https://wiki.geneontology.org/api.php?action=feedcontributions&user=Adiehl&feedformat=atomGO Wiki - User contributions [en]2024-03-29T01:30:45ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=2020_Paris_GOC_Meeting_Logistics&diff=772882020 Paris GOC Meeting Logistics2020-01-23T17:23:37Z<p>Adiehl: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Paris , May 11th - 14th, 2020=<br />
<br />
<span style="color:red">THIS DOCUMENT IS A DRAFT - FINAL VERSION WILL BE ANNOUNCED SOON</span><br />
<br />
==Location==<br />
* [https://research.pasteur.fr/en/network/institut-pasteur-paris-france/#location Pasteur Institute], [https://goo.gl/maps/x5M9YR7Z3urQ8rLM9 25-28 Rue du Dr Roux] - Retrovirus Room.<br />
* Entrance / Security checkin and access to Retrovirus Room: [https://drive.google.com/open?id=1rinBeOdfCaQhChDNfrJOzPWSEYTsXUuS 2D view] [https://drive.google.com/open?id=1XsqfBYeZjVUUHi-zp8HomPk15pGtvREO 3D view]<br />
<br />
==Registration==<br />
* Fee: <span style="color:red">TBD</span> with dinner, or <span style="color:red">TBD</span> for the meeting only<br />
* '''Deadline:''' Friday March 6th, or until full (max 50 people)<br />
<br />
==Overall schedule==<br />
* Monday May 11: User Meeting and discussions with local teams<br />
* Tuesday - Thursday May 12-14: GOC Meeting<br />
<br />
==Consortium dinner==<br />
* <span style="color:red">May 13</span><br />
<br />
<br />
==Hotels==<br />
<br />
<br />
==Getting around==<br />
<br />
===Airports===<br />
From Charles de Gaulles Airport, you can go to Paris through:<br />
* [https://www.parisaeroport.fr/en/passengers/access/paris-charles-de-gaulle/public-transport public transport] and the "RER B" line or "le bus direct"<br />
* [https://www.parisaeroport.fr/en/passengers/access/paris-charles-de-gaulle/taxi/paris-cdg-taxi Taxi] for 50 / 55 euros<br />
<br />
===Public transport===<br />
Public transport (RATP) is usually very good in Paris and can get you pretty much everywhere: [https://www.ratp.fr/sites/default/files/plans-lignes/Plans-essentiels/Plan-Metro.1571994565.pdf Downloadable Map]. Metro are mostly to travel within Paris and RER, faster trains can get you to the suburban, including [https://parisbytrain.com/paris-to-chateau-versailles-by-train/ Versailles] (~ 1h).<br />
<br />
The station to get to the meeting is "Pasteur" (south west) and is deserved by both line 6 and 12. <br />
<br />
If you want more precise / up-to-date itineraries than google map, you can use the [RATP site https://www.ratp.fr/en/itineraires].<br />
<br />
===Taxi===<br />
Official Paris Taxi are easily recognizable thanks to their [https://media.timeout.com/images/100013459/1372/772/image.jpg sign], a green light indicating they are available and will stop if you call them. <br />
<br />
===Shared ride===<br />
Uber is available in Paris but not Lyft.<br />
<br />
===Bicycle===<br />
Paris also has a number of biking stations called [https://www.velib-metropole.fr/en/map#/ velib'].<br />
<br />
==Local activities==<br />
The Institut Pasteur is very close to the "Quartier Latin", a very lively part of Paris which concentrate most universities and engineering schools. The [https://en.wikipedia.org/wiki/Rue_Mouffetard rue Mouffetard] and the [https://www.google.com/maps/@48.8444538,2.3492678,3a,75y,77.02h,91.34t/data=!3m7!1e1!3m5!1sevihytHn5fwm5b4jKwbj-A!2e0!6s%2F%2Fgeo3.ggpht.com%2Fcbk%3Fpanoid%3DevihytHn5fwm5b4jKwbj-A%26output%3Dthumbnail%26cb_client%3Dsearch.revgeo_and_fetch.gps%26thumb%3D2%26w%3D96%26h%3D64%26yaw%3D24.475828%26pitch%3D0%26thumbfov%3D100!7i16384!8i8192 Place de la Contrescarpe] are typical of a Paris student life and hold many restaurants. <br />
<br />
This [https://www.discoverwalks.com/blog/10-things-to-see-in-the-latin-quarter/ article] gives some ideas of what can be seen in the area. In 25mn walk you can get to the Gardens of Luxembourg, 35mn will get you to the medieval museum of Cluny, 45mn to the island of the city with Notre Dame cathedral and the Sainte Chapelle (many classical concerts are usually available). If you prefer to use public transportation, taking the line 12 from Pasteur and line 4 from Montparnasse will get you to Saint Michel Notre Dame in 20mn. <br />
<br />
Walking along the Seine river around that area and by a sunny day is always enjoyable. Along the way, it's easy to find the Louvres, the City town hall (Hotel de Ville), the Orsay museum and the [https://www.cometoparis.com/paris-guide/paris-monuments/pont-des-arts-s959 Pont des arts] which leads to the [https://en.wikipedia.org/wiki/Institut_de_France Institut de France] where the French Academy of Science is.<br />
<br />
A one hour tour of Paris by boat is also possible on the [https://www.bateaux-mouches.fr/en/reservation/tickets bateaux mouches] for 14 euros and can be boarded at [https://goo.gl/maps/GkZn4SfyZPjmgLws9 Pont de l'Alma].<br />
<br />
<br />
==Attendees==<br />
Please add yourself to the table if you plan to attend! (If you don't have edit permission, we will soon provide a form to fill out)<br />
Don't forget to register and pay via <span style="color:red">Eventbrite / TBD</span>.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization?<br />
! GOC meeting (May 12-15)?<br />
! GOC dinner (May 13)?<br />
! User Meeting (May 11)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
| <br />
|-<br />
| Seth Carbon<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Ben Good<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Deepak Unni<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| yes<br />
| yes<br />
| yes<br />
| N/A<br />
| N/A<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Anushya Muruganujan<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Alan Bridge<br />
| SIB/Swiss-Prot/UniProt<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|Petra Fey<br />
|dictyBase<br />
|<br />
| <br />
| <br />
|<br />
|-<br />
|Alexander Diehl<br />
|University at Buffalo<br />
|yes<br />
|yes<br />
|<br />
|<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2020_Paris_GOC_Meeting_Logistics&diff=772862020 Paris GOC Meeting Logistics2020-01-23T17:22:44Z<p>Adiehl: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Paris , May 11th - 14th, 2020=<br />
<br />
<span style="color:red">THIS DOCUMENT IS A DRAFT - FINAL VERSION WILL BE ANNOUNCED SOON</span><br />
<br />
==Location==<br />
* [https://research.pasteur.fr/en/network/institut-pasteur-paris-france/#location Pasteur Institute], [https://goo.gl/maps/x5M9YR7Z3urQ8rLM9 25-28 Rue du Dr Roux] - Retrovirus Room.<br />
* Entrance / Security checkin and access to Retrovirus Room: [https://drive.google.com/open?id=1rinBeOdfCaQhChDNfrJOzPWSEYTsXUuS 2D view] [https://drive.google.com/open?id=1XsqfBYeZjVUUHi-zp8HomPk15pGtvREO 3D view]<br />
<br />
==Registration==<br />
* Fee: <span style="color:red">TBD</span> with dinner, or <span style="color:red">TBD</span> for the meeting only<br />
* '''Deadline:''' Friday March 6th, or until full (max 50 people)<br />
<br />
==Overall schedule==<br />
* Monday May 11: User Meeting and discussions with local teams<br />
* Tuesday - Thursday May 12-14: GOC Meeting<br />
<br />
==Consortium dinner==<br />
* <span style="color:red">May 13</span><br />
<br />
<br />
==Hotels==<br />
<br />
<br />
==Getting around==<br />
<br />
===Airports===<br />
From Charles de Gaulles Airport, you can go to Paris through:<br />
* [https://www.parisaeroport.fr/en/passengers/access/paris-charles-de-gaulle/public-transport public transport] and the "RER B" line or "le bus direct"<br />
* [https://www.parisaeroport.fr/en/passengers/access/paris-charles-de-gaulle/taxi/paris-cdg-taxi Taxi] for 50 / 55 euros<br />
<br />
===Public transport===<br />
Public transport (RATP) is usually very good in Paris and can get you pretty much everywhere: [https://www.ratp.fr/sites/default/files/plans-lignes/Plans-essentiels/Plan-Metro.1571994565.pdf Downloadable Map]. Metro are mostly to travel within Paris and RER, faster trains can get you to the suburban, including [https://parisbytrain.com/paris-to-chateau-versailles-by-train/ Versailles] (~ 1h).<br />
<br />
The station to get to the meeting is "Pasteur" (south west) and is deserved by both line 6 and 12. <br />
<br />
If you want more precise / up-to-date itineraries than google map, you can use the [RATP site https://www.ratp.fr/en/itineraires].<br />
<br />
===Taxi===<br />
Official Paris Taxi are easily recognizable thanks to their [https://media.timeout.com/images/100013459/1372/772/image.jpg sign], a green light indicating they are available and will stop if you call them. <br />
<br />
===Shared ride===<br />
Uber is available in Paris but not Lyft.<br />
<br />
===Bicycle===<br />
Paris also has a number of biking stations called [https://www.velib-metropole.fr/en/map#/ velib'].<br />
<br />
==Local activities==<br />
The Institut Pasteur is very close to the "Quartier Latin", a very lively part of Paris which concentrate most universities and engineering schools. The [https://en.wikipedia.org/wiki/Rue_Mouffetard rue Mouffetard] and the [https://www.google.com/maps/@48.8444538,2.3492678,3a,75y,77.02h,91.34t/data=!3m7!1e1!3m5!1sevihytHn5fwm5b4jKwbj-A!2e0!6s%2F%2Fgeo3.ggpht.com%2Fcbk%3Fpanoid%3DevihytHn5fwm5b4jKwbj-A%26output%3Dthumbnail%26cb_client%3Dsearch.revgeo_and_fetch.gps%26thumb%3D2%26w%3D96%26h%3D64%26yaw%3D24.475828%26pitch%3D0%26thumbfov%3D100!7i16384!8i8192 Place de la Contrescarpe] are typical of a Paris student life and hold many restaurants. <br />
<br />
This [https://www.discoverwalks.com/blog/10-things-to-see-in-the-latin-quarter/ article] gives some ideas of what can be seen in the area. In 25mn walk you can get to the Gardens of Luxembourg, 35mn will get you to the medieval museum of Cluny, 45mn to the island of the city with Notre Dame cathedral and the Sainte Chapelle (many classical concerts are usually available). If you prefer to use public transportation, taking the line 12 from Pasteur and line 4 from Montparnasse will get you to Saint Michel Notre Dame in 20mn. <br />
<br />
Walking along the Seine river around that area and by a sunny day is always enjoyable. Along the way, it's easy to find the Louvres, the City town hall (Hotel de Ville), the Orsay museum and the [https://www.cometoparis.com/paris-guide/paris-monuments/pont-des-arts-s959 Pont des arts] which leads to the [https://en.wikipedia.org/wiki/Institut_de_France Institut de France] where the French Academy of Science is.<br />
<br />
A one hour tour of Paris by boat is also possible on the [https://www.bateaux-mouches.fr/en/reservation/tickets bateaux mouches] for 14 euros and can be boarded at [https://goo.gl/maps/GkZn4SfyZPjmgLws9 Pont de l'Alma].<br />
<br />
<br />
==Attendees==<br />
Please add yourself to the table if you plan to attend! (If you don't have edit permission, we will soon provide a form to fill out)<br />
Don't forget to register and pay via <span style="color:red">Eventbrite / TBD</span>.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization?<br />
! GOC meeting (May 12-15)?<br />
! GOC dinner (May 13)?<br />
! User Meeting (May 11)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
| <br />
|-<br />
| Seth Carbon<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Ben Good<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Deepak Unni<br />
| LBL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
|<br />
|<br />
|<br />
| <br />
|<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| yes<br />
| yes<br />
| yes<br />
| N/A<br />
| N/A<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Anushya Muruganujan<br />
| USC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Alan Bridge<br />
| SIB/Swiss-Prot/UniProt<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|Petra Fey<br />
|dictyBase<br />
|<br />
| <br />
| <br />
|<br />
|-<br />
|Alexander Diehl<br />
|University at Buffalo<br />
|yes<br />
|yes<br />
|<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=730072019 Cambridge GOC Meeting Logistics2019-03-01T15:57:48Z<p>Adiehl: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Fee: '''£65''' with dinner, or £35 for the meeting only<br />
* Link to [https://onlinesales.admin.cam.ac.uk/conferences-and-events/biochemistry/go-consortium-meeting/go-consortium-meeting-april-2019 pay by credit or debit card]<br />
* '''Note that this is also the sign-up for dinner on Thursday evening'''<br />
* Open until Thursday March 28th, or until full (max 50 people)<br />
<br />
==Planned Schedule== <br />
*9am-5pm Thursday April 11th<br />
**New item! Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
*9am-5pm Friday April 12th<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Michele Magrane<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Mike Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Felix Gondwe<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| Yes<br />
|-<br />
| Nick Brown<br />
| FlyBase<br />
| Yes<br />
| No<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 1st March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=729382019 Cambridge GOC Meeting Logistics2019-02-22T17:24:31Z<p>Adiehl: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* '''Update coming soon'''<br />
<br />
==Planned Schedule== <br />
*9am-5pm Thursday April 11th<br />
**New item! Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
*9am-5pm Friday April 12th<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings. If you would like to arrange a focus group on the Saturday, please let Val or Helen know).<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|MIke Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| No<br />
|-|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 1st March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2012-05-09&diff=40646Ontology meeting 2012-05-092012-05-08T12:01:52Z<p>Adiehl: </p>
<hr />
<div>MINUTES: DAVID<br />
<br />
45-minute call<br />
<br />
<br />
===FOLLOW-UP: chemical xps===<br />
<br />
For background, see discussion here: http://wiki.geneontology.org/index.php/Ontology_meeting_2012-05-02#DISCUSSION_ITEM_I:_Follow_up_on_chemical_xps<br />
<br />
The google docs version of the compounds to sort out is here:<br />
<br />
https://docs.google.com/spreadsheet/ccc?key=0AtGZO7sNc8MkdGlyYXlvOVhmMmNIUFVYTnk1SUtJS1E&pli=1#gid=0<br />
<br />
Also, Jane is looking into missing xps using OBO-Edit/Protege - WORK IN PROGRESS<br />
<br />
<br />
===FOLLOW-UP: ChEBI paper===<br />
<br />
Chris, not sure if you've had a chance to work on this, see http://wiki.geneontology.org/index.php/Ontology_meeting_2012-05-02#DISCUSSION_ITEM_III:_Follow-up_on_papers:_ChEBI_and_TermGenie <br />
<br />
<br />
===FOLLOW-UP: TermGenie paper===<br />
<br />
Done since last call: half of all new term requests (51.8% to be precise) between Jan. and June 2010 could have been dealt with, at least in part, using TG templates. See http://gocwiki.geneontology.org/index.php/Template-able_Requests_Prior_To_TG<br />
<br />
The google doc has been update with this info. What do we need to do next?<br />
<br />
<br />
===DISCUSSION ITEM I: Update on Cell Ontology (CL)===<br />
<br />
Is there any update on the Cell Ontology work, especially with regard to new cell-type term requests? Is there any paid editor working on this currently? If not, would it be an option to allow access to CL to the GO Editors, so we can put terms in ourselves when needed? <br />
<br />
This stems from some open requests for neuronal and cardiac cell type terms - the former are long-standing and needed to create new GO terms, and the latter are needed for the cardiac conduction project. <br />
<br />
See e.g. <br />
<br />
https://sourceforge.net/tracker/?func=detail&aid=3403196&group_id=76834&atid=925065<br />
<br />
https://sourceforge.net/tracker/?func=detail&aid=3438262&group_id=76834&atid=925065<br />
<br />
https://sourceforge.net/tracker/?func=detail&aid=3436074&group_id=76834&atid=925065<br />
<br />
<br />
'''Note from Alex:'''<br />
There is no paid editor for CL at this point. I am involved in several projects related to the CL, including some ontology editing work, but have not been good about getting back to the SF items. We are planning to apply for new funding for CL work through one or more grants.<br />
<br />
Chris Mungall, Melissa Haendel, and Ceri van Slyke have all contributed edits to the CL in the past year for particular projects, and Chris has recently transitioned the CL to an svn repository. I will continue doing editing myself among other projects, but I would welcome any contributions from GOC editorial staff. If GOC editors wish to add new terms to the CL, please use the range CL:0009000-CL:0009999, and make comments to your SF entries as you complete them. Otherwise, I will make an effort to attend to these SF entries when I get a chance. Thanks --Alex<br />
<br />
<br />
===DISCUSSION ITEM II: Follow up on "Moving biological_process_xp_cellular_component into live GO"===<br />
<br />
See previous discussion here: http://wiki.geneontology.org/index.php?title=Ontology_meeting_2012-03-07<br />
<br />
* I'm ready for all the transport ones - one hold up has been thinking of a family of relation names that generalizes over both transport and localization that encompasses the different roles (cargo, source, destination, conduit). If we decide on these we can just move this lot in straight away. There was a thread on the list about this w/ Midori a month or two ago -- cjm<br />
<br />
<br />
===DISCUSSION ITEM III (related): Are we going to retrofit logical definitions for cell-type-specific cellular component terms?===<br />
<br />
Some of these (e.g. neuron projection) are in the scratch directory as cellular_component_xp_cell.obo.<br />
<br />
Stems from this SF item: https://sourceforge.net/tracker/?func=detail&aid=3518879&group_id=36855&atid=440764<br />
<br />
Also see this other SF item: https://sourceforge.net/tracker/?func=detail&aid=3410166&group_id=36855&atid=440764</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2012-05-09&diff=40645Ontology meeting 2012-05-092012-05-08T11:59:50Z<p>Adiehl: /* DISCUSSION ITEM I: Update on Cell Ontology (CL) */</p>
<hr />
<div>MINUTES: DAVID<br />
<br />
45-minute call<br />
<br />
<br />
===FOLLOW-UP: chemical xps===<br />
<br />
For background, see discussion here: http://wiki.geneontology.org/index.php/Ontology_meeting_2012-05-02#DISCUSSION_ITEM_I:_Follow_up_on_chemical_xps<br />
<br />
The google docs version of the compounds to sort out is here:<br />
<br />
https://docs.google.com/spreadsheet/ccc?key=0AtGZO7sNc8MkdGlyYXlvOVhmMmNIUFVYTnk1SUtJS1E&pli=1#gid=0<br />
<br />
Also, Jane is looking into missing xps using OBO-Edit/Protege - WORK IN PROGRESS<br />
<br />
<br />
===FOLLOW-UP: ChEBI paper===<br />
<br />
Chris, not sure if you've had a chance to work on this, see http://wiki.geneontology.org/index.php/Ontology_meeting_2012-05-02#DISCUSSION_ITEM_III:_Follow-up_on_papers:_ChEBI_and_TermGenie <br />
<br />
<br />
===FOLLOW-UP: TermGenie paper===<br />
<br />
Done since last call: half of all new term requests (51.8% to be precise) between Jan. and June 2010 could have been dealt with, at least in part, using TG templates. See http://gocwiki.geneontology.org/index.php/Template-able_Requests_Prior_To_TG<br />
<br />
The google doc has been update with this info. What do we need to do next?<br />
<br />
<br />
===DISCUSSION ITEM I: Update on Cell Ontology (CL)===<br />
<br />
Is there any update on the Cell Ontology work, especially with regard to new cell-type term requests? Is there any paid editor working on this currently? If not, would it be an option to allow access to CL to the GO Editors, so we can put terms in ourselves when needed? <br />
<br />
This stems from some open requests for neuronal and cardiac cell type terms - the former are long-standing and needed to create new GO terms, and the latter are needed for the cardiac conduction project. <br />
<br />
See e.g. <br />
<br />
https://sourceforge.net/tracker/?func=detail&aid=3403196&group_id=76834&atid=925065<br />
<br />
https://sourceforge.net/tracker/?func=detail&aid=3438262&group_id=76834&atid=925065<br />
<br />
https://sourceforge.net/tracker/?func=detail&aid=3436074&group_id=76834&atid=925065<br />
<br />
<br />
'''Note from Alex:'''<br />
There is no paid editor for CL at this point. I am involved in several projects related to the CL, including some ontology editing work, but have not been good about getting back to the SF items. We are planning to apply for new funding for CL work through one or more grants.<br />
<br />
Chris Mungall, Melissa Haendel, and Ceri van Slyke have all contributed edits to the CL in the past year for particular projects, and Chris has recently transitioned the CL to an svn repository. I will continue doing editing myself among other projects, but I would welcome any contributions from GOC editorial staff. If GOC editors wish to add new terms to the CL, please use the range CL:0009000-CL:0009999, and make comments to your SF entries as you complete them. Otherwise, I will make an effort to attend to these SF entries when I get a chance. Thanks --Alex<br />
<br />
===DISCUSSION ITEM II: Follow up on "Moving biological_process_xp_cellular_component into live GO"===<br />
<br />
See previous discussion here: http://wiki.geneontology.org/index.php?title=Ontology_meeting_2012-03-07<br />
<br />
* I'm ready for all the transport ones - one hold up has been thinking of a family of relation names that generalizes over both transport and localization that encompasses the different roles (cargo, source, destination, conduit). If we decide on these we can just move this lot in straight away. There was a thread on the list about this w/ Midori a month or two ago -- cjm<br />
<br />
<br />
===DISCUSSION ITEM III (related): Are we going to retrofit logical definitions for cell-type-specific cellular component terms?===<br />
<br />
Some of these (e.g. neuron projection) are in the scratch directory as cellular_component_xp_cell.obo.<br />
<br />
Stems from this SF item: https://sourceforge.net/tracker/?func=detail&aid=3518879&group_id=36855&atid=440764<br />
<br />
Also see this other SF item: https://sourceforge.net/tracker/?func=detail&aid=3410166&group_id=36855&atid=440764</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2011-11-30&diff=38344Ontology meeting 2011-11-302011-11-29T20:07:41Z<p>Adiehl: /* Discussion notes III: RESPONSE TO & DETECTION */</p>
<hr />
<div>'''Report'''<br />
<br />
'''Discussion notes'''<br />
<br />
==Discussion notes I: REGULATION OF X BY REGULATION OF TRANSCRIPTION==<br />
<br />
* Our old favourite: is there progression on making this template in TG, so we can shift the requests out of SF?<br />
<br />
<br />
==Discussion notes II: OBSOLETE TAXON RESTRICTIONS==<br />
<br />
* Rather than having a separate file for obsolete taxon restrictions, could we include it in taxon_go_triggers.obo, in the format (suggested by Tony):<br />
<br />
relationship: only_in_taxon NCBITaxon:5794 {id="GOTAX:0000001", source="PMID:11111111", source="PMID:22222222", source="GOC:al", obsolete="true" } ! Apicomplexa <br />
<br />
<br />
==Discussion notes III: RESPONSE TO & DETECTION==<br />
<br />
* This stems from a [https://sourceforge.net/tracker/?func=detail&aid=3432277&group_id=36855&atid=440764 SF item] from David O-S requesting sensory perception terms for humidity. <br />
<br />
* The sensory perception terms are not linked to 'response terms'. E.g. sensory perception of sound ; GO:0007605 (aka hearing) is not connected to 'response to auditory stimulus ; GO:0010996'.<br />
<br />
* The detection terms are currently is_a children of the response terms:<br />
<br />
response to mechanical stimulus ; GO:0009612<br />
--[isa]detection of mechanical stimulus ; GO:0050982<br />
<br />
response to stimulus ; GO:0050896<br />
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.<br />
<br />
detection of stimulus ; GO:0051606<br />
The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal.<br />
<br />
* I know David H feels strongly that detection comes before the response. What do other editors think? And what was the original reasoning behind the existing layout?<br />
<br />
'''''From Alex:''''' The original reasoning to the layout is found in my comments to [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1290786&group_id=36855 SF1290786] in 2005, and the structure was agreed to at the [http://www.geneontology.org/minutes/20051115_TIGR_Content/20051115_TIGR_Content.pdf TIGR GO Content Meeting] of November 2005. The basic argument is that at the molecular level, a detection event is an induced response in a receptor protein upon binding of a ligand or absorption of a photon etc. that results in a conformational change leading to initiation of a signaling event. I would be interested in alternatives to this structure, possibly based on relation types not in use in 2005.<br />
<br />
* NB: This will have an impact on the signaling terms, since the pathways (ligand-receptor binding down to regulation of a cellular process) are currently children of the cellular response terms...<br />
<br />
==Discussion notes IV: UPDATE ON PROTEGE WORKSHOP==<br />
<br />
* Wiki here: http://wiki.geneontology.org/index.php/Protege_workshop<br />
<br />
* Do we want presentations/demos?<br />
<br />
* Chris will provide us with a list of softwares etc. that we'd need to have downloaded before the workshop begins.<br />
<br />
<br />
<br />
==Discussion notes V: UPDATE ON BP_XP_CC SOURCEFORGE ITEMS==<br />
<br />
* Chris submitted these at<br />
<br />
https://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=440764&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=&category=&artgroup=886159&submitter=&keyword=&artifact_id=&submit=Filter&mass_category=&mass_priority=&mass_resolution=&mass_assignee=&mass_artgroup=&mass_status=&mass_cannedresponse=&_visit_cookie=e69893a83b4d9526a4d95e23b32e856e<br />
<br />
<br />
==Discussion notes VI: OORT OUTPUT==<br />
<br />
* Request for Chris to explain the output of the Oort reasoner, now we have it working.<br />
** What do the Justified asserted subclasses mean (exists entailed, exists not-entailed.....)?<br />
** What do we need to take action on?<br />
<br />
<br />
<br />
'''Task List'''<br />
<br />
<br />
[[Category:Ontology]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2011_UCL_Meeting_Logistics&diff=375892011 UCL Meeting Logistics2011-10-20T14:56:18Z<p>Adiehl: /* Remote Attendees */</p>
<hr />
<div>Return to [[Consortium_Meetings]] page<br />
[[Category:Meetings]]<br />
<br />
=Questions=<br />
please contact Ruth, r.lovering@ucl.ac.uk if you have any questions/queries<br />
<br />
=Dates=<br />
The GO meeting will be begin at 9am on Monday 7th November, 2011 and end at 1pm on Wednesday 9th November, 2011, and will be held at the University College London.<br />
<br />
=Venue=<br />
Wilkins Haldane Room ([http://crf.casa.ucl.ac.uk/screenRoute.aspx?s=1019&d=187&w=False])<br />
Wilkins Building, ([http://maps.google.co.uk/maps?f=q&source=embed&hl=en&geocode=&q=WILKINS+BUILDING@51.524699,-0.13366&ie=UTF8&ll=51.524699,-0.13366&z=16])<br/><br />
University College London,<br/><br />
Gower Street,<br/><br />
London. WC1E 6BT<br />
<br />
<br />
== GOC dinner ==<br />
<br />
Monday 6:30pm<br />
<br />
Sardo <br />
<br />
47 Grafton Way<br />
<br />
http://www.sardo-restaurant.com/index.html<br />
<br />
Menu: based on the Christmas menu http://www.sardo-restaurant.com/setmenu.html<br />
Soup and Main fish course option varies, depending on seasonal supply.<br />
Additional starter: Carpaccio di Manzo (slices of beef)<br />
Main vegetarian option will be Fregola con asparagi e ricotta, (pasta with asparagus and ricotta, not the Christmas option)<br />
<br />
Vegan and Gluten free options available from the main menu, gluten free pasta option. Maybe able to have other vegetarian options too.<br />
<br />
http://www.sardo-restaurant.com/menu.html<br />
<br />
=Registration=<br />
Register by entering your name in the [http://wiki.geneontology.org/index.php/2011_UCL_Meeting_Logistics#Attendees Attendees section] below.<br />
<br />
*Registration fee to be decided (depending on number of participants). Aiming for £140, to include lunches and coffee breaks and 1 evening dinner. This will be payable by credit card the first day of the meeting. Please use the Attendees table below to register for the meeting.<br />
<br />
=Lodging Information=<br />
Please make your own Hotel reservations (see table below). The most reasonable hotels are Ibis and Premier Inn. <br />
<br />
Early booking is recommended as the prices are likely to increase closer to the time, some sites offer free cancellation options. <br />
It might be worth checking hotel costs direct from hotel versus online sites eg [[http://www.booking.com/ booking.com]] filter on bloomsbury, or [[http://www.tripadvisor.co.uk/ Tripadvisor.co.uk]]. <br />
<br />
All hotels below are within a 10-15 min walk from the meeting room. In General London is a pretty safe area, although 20 min east of UCL (around King's cross) is a red light district so I would suggest you avoid this area. None of the hotels below are in the Red Light area! Obviously there are a lot more hotels you could try.<br />
<br />
If anyone has stayed in these hotels please comment on them below.<br />
<br />
----<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Hotel Name<br />
! Cost for 3 nights<br />
! Walking time to UCL<br />
! Address <br />
! Phone number<br />
! Gym (Y/N)<br />
! Internet cost<br />
! Star rating<br />
! Noisy (Y/N)<br />
|-<br />
|[http://www.micentre.com/ MIC] fully booked?<br />
|£225<br />
|5 min<br />
|81 - 103 Euston Street, London NW1 2EZ<br />
|0207 380 0001<br />
|N<br />
|?<br />
|3<br />
|N, shouldn't be<br />
|-<br />
|[http://www.premierinn.com/en/hotel/LONEUS/london-euston Premier Inn]<br />
|£365<br />
|9 min<br />
|1 Dukes Road,London, WC1H 9PJ<br />
|0870 850 5115<br />
|N<br />
|?<br />
|3<br />
|N<br />
|-<br />
|[http://www.ibishotel.com/gb/hotel-0921-ibis-london-euston-st-pancras/index.shtml Ibis]<br />
|£335<br />
|7 min<br />
|3 Cardington Street NW1 2LW<br />
|0207 3887777<br />
|N<br />
|?<br />
|2<br />
|N&Y room dependent<br />
|-<br />
|[http://www.novotel.com/gb/hotel-5309-novotel-london-st-pancras/index.shtml Novatel]<br />
|£440 (now £520)<br />
|10 min<br />
|100 - 110 Euston Road NW1 2AJ<br />
|0207 6669000<br />
|Y<br />
|?<br />
|4<br />
|N<br />
|-<br />
|[http://www.holidayinn.com/hotels/gb/en/london/lonbl/hoteldetail Holiday Inn]<br />
|£512<br />
|11 min<br />
|Coram Street, London, WC1N 1HT<br />
|0871 9429222<br />
|Y<br />
|£5/hour<br />
|4<br />
|N<br />
|-<br />
|[http://www.londonrussellhotel.co.uk/ The Hotel Russell]<br />
|£493<br />
|12 min<br />
|1-8 Russell Square, Bloomsbury, WC1B 5BE<br />
|0870 850 5115<br />
|off site £5<br />
|£15/day<br />
|4<br />
|Y<br />
|-<br />
|[http://centrallondon.stgiles.com/default.aspx?pg=suites St Giles Hotel & Leisure Club]<br />
|£337<br />
|15 min<br />
|Bedford Avenue, Bloomsbury, WC1B 3GH<br />
|0207 300 3000<br />
|yes and pool<br />
|£10/day<br />
|3<br />
|? should be OK<br />
|-<br />
|The White Hall Hotel<br />
|£450**, only executive rooms now free £558**<br />
|12 min<br />
|2-5 Montague Street, WC1B 5BU <br />
|020 7233 7888<br />
|N<br />
|?<br />
|4<br />
|? should be OK<br />
|}<br />
<br />
(**) If you are interested in The White Hall Hotel let me know and I will book these via UCL, to get this discount price (Ruth r.lovering@ucl.ac.uk).<br />
----<br />
<br />
=Maps and Transportation=<br />
<br />
== Airports ==<br />
<br />
You can get to central London from any of the following airports, taxis will be more expensive than trains and all airports have good train services available. Once in a central London train station, either get a taxi to your hotel or the meeting or get on the tube (see information below).<br />
<br />
* Heathrow [http://www.heathrowairport.com/portal/controller/dispatcher.jsp?CiID=759c9b25f9599110VgnVCM10000036821c0a____&ChID=4504abfa784d3110VgnVCM10000036821c0a____&Ct=B2C_CT_GENERAL&CtID=448c6a4c7f1b0010VgnVCM200000357e120a____&ChPath=Home^Heathrow^General^To+and+from+Heathrow^Trains&search=true link to train information ]<br />
<br />
* Gatwick [http://www.gatwickairport.com/transport/gatwick-express/ link to train information ]<br />
<br />
* Stansted [http://www.stanstedairport.com/portal/page/Stansted%5EGeneral%5ETo+and+from+Stansted%5ETrains/a024e37e8077d110VgnVCM10000036821c0a____/448c6a4c7f1b0010VgnVCM200000357e120a____/ link to train information ]<br />
<br />
== Airport to Central London ==<br />
<br />
The meeting is in central London and is walkable from Euston, Euston Square, Warren Street, Goodge Street tube stations. Note Tottenham Court Road Tube station is closed.<br />
<br />
There is a good [http://www.tfl.gov.uk/gettingaround/1106.aspx journey planner site] <br />
<br />
=== From Heathrow: ===<br />
<br />
* Either: catch the Heathrow express train from Heathrow to Paddington, and then get a taxi, to your hotel/UCL from there, or get the tube from Paddington to Euston Square (east bound on the Hammersmith & City Line towards Baker Street or the Circle Line towards Kings Cross St Pancras). <br />
Journey time around 1 hour. Cost around £38 return, £21 single plus tube fare £4 each way (taxi cost unknown).<br />
<br />
* Or get the Piccadilly tube: from Heathrow to Green Park and change onto the Victoria Line (heading north) and either get out at Warren Street (meeting) or Euston (depending on hotel). <br />
Journey time around 1 hour 10 min. Cost around £5 single (Heathrow is zone 6).<br />
<br />
* Or taxi, there are lots of online sites suggesting the cost is around £44, each way, and will take about 40 min (but this will be traffic dependent).<br />
<br />
=== From Gatwick: ===<br />
<br />
* Either: catch the Gatwick express train from Gatwick to Victoria, and then get a taxi, to your hotel/UCL from there, or get the tube from Victoria to Warren Street (north bound on the Victoria Line). <br />
Journey time around 1 hour. Cost around £30 return, £17 single, plus tube fare £4 each way (taxi cost unknown).<br />
<br />
* Or taxi, there are lots of online sites suggesting the cost is around £60, each way, and will take about 1 hour (but this will be traffic dependent).<br />
<br />
=== From Stansted: ===<br />
<br />
* Either: catch the Stansted express train from Stansted to Liverpool Street, and then get a taxi, to your hotel/UCL from there, or get the tube from Liverpool Street to Euston Square (west bound on the Hammersmith & City Line/Metropolitan Line, or the Circle Line towards Kings Cross St Pancras). <br />
Journey time around 1 hour. Cost around £27 return, £20 single, plus tube fare £4 each way (taxi cost unknown).<br />
<br />
* Or taxi, there are lots of online sites suggesting the cost is around £45, each way, and will take about 1 hour (but this will be traffic dependent).<br />
<br />
=Meeting Agenda= <br />
<br />
The agenda can be found here: [[2011_UCL_Meeting_Agenda]]<br />
<br />
=Attendees=<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time at Airport <br />
! Departure Date/Time from Airport<br />
! Hotel booked?<br />
! Vegetarian (Y/N)<br />
|-<br />
|Ruth Lovering <br />
|BHF-UCL<br />
|N/A<br />
|N/A<br />
|Travel from home and St Giles Monday night<br />
|N<br />
|-<br />
|Peter D'Eustachio <br />
|NYU - Reactome<br />
|6 Nov 9:25 AM LHR<br />
|12 Nov 10:25 AM LHR<br />
|Regency House 71 Gower St<br />
|N<br />
|-<br />
|Varsha Khodiyar <br />
|BHF-UCL<br />
|N/A<br />
|N/A<br />
|Travel from home and St Giles Monday night<br />
|N<br />
|-<br />
|Emily Dimmer<br />
|UniProtKB<br />
|N/A<br />
|N/A<br />
|Travel from home and Ibis Monday night<br />
|N<br />
|-<br />
|Tony Sawford<br />
|UniProtKB<br />
|N/A<br />
|N/A<br />
|Travel from home and Ibis Monday night<br />
|N<br />
|-<br />
|Jane Lomax<br />
|GO-EBI<br />
|N/A<br />
|N/A<br />
|Travel from home<br />
|N<br />
|-<br />
|Seth Carbon<br />
|BBOP-LBNL<br />
|N/A<br />
|N/A<br />
|yes<br />
|N<br />
|-<br />
|Chris Mungall<br />
|BBOP-LBNL<br />
|N/A<br />
|N/A<br />
|not yet<br />
|Y<br />
|-<br />
|Suzanna Lewis<br />
|BBOP-LBNL<br />
|N/A<br />
|N/A<br />
|yes<br />
|N<br />
|-<br />
|Paola Roncaglia<br />
|GO-EBI<br />
|N/A<br />
|N/A<br />
|Travel from home & MIC Monday night<br />
|N<br />
|-<br />
|Mike Cherry<br />
|Stanford<br />
|Nov 7, LHR, 6:50AM<br />
|Nov 10, LHR, 1:35PM<br />
|The White Hall Hotel <br />
|N<br />
|-<br />
|Judy Blake<br />
|The Jackson Laboratory<br />
|Nov 6, LHR, 9:25 AM<br />
|Nov 10, LHR, 12:05 PM<br />
|don't know yet.<br />
|N<br />
|-<br />
|Brenley McIntosh <br />
|Tx A&M - EcoliWiki<br />
|?<br />
|?<br />
|not yet<br />
|N<br />
|-<br />
|Val Wood<br />
|PomBase<br />
|n/a<br />
|n/a<br />
|TBD may stay one night<br />
|N<br />
|-<br />
|Yasmin Alam-Faruque<br />
|UniProtKB-GOA<br />
|n/a<br />
|n/a<br />
|Travel from home and Ibis Monday night<br />
|Y<br />
|-<br />
|Rebecca Foulger<br />
|GO-EBI<br />
|N/A<br />
|N/A<br />
|Travel from home & MIC on Monday night<br />
|N<br />
|-<br />
|Rama Balakrishnan<br />
|SGD, Stanford<br />
|n/a<br />
|n/a<br />
|not yet<br />
|Y (vegan if possible)<br />
|-<br />
|Stan Laulederkind<br />
|RGD<br />
|Nov 6<br />
|Nov 11<br />
|not yet<br />
|N<br />
|-<br />
|David Hill <br />
|The Jackson Laboratory<br />
|?<br />
|?<br />
|not yet<br />
|N<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase, Caltech<br />
|Nov 6, LHR, 6:35am<br />
|Nov 10, LHR, 10:30am<br />
|Premier Inn<br />
|Yes, please<br />
|-<br />
|Julie Park<br />
|SGD, Stanford<br />
|N/A<br />
|Nov 10, LHR, 1:35PM<br />
| not yet<br />
|N<br />
|-<br />
|Midori Harris<br />
|PomBase, Cambridge<br />
|N/A<br />
|N/A<br />
|TBD - may stay one night<br />
|N (but don't want meat every meal)<br />
|-<br />
|Tanya Berardini<br />
|TAIR<br />
|?<br />
|?<br />
|not yet<br />
|N<br />
|-<br />
|Claire O'Donovan<br />
|UniProtKB<br />
|N/A<br />
|N/A<br />
|Travel from home and Ibis Monday night<br />
|gluten-free<br />
|-<br />
|Susan Tweedie<br />
|FlyBase<br />
|N/A<br />
|N/A<br />
|not yet<br />
|N<br />
|-<br />
|Prudence Mutowo <br />
|GOA-UniProtKB<br />
|N/A<br />
|N/A<br />
|Travel from home and Ibis Monday night<br />
|no rice<br />
|-<br />
|Donghui Li<br />
|TAIR<br />
|Nov 6 LHR 11:25AM<br />
|Nov 10 LHR 01:35PM<br />
|MIC<br />
|N<br />
|-<br />
|Rachael Huntley <br />
|GOA-UniProtKB<br />
|N/A<br />
|N/A<br />
|Travel from home and Ibis Monday night<br />
|Y<br />
|-<br />
|Heiko Dietze<br />
|BBOP-LBNL<br />
|Nov 6, 11:25 am LHR<br />
|Nov 10, 1:35 pm LHR<br />
|Holiday Inn<br />
|N<br />
|-<br />
|Antonia Lock<br />
|Pombase UCL<br />
|N/A<br />
|N/A<br />
|TBD may stay one night<br />
|N<br />
|}<br />
<br />
=Invited attendees =<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Date presenting<br />
! Arrival Date/Time at Airport <br />
! Departure Date/Time from Airport<br />
! Hotel booked?<br />
! Vegetarian (Y/N)<br />
|-<br />
|Sandra Orchard<br />
|IntAct<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|Philippa Talmud<br />
|BHF-UCL<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Pablo Millan<br />
|IntAct<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|}<br />
<br />
=Remote Attendees=<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! email (needed to set up your remote access)<br />
! Time Zone<br />
|-<br />
|Doug Howe<br />
|ZFIN<br />
|dhowe@zfin.org<br />
|PDT (UTC -7)<br />
|-<br />
|Harold Drabkin<br />
|MGI<br />
|harold.drabkin@jax.org<br />
|EST<br />
|-<br />
|Mary Dolan<br />
|MGI<br />
|mdolan@informatics.jax.org<br />
|EST<br />
|-<br />
|Alexander Diehl<br />
|University at Buffalo<br />
|addiehl@buffalo.edu<br />
|EST<br />
|}<br />
<br />
<br />
<br />
----<br />
Return to [[Consortium_Meetings]] page<br />
[[Category:Meetings]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Main_Page&diff=37305Main Page2011-09-26T03:23:18Z<p>Adiehl: Undo revision 37301 by Aiai00125 (talk)</p>
<hr />
<div><big>'''Welcome to the Gene Ontology Consortium Wiki'''</big><br />
<br />
== GOC Public Resources ==<br />
<br />
[[:Category:FAQ|GO Frequently Asked Questions]]<br />
<br />
=== Community Annotation Pages ===<br />
[[Cardiovascular|Cardiovascular Genes]]<br />
<br />
[[Immunology]]<br />
<br />
[[Muscle Biology|Muscle Biology]]<br />
<br />
[[Reference Genome Genes]]<br />
<br />
[[Lung Development]]<br />
<br />
=== Web Pages ===<br />
<br />
* [http://www.geneontology.org/ GO Home]<br />
* [http://www.geneontology.org/GO.contents.doc.shtml GO Documentation]<br />
* [http://www.geneontology.org/GO.downloads.shtml GO Downloads]<br />
<br />
=== Database Query Pages ===<br />
* [http://amigo.geneontology.org AmiGO]<br />
<br />
== GO Working Group Wiki ==<br />
<br />
These pages are limited to use by members of the GOC.<br />
<br />
*[[User Advocacy]]<br />
*[[Annotation Outreach]]<br />
*[[Ontology Development]]<br />
*[[Reference Genome Annotation Project]]<br />
*[[Software and Utilities]]<br />
*[[GO Leadership]]<br />
*[[GO Managers]]<br />
*[[Consortium Meetings]]<br />
*[[Working Groups]]<br />
**[[AmiGO Hub]]<br />
**[[:Category:OBO-Edit working group|OBO-Edit working group]]<br />
**[[:Category:Web Presence Working Group|Web Presence Working Group]]<br />
**[[:Category:Immunology Annotation working group|Immunology Annotation working group]]<br />
**[[Web Presence Working Group]]<br />
*[[GO Content Checklist]]<br />
*[[Progress Reports]]<br />
*[[Publications%2C_tutorials%2C_talks%2C_posters|Publication list]]<br />
<br />
== Useful Links ==<br />
<br />
Help pages for using wikis: http://meta.wikimedia.org/wiki/Help:Help<br />
<br />
Quick guide to formatting wiki text: http://meta.wikimedia.org/wiki/Help:Wikitext<br />
<br />
[[Wiki_best_practice|Guidelines for using this wiki]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2011_USC_Meeting_Logistics&diff=349322011 USC Meeting Logistics2011-05-11T18:09:35Z<p>Adiehl: /* Remote Attendees */</p>
<hr />
<div>=Dates=<br />
The GO meeting will be begin at 9am on May 19, 2011 and end at 1pm on May 21, 2011, and will be held at the University of Southern California in Los Angeles.<br />
<br />
=Venue=<br />
California Room<br/><br />
Davidson Conference Center ([http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=3415+South+Figueroa+Street,+Los+Angeles,+CA&aq=0&sll=37.0625,-95.677068&sspn=38.690438,61.435547&ie=UTF8&hq=&hnear=3415+S+Figueroa+St,+Los+Angeles,+California+90007&z=16 map])<br/><br />
University of Southern California<br/><br />
3415 South Figueroa Street<br/><br />
Los Angeles, CA 90089-0871<br />
<br />
=Registration=<br />
Register by entering your name in the Attendees section below.<br />
<br />
*There will be a registration fee of $120 to cover the breakfasts, lunches and coffee breaks. This will be payable by credit card the first day of the meeting.<br />
<br />
=Lodging Information=<br />
We are no longer arranging for hotel, so if you register after May 1, please arrange for your own hotel. The JW Marriott below still has availability as of May 1.<br />
<br />
Downtown is only a 10 min. ride away (we will arrange for shuttle service and there is also fast, cheap local transportation on the DASH). If you want to share a room, please contact Pauline Martinez at pauline.martinez@med.usc.edu.<br />
<br />
----<br />
Downtown:<br/><br />
[http://www.marriott.com/hotels/travel/laxjw-jw-marriott-hotel-los-angeles-at-la-live/ JW Marriott Los Angeles L.A. LIVE]<br/><br />
900 West Olympic Boulevard, Los Angeles, CA 90015<br/><br />
----<br />
Campus:<br/><br />
'''NOTE: THIS HOTEL IS NOW FULL (AS OF APRIL 19), PLEASE USE DOWNTOWN OPTION'''<br/><br />
[http://www.radisson.com/los-angeles-hotel-ca-90007/cafiguer Radisson Los Angeles at USC]<br/><br />
3540 S. Figueroa Street, Los Angeles, CA 90007<br/><br />
----<br />
<br />
=Maps and Transportation=<br />
==Airport to Hotel==<br />
* LA taxis have a flat rate to downtown (not the USC campus) of $46.50 (not including tip)<br />
* Prime Time Shuttle<br />
** phone 1(800) 733-8267<br />
** USC rate to any USC location, including downtown: $13.50 per person<br />
==Downtown Hotel to USC Campus==<br />
* We will arrange for a shuttle if enough people stay downtown<br />
* The [http://www.ladottransit.com/dash/routes/downtown/downtown.php DASH bus, route F] runs every 10 min. on weekdays and costs 35 cents.<br />
<br />
=To do=<br />
Coming soon.<br />
<br />
=Meeting Agenda= <br />
<br />
The agenda can be found here: [[2011_USC_Meeting_Agenda]]<br />
<br />
=Attendees=<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time from Airport <br />
! Departure Date/Time to Airport<br />
! Hotel pref. (Downtown/Campus) and confirmation<br />
! Vegetarian (Y/N)<br />
|<br />
|-<br />
|Paul Thomas<br />
|USC/PANTHER<br />
|N/A<br />
|N/A<br />
|Downtown<br />
|N<br />
|-<br />
| Paul Sternberg<br />
| Caltech/Wormbase<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
| Suzi Lewis<br />
| LBNL<br />
|<br />
|<br />
|Downtown Marriott JW Marriott/ Conf. #84481712<br />
|<br />
|-<br />
| Mike Cherry<br />
| Stanford/SGD<br />
| 1900 / May 18<br />
| 1500 / May 21<br />
| Downtown Marriott JW Marriott/ Conf. #84481712<br />
| N<br />
|<br />
|-<br />
| Judy Blake<br />
| Jackson Laboratory/MGI<br />
| 1650 / May 18<br />
| 1110 / May 22<br />
| Downtown Marriott (5 nights) JW Marriott/ Conf. # 84974216<br />
| N<br />
|-<br />
| Rama Balakrishnan<br />
| SGD, Stanford University<br />
| May 18<br />
| May 21<br />
| Downtown Marriott JW Marriott/ Conf. #84481712<br />
| Y<br />
|<br />
|-<br />
| Valerie Wood<br />
| PomBase, Cambridge University<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights) JW Marriott/ Conf. # 84974216<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN, U. Oregon<br />
| May 18 5:40PM<br />
| May 21<br />
| Campus (3 nights) RAD conf. #795754<br />
| N<br />
|-<br />
| David Hill<br />
| Jackson Laboratory/MGI<br />
| May 18th 1:36PM<br />
| May 21st 11:00PM<br />
| Campus RAD conf. #795744<br />
| N<br />
|-<br />
| Harold Drabkin<br />
| Jackson Laboratory/MGI/PRO<br />
| May 18 04:50 PM<br />
| May 21 3:00 PM<br />
| Campus (3 nights) RAD conf. #795751<br />
| N<br />
|-<br />
| Eurie Hong<br />
| Stanford/SGD<br />
| May 18<br />
| May 21<br />
| Downtown JW Marriott/ Conf. #84481712 (Dbl)<br />
| N<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR<br />
| May 18<br />
| May 20<br />
| Campus (2 nights) RAD conf. #795752<br />
| N<br />
|<br />
|-<br />
| Donghui Li<br />
| TAIR<br />
| May 18 16:25<br />
| May 21 14:55<br />
| Campus (3 nights) RAD conf. #795753<br />
| N<br />
|-<br />
| Eva Huala<br />
| TAIR<br />
| May 19 07:40<br />
| May 21 14:30<br />
| Campus (2 nights) RAD conf. # 814958<br />
| N<br />
|-<br />
| Susan Tweedie<br />
| FlyBase<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights) RAD conf. #795761<br />
| N<br />
|-<br />
| Julie Park<br />
| Stanford/SGD<br />
| May 18 <br />
| May 21 <br />
| Downtown<br />
| N<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| May 18<br />
| May 22<br />
| Campus (4 nights) RAD conf. #795760<br />
| N<br />
|-<br />
| Rebecca Foulger<br />
| GO-Editorial<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights: booked by EBI) RAD conf. #795759<br />
| N<br />
|-<br />
| Paola Roncaglia<br />
| GO-Editorial<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights: booked by EBI) RAD conf.#795758<br />
| N<br />
|-<br />
| Emily Dimmer<br />
| GOA<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights: booked by EBI) RAD conf.#795757<br />
| N<br />
|-<br />
| Tony Sawford<br />
| GOA<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights: booked by EBI) RAD conf. #795762<br />
| N<br />
|-<br />
| Claire O'Donovan<br />
| UniProt/GOA<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Campus (4 nights: booked by EBI) RAD conf. #795756<br />
| N (but coeliac)<br />
|-<br />
|Seth Carbon<br />
|BBOP<br />
|May 18<br />
|May 21<br />
|Downtown Marriott (3 nights) JW Marriott/ Conf. # 84455496<br />
|N<br />
|-<br />
| Marcus Chibucos<br />
| Institute for Genome Sciences/ECO<br />
| 18 May, time ?<br />
| 21 May, time ?<br />
| Campus (3 nights) RAD conf. #795755<br />
| Y (pescetarian)<br />
|-<br />
| Hans-Michael Muller<br />
| Textpresso / California Institute of Technology<br />
| N/A<br />
| N/A<br />
| N/A<br />
| N<br />
|-<br />
|Jim Hu<br />
|PortEco/EcoliWiki/Texas A&M<br />
|May 18<br />
|May 21<br />
|Downtown JW Marriott/ Conf. # 84455496<br />
|N (Lac<sup>-</sup>)<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase<br />
|May 16, 9:00pm LAX<br />
|May 21, 10:00pm LAX<br />
|N/A<br />
|Y, please <br />
|-<br />
|Fiona McCarthy<br />
|AgBase<br />
|tbd, LAX<br />
|tbd, LAX<br />
|Campus JW Marriott/ Conf. # 84455496<br />
|N <br />
|-<br />
| Ruth Lovering<br />
| BHF-UCL<br />
| May 18 13:40<br />
| May 22 17:45<br />
| Downtown (4 nights) JW Marriott/ Conf. # 84455496<br />
| N<br />
|-<br />
| Sarah Burge<br />
| InterPro<br />
| May 18 13:40(ish)<br />
| May 22 17:45(ish)<br />
| Campus (4 nights: booked by EBI) RAD conf.#788405<br />
| Y<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| May 18 LAX 17:47<br />
| May 21 LAX 16:00 <br />
| Downtown (3 nights) JW Marriott/ Conf. # 84974216<br />
| Y<br />
|-<br />
| Heiko Dietze<br />
| LBNL<br />
| May 18 (5:25 Pm)<br />
| May 21 (5:20 Pm)<br />
| Downtown (3 nights) JW Marriott/ Conf. # 84972140<br />
| N<br />
|-<br />
| Amelia Ireland<br />
| BBOP<br />
| May 18 tbd<br />
| May 21 tbd<br />
| Downtown JW Marriott/ Conf. # 84972140<br />
| Y<br />
|-<br />
| Chris Mungall<br />
| BBOP<br />
| May 19 am<br />
| May 21 tbd<br />
| Downtown JW Marriott/ Conf. # 84972140<br />
| Y<br />
|-<br />
| Ranjana Kishore<br />
| WormBase/Caltech<br />
| N/A<br />
| N/A<br />
| N/A<br />
| Y<br />
|-<br />
|}<br />
<br />
=Remote Attendees=<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! email (needed to set up your remote access)<br />
! Time Zone<br />
|-<br />
|Anushya Muruganujan<br />
|USC/PANTHER<br />
|muruganu@usc.edu<br />
|PDT<br />
|-<br />
|Peter D'Eustachio<br />
|NYU / Reactome<br />
|deustp01@nyumc.org<br />
|EDT<br />
|-<br />
|Mike Livstone (Friday only)<br />
|Princeton/P-POD<br />
|livstone@genomics.princeton.edu<br />
|EDT<br />
|-<br />
|Li NI<br />
|Jackson / MGI<br />
|ln@informatics.jax.org<br />
|EDT<br />
|-<br />
|Terry Meehan<br />
|Jackson / GOC /CL<br />
|Terry.Meehan@jax.org<br />
|EDT<br />
|-<br />
|Mary Dolan<br />
|Jackson / MGI<br />
|mdolan@informatics.jax.org<br />
|EDT<br />
|-<br />
|Lakshmi Pillai<br />
|AgBase<br />
|laksrp@gmail.com<br />
|CDT<br />
|-<br />
|Cathy Gresham<br />
|AgBase<br />
|gresham@cse.msstate.edu<br />
|CDT<br />
|-<br />
|Trudy Torto-Alalibo<br />
|Microbial ENergy processes Gene Ontology (MENGO)VBI<br />
|trudy@vbi.vt.edu<br />
|EDT<br />
|-<br />
|Biswarup Mukhopadhyay<br />
|Microbial ENergy processes Gene Ontology (MENGO) VBI<br />
|biswarup@vt.edu<br />
|EDT<br />
|-<br />
|Karen Christie<br />
|Stanford/SGD<br />
|kchris@genome.stanford.edu<br />
|PDT<br />
|-<br />
|Alexander Diehl<br />
|SUNY Buffalo<br />
|addiehl@buffalo.edu<br />
|EDT<br />
|}<br />
<br />
<br />
----<br />
Return to [[Consortium_Meetings]] page<br />
[[Category:Meetings]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Immunology&diff=34377Immunology2011-04-03T13:03:36Z<p>Adiehl: Undo revision 34376 by Jameskerry110 (talk)</p>
<hr />
<div><big>'''The Gene Ontology Consortium's Community Annotation Wiki for Immunology'''</big><br />
<br />
=='''Introduction'''==<br />
<br />
In order to promote our work annotating genes of immunological interest using the Gene Ontology, we have set up a wiki to allow members of the community of experimental immunologists and other interested parties to review GO annotation of their genes of interest and provide us with additional information to guide our annotation efforts for these genes. '''Note that at present there is no dedicated funding to support the annotation of genes associated with immunological processes, although some annotation of these genes occurs as part of other annotation efforts.''' <br />
<br />
The wiki consists of a set of gene-specific pages that each provide links to general information and existing GO annotation for a given human gene and its orthologs in other species. A separate section of the gene page is set up for editing by users to provide us with information that we will then use to make additional GO annotations for that gene. We are particularly interested in aspects of the biology for a particular gene that are not currently represented in its existing GO annotation. '''Information regarding a particular gene in any species is welcome.'''<br />
<br />
A second set of pages lists important immunological processes, again providing links to existing GO annotation and having a section for editing by users to provide information that may lead to additional GO annotation.<br />
<br />
Our focus on immunology annotation follows upon an extensive revision of the Gene Ontology to provide a more comprehensive representation of immunologically important processes [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17267433&query_hl=1&itool=pubmed_docsum (1)]. You may explore GO terms for immune system processes using the GO Consortium's [http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?xpand=GO:0002376&search_constraint=terms&query=GO:0002376&view=details&show_associations=list Amigo Browser].<br />
<br />
Scientists are encouraged to provide input for specific genes or processes to the gene or process specific pages. We will review information provided through the wiki on a timely basis, and notify users of how their contributions have resulted in GO annotations.<br />
<br />
=='''The Wiki Pages'''==<br />
<br />
[[Immunologically Important Genes]]<br />
<br />
[[Immunologically Important Biological Processes]]<br />
<br />
[[Explanation of Gene Prioritization]]<br />
<br />
[[Suggestions for New GO Terms Related to Immunology]]<br />
<br />
[[Background and Instructions]]<br />
<br />
[[Related GO Immunology Publications]]<br />
<br />
[[Immunology Wiki Credits|Credits]]<br />
<br />
Example of a gene page: IL1A[http://wiki.geneontology.org/index.php/Example_GO_annotation_submission]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Cell_Ontology_Progress_Report_2010&diff=32723Cell Ontology Progress Report 20102010-12-18T06:08:21Z<p>Adiehl: /* Collaborations */</p>
<hr />
<div>Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL.<br />
<br />
<br />
==Personnel==<br />
<br />
* '''Project Leaders'''<br />
** Alexander Diehl, The Jackson Laboratory/University at Buffalo (50% effort)<br />
** Christopher Mungall, LBNL (10% effort)<br />
<br />
* '''Cell Ontology Curator'''<br />
** Terrence Meehan, The Jackson Laboratory (100% effort)<br />
<br />
* '''Programmers'''<br />
** Amina Abdulla and Nomi Harris, LBNL (75% effort, split)<br />
<br />
* '''Senior Advisors'''<br />
** Judith Blake, The Jackson Laboratory<br />
** Suzanna Lewis, LBNL<br />
<br />
* '''External Consultants'''<br />
** Lindsay Cowell, Duke University<br />
** Anna Maria Masci, Duke University<br />
<br />
<br />
==Collaborations==<br />
<br />
* INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.<br />
* Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL.<br />
* Sirarat Sarntivijai and Oliver He, University of Michigan, development of the Cell Line Ontology.<br />
* The Plant Ontology Consortium, plant cell types.<br />
* David Osumi-Sutherland, Flybase, Drosophila cell types.<br />
* Onard Mejino, Foundation Model of Anatomy, import of FMA cell types<br />
* David Dougall and Richard Scheuermann, UT Southwestern, import of novel hematopoietic cell types identified via flow cytometry<br />
* Helen Parkinson, EBI, assistance in making cell types in CL and the Experimental Factor Ontology compatible and in providing support for experimentally derived cell types in OBI.<br />
* Wasila Dahdul and Paula Mabee, Unversity of South Dakota, for bone cell types.<br />
<br><br><br />
<br />
==Item 1 - Activities==<br />
<br />
===Aim 1: Reforming the Structure of the Cell Ontology===<br />
<br />
*Devise new structure for the Cell Ontology<br />
**A new high level structure for the CL was approved at the May 2010 Cell Ontology Workshop. Parts have been implemented, and more will be in 2011.<br />
<br />
*Add formal logical axioms to the CL.<br />
**A system of OWL macro expansions has been developed for CL relations such as "capable_of" that allow for easy conversion to OWL versions that can be more fully reasoned over using Protege reasoners (see below).<br />
<br />
*Add logical definitions using other OBO ontologies<br />
**Extensive computable definitions (AKA "logical definitions" or "cross-products") have been added to terms in the hematopoietic cell branch of the CL, and to some other terms in the CL.<br />
**We have identified the following ontologies as key to defining cell types:<br />
***PRO - Protein Ontology<br />
***GO - Gene Ontology (particularly biological processes such as immune response)<br />
***PATO - Phenotypic Quality Ontology<br />
***Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.<br />
<br />
*Implement automated reasoner strategy<br />
**This has been an integral part of our ongoing development of the CL.<br />
<br />
* General software support<br />
**Support with managing ontology versions in Open Bio-Ontologies repository<br />
**OBO-Edit bug fixes (see below).<br />
<br><br />
<br />
===Aim 2: Improving and extending the content of CL===<br />
*We held a [http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology workshop], on May 18-19, 2010 at the Jackson Laborotory, Bar Harbor, Maine, and extensively discussed both ontological and biological aspects of CL development.<br />
*A workshop on neurons and nervous system cell types is scheduled for April 12-14, 2011. More information may be found [http://obofoundry.org/wiki/index.php/Cell_Ontology-INCF_Neuron_Workshop here].<br />
*We have implementing the computable defintion (AKA "logical definition" or "cross-product") formulation of the hematopoietic terms. As part of this work, we have improved definitions for a number of cell types and adding many new cell types.<br />
*A paper, "Logical Development of the Cell Ontology" by Meehan, Masci, Abdulla, Cowell, Blake, Mungal, and Diehl, which described the work on the hematopoietic cells in the CL has been accepted (December 2010) for publication in BMC Biouinformatics.<br />
*We have imported a large number of terms from the FMA into the CL.<br />
*We have added is_a parents to all terms in the CL.<br />
*We have prepared textual and logical definitions for current nervous system terms in the CL that lack them, although these are not yet implemented in cell.obo.<br />
*Over 400 new cell types have been added to CL in 2010.<br><br><br />
<br />
===Aim 3: Applying the CL to the GO===<br />
<br />
* We are using manual and automated methods to ensure interoperability between the GO and CL for cell types and the logical relationships between them.<br />
<br />
<br />
==Item 2 -- Percent Completion==<br />
<br />
* Based on current progress towards completion of our aims we are on track, with 60% of the work accomplished.<br><br><br />
<br />
== LBL Contributions to CL development ==<br />
<br />
ONTOLOGY ALIGNMENT AND INTEGRATION: we have supported the JAX ontology editors by providing and executing tools to integrate human cell types represented in the FMA (Foundational Model of Anatomy) into CL. These tools identified generic cell types in common between the two ontologies, and used the Obol toolkit (developed at Berkeley) to identify compositional class expressions for specific cell types (e.g. "smooth muscle cell of jejunum"). These compositional classes can then be integrated automatically, using the cross-species gross anatomy ontology UBERON.<br />
<br />
ONTOLOGY EDITOR SUPPORT: we have provided ontology editor support to the JAX editors of the ontology, improving the OBO-Edit ontology editing environment in reponse to curator requests. We have also implemented a variant of the MIREOT (Minimal Information Retrieved for External Ontology Terms) strategy which allows scalable integration across multiple ontologies. We have also devised a build environment for the CL, which allows the easy distribution of multiple versions for different purposes, and uses OWL reasoners to classify and perform logical consistency analysis on the ontology automatically.<br />
<br />
ONTOLOGY LANGUAGE SUPPORT: we identified key areas in which the ontology format used by the Gene Ontology was insufficient for representing cell types. Rather than move wholesale to the more expressive OWL (Ontology Web Langauge) formalism, which would have entailed abandoning tools and interoperation with model organism databases, we enhanced obo format using a macro mechanism and implemented a prototype macro expansion engine (http://precedings.nature.com/documents/5292/version/1). This allowed us to have the best of both worlds, and to be able to transition between the oboedit environment, and the Protege 4 editors environment, and to use OWL reasoners to classify the ontology.<br />
<br />
This work also necessitated creation of a formal specification of obo format and its translation to OWL ([http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html]), which significantly extends on previous efforts made in 2007, before the OWL2 language was finalized.<br><br><br />
<br />
==Related Publications for 2010==<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002].<br />
<br />
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD, 2010, Logical Development of the Cell Ontology, accepted for publication in BMC Bioinformatics.<br />
<br />
<br><br />
<br />
[[http://wiki.geneontology.org/index.php/Grant_Progress_Reports_December_2010 Return to 2010 Progress Reports]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Cell_Ontology_Progress_Report_2010&diff=32722Cell Ontology Progress Report 20102010-12-18T06:05:56Z<p>Adiehl: /* Aim 2: Improving and extending the content of CL */</p>
<hr />
<div>Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL.<br />
<br />
<br />
==Personnel==<br />
<br />
* '''Project Leaders'''<br />
** Alexander Diehl, The Jackson Laboratory/University at Buffalo (50% effort)<br />
** Christopher Mungall, LBNL (10% effort)<br />
<br />
* '''Cell Ontology Curator'''<br />
** Terrence Meehan, The Jackson Laboratory (100% effort)<br />
<br />
* '''Programmers'''<br />
** Amina Abdulla and Nomi Harris, LBNL (75% effort, split)<br />
<br />
* '''Senior Advisors'''<br />
** Judith Blake, The Jackson Laboratory<br />
** Suzanna Lewis, LBNL<br />
<br />
* '''External Consultants'''<br />
** Lindsay Cowell, Duke University<br />
** Anna Maria Masci, Duke University<br />
<br />
<br />
==Collaborations==<br />
<br />
* INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.<br />
* Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL.<br />
* Sirarat Sarntivijai and Oliver He, University of Michigan, development of the Cell Line Ontology.<br />
* The Plant Ontology Consortium, plant cell types.<br />
* David Osumi-Sutherland, Flybase, Drosophila cell types.<br />
* Onard Mejino, Foundation Model of Anatomy, import of FMA cell types<br />
* David Dougall and Richard Scheuermann, UT Southwestern, import of novel hematopoietic cell types identified via flow cytometry<br />
* Helen Parkinson, EBI, assistance in making cell types in CL and the Experimental Factor Ontology compatible and in providing support for experimentally derived cell types in OBI.<br />
<br><br><br />
<br />
==Item 1 - Activities==<br />
<br />
===Aim 1: Reforming the Structure of the Cell Ontology===<br />
<br />
*Devise new structure for the Cell Ontology<br />
**A new high level structure for the CL was approved at the May 2010 Cell Ontology Workshop. Parts have been implemented, and more will be in 2011.<br />
<br />
*Add formal logical axioms to the CL.<br />
**A system of OWL macro expansions has been developed for CL relations such as "capable_of" that allow for easy conversion to OWL versions that can be more fully reasoned over using Protege reasoners (see below).<br />
<br />
*Add logical definitions using other OBO ontologies<br />
**Extensive computable definitions (AKA "logical definitions" or "cross-products") have been added to terms in the hematopoietic cell branch of the CL, and to some other terms in the CL.<br />
**We have identified the following ontologies as key to defining cell types:<br />
***PRO - Protein Ontology<br />
***GO - Gene Ontology (particularly biological processes such as immune response)<br />
***PATO - Phenotypic Quality Ontology<br />
***Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.<br />
<br />
*Implement automated reasoner strategy<br />
**This has been an integral part of our ongoing development of the CL.<br />
<br />
* General software support<br />
**Support with managing ontology versions in Open Bio-Ontologies repository<br />
**OBO-Edit bug fixes (see below).<br />
<br><br />
<br />
===Aim 2: Improving and extending the content of CL===<br />
*We held a [http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology workshop], on May 18-19, 2010 at the Jackson Laborotory, Bar Harbor, Maine, and extensively discussed both ontological and biological aspects of CL development.<br />
*A workshop on neurons and nervous system cell types is scheduled for April 12-14, 2011. More information may be found [http://obofoundry.org/wiki/index.php/Cell_Ontology-INCF_Neuron_Workshop here].<br />
*We have implementing the computable defintion (AKA "logical definition" or "cross-product") formulation of the hematopoietic terms. As part of this work, we have improved definitions for a number of cell types and adding many new cell types.<br />
*A paper, "Logical Development of the Cell Ontology" by Meehan, Masci, Abdulla, Cowell, Blake, Mungal, and Diehl, which described the work on the hematopoietic cells in the CL has been accepted (December 2010) for publication in BMC Biouinformatics.<br />
*We have imported a large number of terms from the FMA into the CL.<br />
*We have added is_a parents to all terms in the CL.<br />
*We have prepared textual and logical definitions for current nervous system terms in the CL that lack them, although these are not yet implemented in cell.obo.<br />
*Over 400 new cell types have been added to CL in 2010.<br><br><br />
<br />
===Aim 3: Applying the CL to the GO===<br />
<br />
* We are using manual and automated methods to ensure interoperability between the GO and CL for cell types and the logical relationships between them.<br />
<br />
<br />
==Item 2 -- Percent Completion==<br />
<br />
* Based on current progress towards completion of our aims we are on track, with 60% of the work accomplished.<br><br><br />
<br />
== LBL Contributions to CL development ==<br />
<br />
ONTOLOGY ALIGNMENT AND INTEGRATION: we have supported the JAX ontology editors by providing and executing tools to integrate human cell types represented in the FMA (Foundational Model of Anatomy) into CL. These tools identified generic cell types in common between the two ontologies, and used the Obol toolkit (developed at Berkeley) to identify compositional class expressions for specific cell types (e.g. "smooth muscle cell of jejunum"). These compositional classes can then be integrated automatically, using the cross-species gross anatomy ontology UBERON.<br />
<br />
ONTOLOGY EDITOR SUPPORT: we have provided ontology editor support to the JAX editors of the ontology, improving the OBO-Edit ontology editing environment in reponse to curator requests. We have also implemented a variant of the MIREOT (Minimal Information Retrieved for External Ontology Terms) strategy which allows scalable integration across multiple ontologies. We have also devised a build environment for the CL, which allows the easy distribution of multiple versions for different purposes, and uses OWL reasoners to classify and perform logical consistency analysis on the ontology automatically.<br />
<br />
ONTOLOGY LANGUAGE SUPPORT: we identified key areas in which the ontology format used by the Gene Ontology was insufficient for representing cell types. Rather than move wholesale to the more expressive OWL (Ontology Web Langauge) formalism, which would have entailed abandoning tools and interoperation with model organism databases, we enhanced obo format using a macro mechanism and implemented a prototype macro expansion engine (http://precedings.nature.com/documents/5292/version/1). This allowed us to have the best of both worlds, and to be able to transition between the oboedit environment, and the Protege 4 editors environment, and to use OWL reasoners to classify the ontology.<br />
<br />
This work also necessitated creation of a formal specification of obo format and its translation to OWL ([http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html]), which significantly extends on previous efforts made in 2007, before the OWL2 language was finalized.<br><br><br />
<br />
==Related Publications for 2010==<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002].<br />
<br />
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD, 2010, Logical Development of the Cell Ontology, accepted for publication in BMC Bioinformatics.<br />
<br />
<br><br />
<br />
[[http://wiki.geneontology.org/index.php/Grant_Progress_Reports_December_2010 Return to 2010 Progress Reports]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Cell_Ontology_Progress_Report_2010&diff=32721Cell Ontology Progress Report 20102010-12-18T06:04:35Z<p>Adiehl: /* LBL Contributions to CL development */</p>
<hr />
<div>Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL.<br />
<br />
<br />
==Personnel==<br />
<br />
* '''Project Leaders'''<br />
** Alexander Diehl, The Jackson Laboratory/University at Buffalo (50% effort)<br />
** Christopher Mungall, LBNL (10% effort)<br />
<br />
* '''Cell Ontology Curator'''<br />
** Terrence Meehan, The Jackson Laboratory (100% effort)<br />
<br />
* '''Programmers'''<br />
** Amina Abdulla and Nomi Harris, LBNL (75% effort, split)<br />
<br />
* '''Senior Advisors'''<br />
** Judith Blake, The Jackson Laboratory<br />
** Suzanna Lewis, LBNL<br />
<br />
* '''External Consultants'''<br />
** Lindsay Cowell, Duke University<br />
** Anna Maria Masci, Duke University<br />
<br />
<br />
==Collaborations==<br />
<br />
* INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.<br />
* Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL.<br />
* Sirarat Sarntivijai and Oliver He, University of Michigan, development of the Cell Line Ontology.<br />
* The Plant Ontology Consortium, plant cell types.<br />
* David Osumi-Sutherland, Flybase, Drosophila cell types.<br />
* Onard Mejino, Foundation Model of Anatomy, import of FMA cell types<br />
* David Dougall and Richard Scheuermann, UT Southwestern, import of novel hematopoietic cell types identified via flow cytometry<br />
* Helen Parkinson, EBI, assistance in making cell types in CL and the Experimental Factor Ontology compatible and in providing support for experimentally derived cell types in OBI.<br />
<br><br><br />
<br />
==Item 1 - Activities==<br />
<br />
===Aim 1: Reforming the Structure of the Cell Ontology===<br />
<br />
*Devise new structure for the Cell Ontology<br />
**A new high level structure for the CL was approved at the May 2010 Cell Ontology Workshop. Parts have been implemented, and more will be in 2011.<br />
<br />
*Add formal logical axioms to the CL.<br />
**A system of OWL macro expansions has been developed for CL relations such as "capable_of" that allow for easy conversion to OWL versions that can be more fully reasoned over using Protege reasoners (see below).<br />
<br />
*Add logical definitions using other OBO ontologies<br />
**Extensive computable definitions (AKA "logical definitions" or "cross-products") have been added to terms in the hematopoietic cell branch of the CL, and to some other terms in the CL.<br />
**We have identified the following ontologies as key to defining cell types:<br />
***PRO - Protein Ontology<br />
***GO - Gene Ontology (particularly biological processes such as immune response)<br />
***PATO - Phenotypic Quality Ontology<br />
***Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.<br />
<br />
*Implement automated reasoner strategy<br />
**This has been an integral part of our ongoing development of the CL.<br />
<br />
* General software support<br />
**Support with managing ontology versions in Open Bio-Ontologies repository<br />
**OBO-Edit bug fixes (see below).<br />
<br><br />
<br />
===Aim 2: Improving and extending the content of CL===<br />
*We held a [http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology workshop], on May 18-19, 2010 at the Jackson Laborotory, Bar Harbor, Maine, and extensively discussed both ontological and biological aspects of CL development.<br />
*A workshop on neurons and nervous system cell types is scheduled for April 12-14, 2011. More information may be found [http://obofoundry.org/wiki/index.php/Cell_Ontology-INCF_Neuron_Workshop here].<br />
*We have implementing the computable defintion (AKA "logical definition" or "cross-product") formulation of the hematopoietic terms. As part of this work, we have improved definitions for a number of cell types and adding many new cell types.<br />
*A paper, "Logical Development of the Cell Ontology" by Meehan, Masci, Abdulla, Cowell, Blake, Mungal, and Diehl, which described the work on the hematopoietic cells in the CL has been accepted (December 2010) for publication in BMC Biouinformatics.<br />
*We have imported a large number of terms from the FMA into the CL.<br />
*We have added is_a parents to all terms in the CL.<br />
*We have prepared textual and logical definitions for current nervous system terms in the CL that lack them, although these are not yet implemented in cell.obo.<br><br><br />
<br />
===Aim 3: Applying the CL to the GO===<br />
<br />
* We are using manual and automated methods to ensure interoperability between the GO and CL for cell types and the logical relationships between them.<br />
<br />
<br />
==Item 2 -- Percent Completion==<br />
<br />
* Based on current progress towards completion of our aims we are on track, with 60% of the work accomplished.<br><br><br />
<br />
== LBL Contributions to CL development ==<br />
<br />
ONTOLOGY ALIGNMENT AND INTEGRATION: we have supported the JAX ontology editors by providing and executing tools to integrate human cell types represented in the FMA (Foundational Model of Anatomy) into CL. These tools identified generic cell types in common between the two ontologies, and used the Obol toolkit (developed at Berkeley) to identify compositional class expressions for specific cell types (e.g. "smooth muscle cell of jejunum"). These compositional classes can then be integrated automatically, using the cross-species gross anatomy ontology UBERON.<br />
<br />
ONTOLOGY EDITOR SUPPORT: we have provided ontology editor support to the JAX editors of the ontology, improving the OBO-Edit ontology editing environment in reponse to curator requests. We have also implemented a variant of the MIREOT (Minimal Information Retrieved for External Ontology Terms) strategy which allows scalable integration across multiple ontologies. We have also devised a build environment for the CL, which allows the easy distribution of multiple versions for different purposes, and uses OWL reasoners to classify and perform logical consistency analysis on the ontology automatically.<br />
<br />
ONTOLOGY LANGUAGE SUPPORT: we identified key areas in which the ontology format used by the Gene Ontology was insufficient for representing cell types. Rather than move wholesale to the more expressive OWL (Ontology Web Langauge) formalism, which would have entailed abandoning tools and interoperation with model organism databases, we enhanced obo format using a macro mechanism and implemented a prototype macro expansion engine (http://precedings.nature.com/documents/5292/version/1). This allowed us to have the best of both worlds, and to be able to transition between the oboedit environment, and the Protege 4 editors environment, and to use OWL reasoners to classify the ontology.<br />
<br />
This work also necessitated creation of a formal specification of obo format and its translation to OWL ([http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html]), which significantly extends on previous efforts made in 2007, before the OWL2 language was finalized.<br><br><br />
<br />
==Related Publications for 2010==<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002].<br />
<br />
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD, 2010, Logical Development of the Cell Ontology, accepted for publication in BMC Bioinformatics.<br />
<br />
<br><br />
<br />
[[http://wiki.geneontology.org/index.php/Grant_Progress_Reports_December_2010 Return to 2010 Progress Reports]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Cell_Ontology_Progress_Report_2010&diff=32720Cell Ontology Progress Report 20102010-12-18T06:03:27Z<p>Adiehl: /* LBL Contributions to CL development */</p>
<hr />
<div>Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL.<br />
<br />
<br />
==Personnel==<br />
<br />
* '''Project Leaders'''<br />
** Alexander Diehl, The Jackson Laboratory/University at Buffalo (50% effort)<br />
** Christopher Mungall, LBNL (10% effort)<br />
<br />
* '''Cell Ontology Curator'''<br />
** Terrence Meehan, The Jackson Laboratory (100% effort)<br />
<br />
* '''Programmers'''<br />
** Amina Abdulla and Nomi Harris, LBNL (75% effort, split)<br />
<br />
* '''Senior Advisors'''<br />
** Judith Blake, The Jackson Laboratory<br />
** Suzanna Lewis, LBNL<br />
<br />
* '''External Consultants'''<br />
** Lindsay Cowell, Duke University<br />
** Anna Maria Masci, Duke University<br />
<br />
<br />
==Collaborations==<br />
<br />
* INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.<br />
* Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL.<br />
* Sirarat Sarntivijai and Oliver He, University of Michigan, development of the Cell Line Ontology.<br />
* The Plant Ontology Consortium, plant cell types.<br />
* David Osumi-Sutherland, Flybase, Drosophila cell types.<br />
* Onard Mejino, Foundation Model of Anatomy, import of FMA cell types<br />
* David Dougall and Richard Scheuermann, UT Southwestern, import of novel hematopoietic cell types identified via flow cytometry<br />
* Helen Parkinson, EBI, assistance in making cell types in CL and the Experimental Factor Ontology compatible and in providing support for experimentally derived cell types in OBI.<br />
<br><br><br />
<br />
==Item 1 - Activities==<br />
<br />
===Aim 1: Reforming the Structure of the Cell Ontology===<br />
<br />
*Devise new structure for the Cell Ontology<br />
**A new high level structure for the CL was approved at the May 2010 Cell Ontology Workshop. Parts have been implemented, and more will be in 2011.<br />
<br />
*Add formal logical axioms to the CL.<br />
**A system of OWL macro expansions has been developed for CL relations such as "capable_of" that allow for easy conversion to OWL versions that can be more fully reasoned over using Protege reasoners (see below).<br />
<br />
*Add logical definitions using other OBO ontologies<br />
**Extensive computable definitions (AKA "logical definitions" or "cross-products") have been added to terms in the hematopoietic cell branch of the CL, and to some other terms in the CL.<br />
**We have identified the following ontologies as key to defining cell types:<br />
***PRO - Protein Ontology<br />
***GO - Gene Ontology (particularly biological processes such as immune response)<br />
***PATO - Phenotypic Quality Ontology<br />
***Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.<br />
<br />
*Implement automated reasoner strategy<br />
**This has been an integral part of our ongoing development of the CL.<br />
<br />
* General software support<br />
**Support with managing ontology versions in Open Bio-Ontologies repository<br />
**OBO-Edit bug fixes (see below).<br />
<br><br />
<br />
===Aim 2: Improving and extending the content of CL===<br />
*We held a [http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology workshop], on May 18-19, 2010 at the Jackson Laborotory, Bar Harbor, Maine, and extensively discussed both ontological and biological aspects of CL development.<br />
*A workshop on neurons and nervous system cell types is scheduled for April 12-14, 2011. More information may be found [http://obofoundry.org/wiki/index.php/Cell_Ontology-INCF_Neuron_Workshop here].<br />
*We have implementing the computable defintion (AKA "logical definition" or "cross-product") formulation of the hematopoietic terms. As part of this work, we have improved definitions for a number of cell types and adding many new cell types.<br />
*A paper, "Logical Development of the Cell Ontology" by Meehan, Masci, Abdulla, Cowell, Blake, Mungal, and Diehl, which described the work on the hematopoietic cells in the CL has been accepted (December 2010) for publication in BMC Biouinformatics.<br />
*We have imported a large number of terms from the FMA into the CL.<br />
*We have added is_a parents to all terms in the CL.<br />
*We have prepared textual and logical definitions for current nervous system terms in the CL that lack them, although these are not yet implemented in cell.obo.<br><br><br />
<br />
===Aim 3: Applying the CL to the GO===<br />
<br />
* We are using manual and automated methods to ensure interoperability between the GO and CL for cell types and the logical relationships between them.<br />
<br />
<br />
==Item 2 -- Percent Completion==<br />
<br />
* Based on current progress towards completion of our aims we are on track, with 60% of the work accomplished.<br><br><br />
<br />
== LBL Contributions to CL development ==<br />
<br />
ONTOLOGY ALIGNMENT AND INTEGRATION: we have supported the JAX ontology editors by providing and executing tools to integrate human cell types represented in the FMA (Foundational Model of Anatomy) into CL. These tools identified generic cell types in common between the two ontologies, and used the Obol toolkit (developed at Berkeley) to identify compositional class expressions for specific cell types (e.g. "smooth muscle cell of jejunum"). These compositional classes can then be integrated automatically, using the cross-species gross anatomy ontology UBERON.<br />
<br />
ONTOLOGY EDITOR SUPPORT: we have provided ontology editor support to the JAX editors of the ontology, improving the OBO-Edit ontology editing environment in reponse to curator requests. We have also implemented a variant of the MIREOT (Minimal Information Retrieved for External Ontology Terms) strategy which allows scalable integration across multiple ontologies. We have also devised a build environment for the CL, which allows the easy distribution of multiple versions for different purposes, and uses OWL reasoners to classify and perform logical consistency analysis on the ontology automatically.<br />
<br />
ONTOLOGY LANGUAGE SUPPORT: we identified key areas in which the ontology format used by the Gene Ontology was insufficient for representing cell types. Rather than move wholesale to the more expressive OWL (Ontology Web Langauge) formalism, which would have entailed abandoning tools and interoperation with model organism databases, we enhanced obo format using a macro mechanism and implemented a prototype macro expansion engine (http://precedings.nature.com/documents/5292/version/1). This allowed us to have the best of both worlds, and to be able to transition between the oboedit environment, and the Protege 4 editors environment, and to use OWL reasoners to classify the ontology.<br />
<br />
This work also necessitated creation of a formal specification of obo format and its translation to OWL ([http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html]), which significantly extends on previous efforts made in 2007, before theOWL2 language was finalized.<br><br><br />
<br />
==Related Publications for 2010==<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002].<br />
<br />
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD, 2010, Logical Development of the Cell Ontology, accepted for publication in BMC Bioinformatics.<br />
<br />
<br><br />
<br />
[[http://wiki.geneontology.org/index.php/Grant_Progress_Reports_December_2010 Return to 2010 Progress Reports]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Cell_Ontology_Progress_Report_2010&diff=32719Cell Ontology Progress Report 20102010-12-18T06:02:21Z<p>Adiehl: /* LBL Contributions to CL development */</p>
<hr />
<div>Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL.<br />
<br />
<br />
==Personnel==<br />
<br />
* '''Project Leaders'''<br />
** Alexander Diehl, The Jackson Laboratory/University at Buffalo (50% effort)<br />
** Christopher Mungall, LBNL (10% effort)<br />
<br />
* '''Cell Ontology Curator'''<br />
** Terrence Meehan, The Jackson Laboratory (100% effort)<br />
<br />
* '''Programmers'''<br />
** Amina Abdulla and Nomi Harris, LBNL (75% effort, split)<br />
<br />
* '''Senior Advisors'''<br />
** Judith Blake, The Jackson Laboratory<br />
** Suzanna Lewis, LBNL<br />
<br />
* '''External Consultants'''<br />
** Lindsay Cowell, Duke University<br />
** Anna Maria Masci, Duke University<br />
<br />
<br />
==Collaborations==<br />
<br />
* INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.<br />
* Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL.<br />
* Sirarat Sarntivijai and Oliver He, University of Michigan, development of the Cell Line Ontology.<br />
* The Plant Ontology Consortium, plant cell types.<br />
* David Osumi-Sutherland, Flybase, Drosophila cell types.<br />
* Onard Mejino, Foundation Model of Anatomy, import of FMA cell types<br />
* David Dougall and Richard Scheuermann, UT Southwestern, import of novel hematopoietic cell types identified via flow cytometry<br />
* Helen Parkinson, EBI, assistance in making cell types in CL and the Experimental Factor Ontology compatible and in providing support for experimentally derived cell types in OBI.<br />
<br><br><br />
<br />
==Item 1 - Activities==<br />
<br />
===Aim 1: Reforming the Structure of the Cell Ontology===<br />
<br />
*Devise new structure for the Cell Ontology<br />
**A new high level structure for the CL was approved at the May 2010 Cell Ontology Workshop. Parts have been implemented, and more will be in 2011.<br />
<br />
*Add formal logical axioms to the CL.<br />
**A system of OWL macro expansions has been developed for CL relations such as "capable_of" that allow for easy conversion to OWL versions that can be more fully reasoned over using Protege reasoners (see below).<br />
<br />
*Add logical definitions using other OBO ontologies<br />
**Extensive computable definitions (AKA "logical definitions" or "cross-products") have been added to terms in the hematopoietic cell branch of the CL, and to some other terms in the CL.<br />
**We have identified the following ontologies as key to defining cell types:<br />
***PRO - Protein Ontology<br />
***GO - Gene Ontology (particularly biological processes such as immune response)<br />
***PATO - Phenotypic Quality Ontology<br />
***Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.<br />
<br />
*Implement automated reasoner strategy<br />
**This has been an integral part of our ongoing development of the CL.<br />
<br />
* General software support<br />
**Support with managing ontology versions in Open Bio-Ontologies repository<br />
**OBO-Edit bug fixes (see below).<br />
<br><br />
<br />
===Aim 2: Improving and extending the content of CL===<br />
*We held a [http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology workshop], on May 18-19, 2010 at the Jackson Laborotory, Bar Harbor, Maine, and extensively discussed both ontological and biological aspects of CL development.<br />
*A workshop on neurons and nervous system cell types is scheduled for April 12-14, 2011. More information may be found [http://obofoundry.org/wiki/index.php/Cell_Ontology-INCF_Neuron_Workshop here].<br />
*We have implementing the computable defintion (AKA "logical definition" or "cross-product") formulation of the hematopoietic terms. As part of this work, we have improved definitions for a number of cell types and adding many new cell types.<br />
*A paper, "Logical Development of the Cell Ontology" by Meehan, Masci, Abdulla, Cowell, Blake, Mungal, and Diehl, which described the work on the hematopoietic cells in the CL has been accepted (December 2010) for publication in BMC Biouinformatics.<br />
*We have imported a large number of terms from the FMA into the CL.<br />
*We have added is_a parents to all terms in the CL.<br />
*We have prepared textual and logical definitions for current nervous system terms in the CL that lack them, although these are not yet implemented in cell.obo.<br><br><br />
<br />
===Aim 3: Applying the CL to the GO===<br />
<br />
* We are using manual and automated methods to ensure interoperability between the GO and CL for cell types and the logical relationships between them.<br />
<br />
<br />
==Item 2 -- Percent Completion==<br />
<br />
* Based on current progress towards completion of our aims we are on track, with 60% of the work accomplished.<br><br><br />
<br />
== LBL Contributions to CL development ==<br />
<br />
ONTOLOGY ALIGNMENT AND INTEGRATION: we have supported the JAX ontology editors by providing and executing tools to integrate human cell types represented in the FMA (Foundational Model of Anatomy) into CL. These tools identified generic cell types in common between the two ontologies, and used the Obol toolkit (developed at Berkeley) to identify compositional class expressions for specific cell types (e.g. "smooth muscle cell of jejunum"). These compositional classes can then be integrated automatically, using the cross-species gross anatomy ontology UBERON.<br />
<br />
ONTOLOGY EDITOR SUPPORT: we have provided ontology editor support to the JAX editors of the ontology, improving the OBO-Edit ontology editing environment in reponse to curator requests. We have also implemented a variant of the MIREOT (Minimal Information Retrieved for External Ontology Terms) strategy which allows scalable integration across multiple ontologies. We have also devised a build environment for the CL, which allows the easy distribution of multiple versions for different purposes, and uses OWL reasoners to classify and perform logical consistency analysis on the ontology automatically.<br />
<br />
ONTOLOGY LANGUAGE SUPPORT: we identified key areas in which the ontology format used by the Gene Ontology was insufficient for representing cell types. Rather than move wholesale to the more expressive OWL (Ontology Web Langauge) formalism, which would have entailed abandoning tools and interoperation with model organism databases, we enhanced obo format using a macro mechanism and implemented a prototype macro expansion engine (http://precedings.nature.com/documents/5292/version/1). This allowed us to have the best of both worlds, and to be able to transition between the oboedit environment, and the Protege 4 editors environment, and to use OWL reasoners to classify the ontology.<br />
<br />
This work also necessitated creation of a formal specification of obo format and its translation to OWL ([http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html]), which significantly extends on previous efforts made in 2007, before theOWL2 language was finalized.<br />
<br />
==Related Publications for 2010==<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002].<br />
<br />
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD, 2010, Logical Development of the Cell Ontology, accepted for publication in BMC Bioinformatics.<br />
<br />
<br><br />
<br />
[[http://wiki.geneontology.org/index.php/Grant_Progress_Reports_December_2010 Return to 2010 Progress Reports]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Cell_Ontology_Progress_Report_2010&diff=32718Cell Ontology Progress Report 20102010-12-18T06:02:01Z<p>Adiehl: /* LBL Contributions to CL development */</p>
<hr />
<div>Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL.<br />
<br />
<br />
==Personnel==<br />
<br />
* '''Project Leaders'''<br />
** Alexander Diehl, The Jackson Laboratory/University at Buffalo (50% effort)<br />
** Christopher Mungall, LBNL (10% effort)<br />
<br />
* '''Cell Ontology Curator'''<br />
** Terrence Meehan, The Jackson Laboratory (100% effort)<br />
<br />
* '''Programmers'''<br />
** Amina Abdulla and Nomi Harris, LBNL (75% effort, split)<br />
<br />
* '''Senior Advisors'''<br />
** Judith Blake, The Jackson Laboratory<br />
** Suzanna Lewis, LBNL<br />
<br />
* '''External Consultants'''<br />
** Lindsay Cowell, Duke University<br />
** Anna Maria Masci, Duke University<br />
<br />
<br />
==Collaborations==<br />
<br />
* INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.<br />
* Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL.<br />
* Sirarat Sarntivijai and Oliver He, University of Michigan, development of the Cell Line Ontology.<br />
* The Plant Ontology Consortium, plant cell types.<br />
* David Osumi-Sutherland, Flybase, Drosophila cell types.<br />
* Onard Mejino, Foundation Model of Anatomy, import of FMA cell types<br />
* David Dougall and Richard Scheuermann, UT Southwestern, import of novel hematopoietic cell types identified via flow cytometry<br />
* Helen Parkinson, EBI, assistance in making cell types in CL and the Experimental Factor Ontology compatible and in providing support for experimentally derived cell types in OBI.<br />
<br><br><br />
<br />
==Item 1 - Activities==<br />
<br />
===Aim 1: Reforming the Structure of the Cell Ontology===<br />
<br />
*Devise new structure for the Cell Ontology<br />
**A new high level structure for the CL was approved at the May 2010 Cell Ontology Workshop. Parts have been implemented, and more will be in 2011.<br />
<br />
*Add formal logical axioms to the CL.<br />
**A system of OWL macro expansions has been developed for CL relations such as "capable_of" that allow for easy conversion to OWL versions that can be more fully reasoned over using Protege reasoners (see below).<br />
<br />
*Add logical definitions using other OBO ontologies<br />
**Extensive computable definitions (AKA "logical definitions" or "cross-products") have been added to terms in the hematopoietic cell branch of the CL, and to some other terms in the CL.<br />
**We have identified the following ontologies as key to defining cell types:<br />
***PRO - Protein Ontology<br />
***GO - Gene Ontology (particularly biological processes such as immune response)<br />
***PATO - Phenotypic Quality Ontology<br />
***Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.<br />
<br />
*Implement automated reasoner strategy<br />
**This has been an integral part of our ongoing development of the CL.<br />
<br />
* General software support<br />
**Support with managing ontology versions in Open Bio-Ontologies repository<br />
**OBO-Edit bug fixes (see below).<br />
<br><br />
<br />
===Aim 2: Improving and extending the content of CL===<br />
*We held a [http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology workshop], on May 18-19, 2010 at the Jackson Laborotory, Bar Harbor, Maine, and extensively discussed both ontological and biological aspects of CL development.<br />
*A workshop on neurons and nervous system cell types is scheduled for April 12-14, 2011. More information may be found [http://obofoundry.org/wiki/index.php/Cell_Ontology-INCF_Neuron_Workshop here].<br />
*We have implementing the computable defintion (AKA "logical definition" or "cross-product") formulation of the hematopoietic terms. As part of this work, we have improved definitions for a number of cell types and adding many new cell types.<br />
*A paper, "Logical Development of the Cell Ontology" by Meehan, Masci, Abdulla, Cowell, Blake, Mungal, and Diehl, which described the work on the hematopoietic cells in the CL has been accepted (December 2010) for publication in BMC Biouinformatics.<br />
*We have imported a large number of terms from the FMA into the CL.<br />
*We have added is_a parents to all terms in the CL.<br />
*We have prepared textual and logical definitions for current nervous system terms in the CL that lack them, although these are not yet implemented in cell.obo.<br><br><br />
<br />
===Aim 3: Applying the CL to the GO===<br />
<br />
* We are using manual and automated methods to ensure interoperability between the GO and CL for cell types and the logical relationships between them.<br />
<br />
<br />
==Item 2 -- Percent Completion==<br />
<br />
* Based on current progress towards completion of our aims we are on track, with 60% of the work accomplished.<br><br><br />
<br />
== LBL Contributions to CL development ==<br />
<br />
ONTOLOGY ALIGNMENT AND INTEGRATION: we have supported the JAX ontology editors by providing and executing tools to integrate human cell types represented in the FMA (Foundational Model of Anatomy) into CL. These tools identified generic cell types in common between the two ontologies, and used the Obol toolkit (developed at Berkeley) to identify compositional class expressions for specific cell types (e.g. "smooth muscle cell of jejunum"). These compositional classescan then be integrated automatically, using the cross-species gross anatomy ontology UBERON.<br />
<br />
ONTOLOGY EDITOR SUPPORT: we have provided ontology editor support to the JAX editors of the ontology, improving the OBO-Edit ontology editing environment in reponse to curator requests. We have also implemented a variant of the MIREOT (Minimal Information Retrieved for External Ontology Terms) strategy which allows scalable integration across multiple ontologies. We have also devised a build environment for the CL, which allows the easy distribution of multiple versions for different purposes, and uses OWL reasoners to classify and perform logical consistency analysis on the ontology automatically.<br />
<br />
ONTOLOGY LANGUAGE SUPPORT: we identified key areas in which the ontology format used by the Gene Ontology was insufficient for representing cell types. Rather than move wholesale to the more expressive OWL (Ontology Web Langauge) formalism, which would have entailed abandoning tools and interoperation with model organism databases, we enhanced obo format using a macro mechanism and implemented a prototype macro expansion engine (http://precedings.nature.com/documents/5292/version/1). This allowed us to have the best of both worlds, and to be able to transition between the oboedit environment, and the Protege 4 editors environment, and to use OWL reasoners to classify the ontology.<br />
<br />
This work also necessitated creation of a formal specification of obo format and its translation to OWL ([http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html]), which significantly extends on previous efforts made in 2007, before theOWL2 language was finalized.<br />
<br />
==Related Publications for 2010==<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002].<br />
<br />
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD, 2010, Logical Development of the Cell Ontology, accepted for publication in BMC Bioinformatics.<br />
<br />
<br><br />
<br />
[[http://wiki.geneontology.org/index.php/Grant_Progress_Reports_December_2010 Return to 2010 Progress Reports]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Cell_Ontology_Progress_Report_2010&diff=32717Cell Ontology Progress Report 20102010-12-18T06:01:30Z<p>Adiehl: /* Item 2 -- Percent Completion */</p>
<hr />
<div>Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL.<br />
<br />
<br />
==Personnel==<br />
<br />
* '''Project Leaders'''<br />
** Alexander Diehl, The Jackson Laboratory/University at Buffalo (50% effort)<br />
** Christopher Mungall, LBNL (10% effort)<br />
<br />
* '''Cell Ontology Curator'''<br />
** Terrence Meehan, The Jackson Laboratory (100% effort)<br />
<br />
* '''Programmers'''<br />
** Amina Abdulla and Nomi Harris, LBNL (75% effort, split)<br />
<br />
* '''Senior Advisors'''<br />
** Judith Blake, The Jackson Laboratory<br />
** Suzanna Lewis, LBNL<br />
<br />
* '''External Consultants'''<br />
** Lindsay Cowell, Duke University<br />
** Anna Maria Masci, Duke University<br />
<br />
<br />
==Collaborations==<br />
<br />
* INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.<br />
* Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL.<br />
* Sirarat Sarntivijai and Oliver He, University of Michigan, development of the Cell Line Ontology.<br />
* The Plant Ontology Consortium, plant cell types.<br />
* David Osumi-Sutherland, Flybase, Drosophila cell types.<br />
* Onard Mejino, Foundation Model of Anatomy, import of FMA cell types<br />
* David Dougall and Richard Scheuermann, UT Southwestern, import of novel hematopoietic cell types identified via flow cytometry<br />
* Helen Parkinson, EBI, assistance in making cell types in CL and the Experimental Factor Ontology compatible and in providing support for experimentally derived cell types in OBI.<br />
<br><br><br />
<br />
==Item 1 - Activities==<br />
<br />
===Aim 1: Reforming the Structure of the Cell Ontology===<br />
<br />
*Devise new structure for the Cell Ontology<br />
**A new high level structure for the CL was approved at the May 2010 Cell Ontology Workshop. Parts have been implemented, and more will be in 2011.<br />
<br />
*Add formal logical axioms to the CL.<br />
**A system of OWL macro expansions has been developed for CL relations such as "capable_of" that allow for easy conversion to OWL versions that can be more fully reasoned over using Protege reasoners (see below).<br />
<br />
*Add logical definitions using other OBO ontologies<br />
**Extensive computable definitions (AKA "logical definitions" or "cross-products") have been added to terms in the hematopoietic cell branch of the CL, and to some other terms in the CL.<br />
**We have identified the following ontologies as key to defining cell types:<br />
***PRO - Protein Ontology<br />
***GO - Gene Ontology (particularly biological processes such as immune response)<br />
***PATO - Phenotypic Quality Ontology<br />
***Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.<br />
<br />
*Implement automated reasoner strategy<br />
**This has been an integral part of our ongoing development of the CL.<br />
<br />
* General software support<br />
**Support with managing ontology versions in Open Bio-Ontologies repository<br />
**OBO-Edit bug fixes (see below).<br />
<br><br />
<br />
===Aim 2: Improving and extending the content of CL===<br />
*We held a [http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology workshop], on May 18-19, 2010 at the Jackson Laborotory, Bar Harbor, Maine, and extensively discussed both ontological and biological aspects of CL development.<br />
*A workshop on neurons and nervous system cell types is scheduled for April 12-14, 2011. More information may be found [http://obofoundry.org/wiki/index.php/Cell_Ontology-INCF_Neuron_Workshop here].<br />
*We have implementing the computable defintion (AKA "logical definition" or "cross-product") formulation of the hematopoietic terms. As part of this work, we have improved definitions for a number of cell types and adding many new cell types.<br />
*A paper, "Logical Development of the Cell Ontology" by Meehan, Masci, Abdulla, Cowell, Blake, Mungal, and Diehl, which described the work on the hematopoietic cells in the CL has been accepted (December 2010) for publication in BMC Biouinformatics.<br />
*We have imported a large number of terms from the FMA into the CL.<br />
*We have added is_a parents to all terms in the CL.<br />
*We have prepared textual and logical definitions for current nervous system terms in the CL that lack them, although these are not yet implemented in cell.obo.<br><br><br />
<br />
===Aim 3: Applying the CL to the GO===<br />
<br />
* We are using manual and automated methods to ensure interoperability between the GO and CL for cell types and the logical relationships between them.<br />
<br />
<br />
==Item 2 -- Percent Completion==<br />
<br />
* Based on current progress towards completion of our aims we are on track, with 60% of the work accomplished.<br><br><br />
<br />
== LBL Contributions to CL development ==<br />
<br />
ONTOLOGY ALIGNMENT AND INTEGRATION: we have supported the JAX ontology editors by providing and executing tools to integrate human cell types represented in the FMA (Foundational Model of Anatomy) into CL. These tools identified generic cell types in common between the two ontologies, and used the Obol toolkit (developed at Berkeley) to identify compositional class expressions for specific cell types (e.g. "smooth muscle cell of jejunum"). These compositional classescan then be integrated automatically, using the cross-species gross anatomy ontology UBERON.<br />
<br />
ONTOLOGY EDITOR SUPPORT: we have provided ontology editor support to the JAX editors of the ontology, improving the OBO-Edit ontology editing environment in reponse to curator requests. We have also implemented a variant of the MIREOT (Minimal Information Retrieved for External Ontology Terms) strategy which allows scalable integration across multiple ontologies. We have also devised a build environment for the CL, which allows the easy distribution of multiple versions for different purposes, and uses OWL reasoners to classify and perform logical consistency analysis on the ontology automatically.<br />
<br />
ONTOLOGY LANGUAGE SUPPORT: we identified key areas in which the ontology format used by the Gene Ontology was insufficient for representing cell types. Rather than move wholesale to the more expressive OWL (Ontology Web Langauge) formalism, which would have entailed abandoning tools and interoperation with model organism databases, we enhanced obo format using a macro mechanism and implemented a prototype macro expansion engine (http://precedings.nature.com/documents/5292/version/1). This allowed us to have the best of both worlds, and to be able to transition between the oboedit environment, and the Protege4 editors environment, and to use OWL reasoners to classify the ontology.<br />
<br />
This work also necessitated creation of a formal specification of obo format and its translation to OWL ([http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html]), which significantly extends on previous efforts made in 2007, before theOWL2 language was finalized.<br />
<br />
<br />
<br />
==Related Publications for 2010==<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002].<br />
<br />
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD, 2010, Logical Development of the Cell Ontology, accepted for publication in BMC Bioinformatics.<br />
<br />
<br><br />
<br />
[[http://wiki.geneontology.org/index.php/Grant_Progress_Reports_December_2010 Return to 2010 Progress Reports]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Cell_Ontology_Progress_Report_2010&diff=32716Cell Ontology Progress Report 20102010-12-18T06:01:04Z<p>Adiehl: /* Aim 1: Reforming the Structure of the Cell Ontology */</p>
<hr />
<div>Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL.<br />
<br />
<br />
==Personnel==<br />
<br />
* '''Project Leaders'''<br />
** Alexander Diehl, The Jackson Laboratory/University at Buffalo (50% effort)<br />
** Christopher Mungall, LBNL (10% effort)<br />
<br />
* '''Cell Ontology Curator'''<br />
** Terrence Meehan, The Jackson Laboratory (100% effort)<br />
<br />
* '''Programmers'''<br />
** Amina Abdulla and Nomi Harris, LBNL (75% effort, split)<br />
<br />
* '''Senior Advisors'''<br />
** Judith Blake, The Jackson Laboratory<br />
** Suzanna Lewis, LBNL<br />
<br />
* '''External Consultants'''<br />
** Lindsay Cowell, Duke University<br />
** Anna Maria Masci, Duke University<br />
<br />
<br />
==Collaborations==<br />
<br />
* INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.<br />
* Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL.<br />
* Sirarat Sarntivijai and Oliver He, University of Michigan, development of the Cell Line Ontology.<br />
* The Plant Ontology Consortium, plant cell types.<br />
* David Osumi-Sutherland, Flybase, Drosophila cell types.<br />
* Onard Mejino, Foundation Model of Anatomy, import of FMA cell types<br />
* David Dougall and Richard Scheuermann, UT Southwestern, import of novel hematopoietic cell types identified via flow cytometry<br />
* Helen Parkinson, EBI, assistance in making cell types in CL and the Experimental Factor Ontology compatible and in providing support for experimentally derived cell types in OBI.<br />
<br><br><br />
<br />
==Item 1 - Activities==<br />
<br />
===Aim 1: Reforming the Structure of the Cell Ontology===<br />
<br />
*Devise new structure for the Cell Ontology<br />
**A new high level structure for the CL was approved at the May 2010 Cell Ontology Workshop. Parts have been implemented, and more will be in 2011.<br />
<br />
*Add formal logical axioms to the CL.<br />
**A system of OWL macro expansions has been developed for CL relations such as "capable_of" that allow for easy conversion to OWL versions that can be more fully reasoned over using Protege reasoners (see below).<br />
<br />
*Add logical definitions using other OBO ontologies<br />
**Extensive computable definitions (AKA "logical definitions" or "cross-products") have been added to terms in the hematopoietic cell branch of the CL, and to some other terms in the CL.<br />
**We have identified the following ontologies as key to defining cell types:<br />
***PRO - Protein Ontology<br />
***GO - Gene Ontology (particularly biological processes such as immune response)<br />
***PATO - Phenotypic Quality Ontology<br />
***Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.<br />
<br />
*Implement automated reasoner strategy<br />
**This has been an integral part of our ongoing development of the CL.<br />
<br />
* General software support<br />
**Support with managing ontology versions in Open Bio-Ontologies repository<br />
**OBO-Edit bug fixes (see below).<br />
<br><br />
<br />
===Aim 2: Improving and extending the content of CL===<br />
*We held a [http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology workshop], on May 18-19, 2010 at the Jackson Laborotory, Bar Harbor, Maine, and extensively discussed both ontological and biological aspects of CL development.<br />
*A workshop on neurons and nervous system cell types is scheduled for April 12-14, 2011. More information may be found [http://obofoundry.org/wiki/index.php/Cell_Ontology-INCF_Neuron_Workshop here].<br />
*We have implementing the computable defintion (AKA "logical definition" or "cross-product") formulation of the hematopoietic terms. As part of this work, we have improved definitions for a number of cell types and adding many new cell types.<br />
*A paper, "Logical Development of the Cell Ontology" by Meehan, Masci, Abdulla, Cowell, Blake, Mungal, and Diehl, which described the work on the hematopoietic cells in the CL has been accepted (December 2010) for publication in BMC Biouinformatics.<br />
*We have imported a large number of terms from the FMA into the CL.<br />
*We have added is_a parents to all terms in the CL.<br />
*We have prepared textual and logical definitions for current nervous system terms in the CL that lack them, although these are not yet implemented in cell.obo.<br><br><br />
<br />
===Aim 3: Applying the CL to the GO===<br />
<br />
* We are using manual and automated methods to ensure interoperability between the GO and CL for cell types and the logical relationships between them.<br />
<br />
<br />
==Item 2 -- Percent Completion==<br />
<br />
* Based on current progress towards completion of our aims we are on track, with 60% of the work accomplished.<br />
<br />
== LBL Contributions to CL development ==<br />
<br />
ONTOLOGY ALIGNMENT AND INTEGRATION: we have supported the JAX ontology editors by providing and executing tools to integrate human cell types represented in the FMA (Foundational Model of Anatomy) into CL. These tools identified generic cell types in common between the two ontologies, and used the Obol toolkit (developed at Berkeley) to identify compositional class expressions for specific cell types (e.g. "smooth muscle cell of jejunum"). These compositional classescan then be integrated automatically, using the cross-species gross anatomy ontology UBERON.<br />
<br />
ONTOLOGY EDITOR SUPPORT: we have provided ontology editor support to the JAX editors of the ontology, improving the OBO-Edit ontology editing environment in reponse to curator requests. We have also implemented a variant of the MIREOT (Minimal Information Retrieved for External Ontology Terms) strategy which allows scalable integration across multiple ontologies. We have also devised a build environment for the CL, which allows the easy distribution of multiple versions for different purposes, and uses OWL reasoners to classify and perform logical consistency analysis on the ontology automatically.<br />
<br />
ONTOLOGY LANGUAGE SUPPORT: we identified key areas in which the ontology format used by the Gene Ontology was insufficient for representing cell types. Rather than move wholesale to the more expressive OWL (Ontology Web Langauge) formalism, which would have entailed abandoning tools and interoperation with model organism databases, we enhanced obo format using a macro mechanism and implemented a prototype macro expansion engine (http://precedings.nature.com/documents/5292/version/1). This allowed us to have the best of both worlds, and to be able to transition between the oboedit environment, and the Protege4 editors environment, and to use OWL reasoners to classify the ontology.<br />
<br />
This work also necessitated creation of a formal specification of obo format and its translation to OWL ([http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html]), which significantly extends on previous efforts made in 2007, before theOWL2 language was finalized.<br />
<br />
<br />
<br />
==Related Publications for 2010==<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002].<br />
<br />
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD, 2010, Logical Development of the Cell Ontology, accepted for publication in BMC Bioinformatics.<br />
<br />
<br><br />
<br />
[[http://wiki.geneontology.org/index.php/Grant_Progress_Reports_December_2010 Return to 2010 Progress Reports]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Cell_Ontology_Progress_Report_2010&diff=32715Cell Ontology Progress Report 20102010-12-18T05:59:11Z<p>Adiehl: </p>
<hr />
<div>Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL.<br />
<br />
<br />
==Personnel==<br />
<br />
* '''Project Leaders'''<br />
** Alexander Diehl, The Jackson Laboratory/University at Buffalo (50% effort)<br />
** Christopher Mungall, LBNL (10% effort)<br />
<br />
* '''Cell Ontology Curator'''<br />
** Terrence Meehan, The Jackson Laboratory (100% effort)<br />
<br />
* '''Programmers'''<br />
** Amina Abdulla and Nomi Harris, LBNL (75% effort, split)<br />
<br />
* '''Senior Advisors'''<br />
** Judith Blake, The Jackson Laboratory<br />
** Suzanna Lewis, LBNL<br />
<br />
* '''External Consultants'''<br />
** Lindsay Cowell, Duke University<br />
** Anna Maria Masci, Duke University<br />
<br />
<br />
==Collaborations==<br />
<br />
* INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.<br />
* Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL.<br />
* Sirarat Sarntivijai and Oliver He, University of Michigan, development of the Cell Line Ontology.<br />
* The Plant Ontology Consortium, plant cell types.<br />
* David Osumi-Sutherland, Flybase, Drosophila cell types.<br />
* Onard Mejino, Foundation Model of Anatomy, import of FMA cell types<br />
* David Dougall and Richard Scheuermann, UT Southwestern, import of novel hematopoietic cell types identified via flow cytometry<br />
* Helen Parkinson, EBI, assistance in making cell types in CL and the Experimental Factor Ontology compatible and in providing support for experimentally derived cell types in OBI.<br />
<br><br><br />
<br />
==Item 1 - Activities==<br />
<br />
===Aim 1: Reforming the Structure of the Cell Ontology===<br />
<br />
*Devise new structure for the Cell Ontology<br />
**A new high level structure for the CL was approved at the May 2010 Cell Ontology Workshop. Parts have been implemented, and more will be in 2011.<br />
<br />
*Add formal logical axioms to the CL.<br />
**A system of OWL macro expansions has been developed for CL relations such as "capable_of" that allow for easy conversion to OWL versions that can be more fully reasoned over using Protege reasoners.<br />
<br />
*Add logical definitions using other OBO ontologies<br />
**Extensive computable definitions (AKA "logical definitions" or "cross-products") have been added to terms in the hematopoietic cell branch of the CL, and to some other terms in the CL.<br />
**We have identified the following ontologies as key to defining cell types:<br />
***PRO - Protein Ontology<br />
***GO - Gene Ontology (particularly biological processes such as immune response)<br />
*** PATO - Phenotypic Quality Ontology<br />
*** Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.<br />
<br />
*Implement automated reasoner strategy<br />
**This has been an integral part of our ongoing development of the CL.<br />
<br />
* General software support<br />
**Support with managing ontology versions in Open Bio-Ontologies repository<br />
**OBO-Edit bug fixes<br />
<br><br />
<br />
===Aim 2: Improving and extending the content of CL===<br />
*We held a [http://obofoundry.org/wiki/index.php/Cell_Ontology_Workshop_2010 Cell Ontology workshop], on May 18-19, 2010 at the Jackson Laborotory, Bar Harbor, Maine, and extensively discussed both ontological and biological aspects of CL development.<br />
*A workshop on neurons and nervous system cell types is scheduled for April 12-14, 2011. More information may be found [http://obofoundry.org/wiki/index.php/Cell_Ontology-INCF_Neuron_Workshop here].<br />
*We have implementing the computable defintion (AKA "logical definition" or "cross-product") formulation of the hematopoietic terms. As part of this work, we have improved definitions for a number of cell types and adding many new cell types.<br />
*A paper, "Logical Development of the Cell Ontology" by Meehan, Masci, Abdulla, Cowell, Blake, Mungal, and Diehl, which described the work on the hematopoietic cells in the CL has been accepted (December 2010) for publication in BMC Biouinformatics.<br />
*We have imported a large number of terms from the FMA into the CL.<br />
*We have added is_a parents to all terms in the CL.<br />
*We have prepared textual and logical definitions for current nervous system terms in the CL that lack them, although these are not yet implemented in cell.obo.<br><br><br />
<br />
===Aim 3: Applying the CL to the GO===<br />
<br />
* We are using manual and automated methods to ensure interoperability between the GO and CL for cell types and the logical relationships between them.<br />
<br />
<br />
==Item 2 -- Percent Completion==<br />
<br />
* Based on current progress towards completion of our aims we are on track, with 60% of the work accomplished.<br />
<br />
== LBL Contributions to CL development ==<br />
<br />
ONTOLOGY ALIGNMENT AND INTEGRATION: we have supported the JAX ontology editors by providing and executing tools to integrate human cell types represented in the FMA (Foundational Model of Anatomy) into CL. These tools identified generic cell types in common between the two ontologies, and used the Obol toolkit (developed at Berkeley) to identify compositional class expressions for specific cell types (e.g. "smooth muscle cell of jejunum"). These compositional classescan then be integrated automatically, using the cross-species gross anatomy ontology UBERON.<br />
<br />
ONTOLOGY EDITOR SUPPORT: we have provided ontology editor support to the JAX editors of the ontology, improving the OBO-Edit ontology editing environment in reponse to curator requests. We have also implemented a variant of the MIREOT (Minimal Information Retrieved for External Ontology Terms) strategy which allows scalable integration across multiple ontologies. We have also devised a build environment for the CL, which allows the easy distribution of multiple versions for different purposes, and uses OWL reasoners to classify and perform logical consistency analysis on the ontology automatically.<br />
<br />
ONTOLOGY LANGUAGE SUPPORT: we identified key areas in which the ontology format used by the Gene Ontology was insufficient for representing cell types. Rather than move wholesale to the more expressive OWL (Ontology Web Langauge) formalism, which would have entailed abandoning tools and interoperation with model organism databases, we enhanced obo format using a macro mechanism and implemented a prototype macro expansion engine (http://precedings.nature.com/documents/5292/version/1). This allowed us to have the best of both worlds, and to be able to transition between the oboedit environment, and the Protege4 editors environment, and to use OWL reasoners to classify the ontology.<br />
<br />
This work also necessitated creation of a formal specification of obo format and its translation to OWL ([http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html]), which significantly extends on previous efforts made in 2007, before theOWL2 language was finalized.<br />
<br />
<br />
<br />
==Related Publications for 2010==<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002].<br />
<br />
Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD, 2010, Logical Development of the Cell Ontology, accepted for publication in BMC Bioinformatics.<br />
<br />
<br><br />
<br />
[[http://wiki.geneontology.org/index.php/Grant_Progress_Reports_December_2010 Return to 2010 Progress Reports]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Cell_Ontology_Progress_Report_2010&diff=32527Cell Ontology Progress Report 20102010-12-10T20:38:20Z<p>Adiehl: </p>
<hr />
<div><big>STILL UNDER REVISION (12-10-10)</big><br />
<br />
Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL.<br />
<br />
<br />
==Personnel==<br />
<br />
* '''Project Leaders'''<br />
** Alexander Diehl, The Jackson Laboratory/University at Buffalo (50% effort)<br />
** Christopher Mungall, LBNL (10% effort)<br />
<br />
* '''Cell Ontology Curator'''<br />
** Terrence Meehan, The Jackson Laboratory (100% effort)<br />
<br />
* '''Programmers'''<br />
** Amina Abdulla and Nomi Harris, LBNL (75% effort, split)<br />
<br />
* '''Senior Advisors'''<br />
** Judith Blake, The Jackson Laboratory<br />
** Suzanna Lewis, LBNL<br />
<br />
* '''External Consultants'''<br />
** Lindsay Cowell, Duke University<br />
** Anna Maria Masci, Duke University<br />
<br />
<br />
==Collaborations==<br />
<br />
* INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.<br />
* Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL.<br />
* Sirarat Sarntivijai and Oliver He, University of Michigan, development of the Cell Line Ontology.<br />
* The Plant Ontology Consortium, plant cell types.<br />
* David Osumi-Sutherland, Flybase, Drosophila cell types.<br />
* Onard Mejino, Foundation Model of Anatomy, import of FMA cell types<br />
* David Dougall and Richard Scheuermann, UT Southwestern, import of novel hematopoietic cell types identified via flow cytometry<br />
* Helen Parkinson, EBI, assistance in making cell types in CL and the Experimental Factor Ontology compatible and in providing support for experimentally derived cell types in OBI.<br />
<br><br><br />
<br />
==Item 1 - Activities==<br />
<br />
===Aim 1: Reforming the Structure of the Cell Ontology===<br />
<br />
*Devise new structure for the Cell Ontology<br />
**We have been prototyping the new CL structure using the hematopoeitic cell types as a test case.<br />
**Started month: 1<br />
**Estimated duration: 6 months<br />
<br />
*Add formal logical axioms to the CL.<br />
**We have made the first steps towards adding logical axioms to theCL. The first is the formal definition of the capable_of relation, required for linking cell types to biological processes (for example, Tr1 cells to IL-10 production). The LBL group has created the formal definition in terms of the Basic Formal Ontology (BFO) "disposition" class, and whilst the Jackson group has applied this in the prototype ontology.<br />
**Started month: 1<br />
**Estimated duration: 6 months<br />
<br />
*Add logical definitions using other OBO ontologies<br />
**We have identified the following ontologies as key to defining cell types:<br />
***PRO - Protein Ontology<br />
***GO - Gene Ontology (particularly biological processes such as immune response)<br />
*** PATO - Phenotypic Quality Ontology<br />
*** Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.<br />
**Started month: 1<br />
**Estimated duration: 6 months<br />
<br />
*Implement automated reasoner strategy<br />
**Although we do not estimate commencing this until month 6 we have made some preliminary steps, partially implementing the MIREOT methodology within OBO-Edit. This allows the CL editors at Jackson to select classes from external ontologies and bring in only the subset of those ontologies that pertain to these referenced classes. This improves reasoner performance.<br />
**Estimated start month: 6<br />
**Estimated duration: 3 months<br />
<br />
* General software support<br />
**Support with managing ontology versions in Open Bio-Ontologies repository<br />
**OBO-Edit bug fixes<br />
**OBO-Edit tutorials for CL curators<br />
<br><br />
<br />
===Aim 2: Improving and extending the content of CL===<br />
*We have begun planning for a Cell Ontology workshop, to be held May 18-19, 2009 at the Jackson Laborotory, Bar Harbor, Maine. The workshop will be used for discussion of general issues involved in the revision of the Cell Ontology.<br />
*We are implementing the cross-product/logical definition formulation of the hematopoietic terms. As part of this work, we are improving definitions for a number of cell types and adding new cell types.<br />
*We are working to add is_a parents to all terms in the CL.<br />
*We are preparing definitions for current nervous system terms in the CL that lack them.<br><br><br />
<br />
===Aim 3: Applying the CL to the GO===<br />
<br />
* This work is to commence in month 6<br />
<br />
<br />
==Item 2 -- Percent Completion==<br />
<br />
* Based on current progress towards completion of our aims we are on track, with 60% of the work accomplished.<br />
<br />
== LBL Portion ==<br />
<br />
ONTOLOGY ALIGNMENT AND INTEGRATION: we have supported the JAX ontology<br />
editors by providing and executing tools to integrate human cell types<br />
represented in the FMA (Foundational Model of Anatomy) into CL. These<br />
tools identified generic cell types in common between the two<br />
ontologies, and used the Obol toolkit (developed at Berkeley) to<br />
identify compositional class expressions for specific cell types<br />
(e.g. "smooth muscle cell of jejunum"). These compositional classes<br />
can then be integrated automatically, using the cross-species gross<br />
anatomy ontology UBERON.<br />
<br />
ONTOLOGY EDITOR SUPPORT: we have provided ontology editor support to<br />
the JAX editors of the ontology, improving the oboedit ontology<br />
editing environment in reponse to curator requests. We have also<br />
implemented a variant of the MIREOT (Minimal Information Retrieved for<br />
External Ontology Terms) strategy which allows scalable integration<br />
across multiple ontologies. We have also devised a build environment<br />
for the CL, which allows the easy distribution of multiple versions<br />
for different purposes, and uses OWL reasoners to classify and perform<br />
logical consistency analysis on the ontology automatically.<br />
<br />
ONTOLOGY LANGUAGE SUPPORT: we identified key areas in which the<br />
ontology format used by the Gene Ontology was insufficient for<br />
representing cell types. Rather than move wholesale to the more<br />
expressive OWL (Ontology Web Langauge) formalism, which would have<br />
entailed abandoning tools and interoperation with model organism<br />
databases, we enhanced obo format using a macro mechanism and<br />
implemented a prototype macro expansion engine<br />
(http://precedings.nature.com/documents/5292/version/1). This allowed<br />
us to have the best of both worlds, and to be able to transition<br />
between the oboedit environment, and the Protege4 editors environment,<br />
and to use OWL reasoners to classify the ontology.<br />
<br />
This work also necessitated creation of a formal specification of obo<br />
format and its translation to OWL<br />
(http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html), which<br />
significantly extends on previous efforts made in 2007, before the<br />
OWL2 language was finalized.<br />
<br />
<br />
<br />
==Related Publications for 2010==<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002].<br />
<br />
<br><br />
<br />
[[http://wiki.geneontology.org/index.php/Grant_Progress_Reports_December_2010 Return to 2010 Progress Reports]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Cell_Ontology_Progress_Report_2010&diff=32526Cell Ontology Progress Report 20102010-12-10T20:37:44Z<p>Adiehl: Created page with 'STILL UNDER REVISION (12-10-10) Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The …'</p>
<hr />
<div>STILL UNDER REVISION (12-10-10)<br />
<br />
Work on the Cell Ontology is funded by an ARRA Competitive Revision to the GO Consortium Grant. This work commenced on September 30, 2009. The project is based at MGI, with sub-contract work at LBNL.<br />
<br />
<br />
==Personnel==<br />
<br />
* '''Project Leaders'''<br />
** Alexander Diehl, The Jackson Laboratory/University at Buffalo (50% effort)<br />
** Christopher Mungall, LBNL (10% effort)<br />
<br />
* '''Cell Ontology Curator'''<br />
** Terrence Meehan, The Jackson Laboratory (100% effort)<br />
<br />
* '''Programmers'''<br />
** Amina Abdulla and Nomi Harris, LBNL (75% effort, split)<br />
<br />
* '''Senior Advisors'''<br />
** Judith Blake, The Jackson Laboratory<br />
** Suzanna Lewis, LBNL<br />
<br />
* '''External Consultants'''<br />
** Lindsay Cowell, Duke University<br />
** Anna Maria Masci, Duke University<br />
<br />
<br />
==Collaborations==<br />
<br />
* INCF Program on Ontologies for Neuroscience Task Force for Representation and Deployment, identification of nervous system cell types for addition to the CL.<br />
* Ceri van Slyke, ZFIN, addition of fish cell types and other revisions to CL.<br />
* Sirarat Sarntivijai and Oliver He, University of Michigan, development of the Cell Line Ontology.<br />
* The Plant Ontology Consortium, plant cell types.<br />
* David Osumi-Sutherland, Flybase, Drosophila cell types.<br />
* Onard Mejino, Foundation Model of Anatomy, import of FMA cell types<br />
* David Dougall and Richard Scheuermann, UT Southwestern, import of novel hematopoietic cell types identified via flow cytometry<br />
* Helen Parkinson, EBI, assistance in making cell types in CL and the Experimental Factor Ontology compatible and in providing support for experimentally derived cell types in OBI.<br />
<br><br><br />
<br />
==Item 1 - Activities==<br />
<br />
===Aim 1: Reforming the Structure of the Cell Ontology===<br />
<br />
*Devise new structure for the Cell Ontology<br />
**We have been prototyping the new CL structure using the hematopoeitic cell types as a test case.<br />
**Started month: 1<br />
**Estimated duration: 6 months<br />
<br />
*Add formal logical axioms to the CL.<br />
**We have made the first steps towards adding logical axioms to theCL. The first is the formal definition of the capable_of relation, required for linking cell types to biological processes (for example, Tr1 cells to IL-10 production). The LBL group has created the formal definition in terms of the Basic Formal Ontology (BFO) "disposition" class, and whilst the Jackson group has applied this in the prototype ontology.<br />
**Started month: 1<br />
**Estimated duration: 6 months<br />
<br />
*Add logical definitions using other OBO ontologies<br />
**We have identified the following ontologies as key to defining cell types:<br />
***PRO - Protein Ontology<br />
***GO - Gene Ontology (particularly biological processes such as immune response)<br />
*** PATO - Phenotypic Quality Ontology<br />
*** Uberon - We are also evaluating the use of a general-purpose gross anatomical ontology (Uberon) for certain cell types defined by location in the body.<br />
**Started month: 1<br />
**Estimated duration: 6 months<br />
<br />
*Implement automated reasoner strategy<br />
**Although we do not estimate commencing this until month 6 we have made some preliminary steps, partially implementing the MIREOT methodology within OBO-Edit. This allows the CL editors at Jackson to select classes from external ontologies and bring in only the subset of those ontologies that pertain to these referenced classes. This improves reasoner performance.<br />
**Estimated start month: 6<br />
**Estimated duration: 3 months<br />
<br />
* General software support<br />
**Support with managing ontology versions in Open Bio-Ontologies repository<br />
**OBO-Edit bug fixes<br />
**OBO-Edit tutorials for CL curators<br />
<br><br />
<br />
===Aim 2: Improving and extending the content of CL===<br />
*We have begun planning for a Cell Ontology workshop, to be held May 18-19, 2009 at the Jackson Laborotory, Bar Harbor, Maine. The workshop will be used for discussion of general issues involved in the revision of the Cell Ontology.<br />
*We are implementing the cross-product/logical definition formulation of the hematopoietic terms. As part of this work, we are improving definitions for a number of cell types and adding new cell types.<br />
*We are working to add is_a parents to all terms in the CL.<br />
*We are preparing definitions for current nervous system terms in the CL that lack them.<br><br><br />
<br />
===Aim 3: Applying the CL to the GO===<br />
<br />
* This work is to commence in month 6<br />
<br />
<br />
==Item 2 -- Percent Completion==<br />
<br />
* Based on current progress towards completion of our aims we are on track, with 60% of the work accomplished.<br />
<br />
== LBL Portion ==<br />
<br />
ONTOLOGY ALIGNMENT AND INTEGRATION: we have supported the JAX ontology<br />
editors by providing and executing tools to integrate human cell types<br />
represented in the FMA (Foundational Model of Anatomy) into CL. These<br />
tools identified generic cell types in common between the two<br />
ontologies, and used the Obol toolkit (developed at Berkeley) to<br />
identify compositional class expressions for specific cell types<br />
(e.g. "smooth muscle cell of jejunum"). These compositional classes<br />
can then be integrated automatically, using the cross-species gross<br />
anatomy ontology UBERON.<br />
<br />
ONTOLOGY EDITOR SUPPORT: we have provided ontology editor support to<br />
the JAX editors of the ontology, improving the oboedit ontology<br />
editing environment in reponse to curator requests. We have also<br />
implemented a variant of the MIREOT (Minimal Information Retrieved for<br />
External Ontology Terms) strategy which allows scalable integration<br />
across multiple ontologies. We have also devised a build environment<br />
for the CL, which allows the easy distribution of multiple versions<br />
for different purposes, and uses OWL reasoners to classify and perform<br />
logical consistency analysis on the ontology automatically.<br />
<br />
ONTOLOGY LANGUAGE SUPPORT: we identified key areas in which the<br />
ontology format used by the Gene Ontology was insufficient for<br />
representing cell types. Rather than move wholesale to the more<br />
expressive OWL (Ontology Web Langauge) formalism, which would have<br />
entailed abandoning tools and interoperation with model organism<br />
databases, we enhanced obo format using a macro mechanism and<br />
implemented a prototype macro expansion engine<br />
(http://precedings.nature.com/documents/5292/version/1). This allowed<br />
us to have the best of both worlds, and to be able to transition<br />
between the oboedit environment, and the Protege4 editors environment,<br />
and to use OWL reasoners to classify the ontology.<br />
<br />
This work also necessitated creation of a formal specification of obo<br />
format and its translation to OWL<br />
(http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html), which<br />
significantly extends on previous efforts made in 2007, before the<br />
OWL2 language was finalized.<br />
<br />
<br />
<br />
==Related Publications for 2010==<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. 2010. Hematopoietic Cell Types: Prototype for a Revised Cell Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. 2010. Cross-product extensions of the Gene Ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002].<br />
<br />
<br><br />
<br />
[[http://wiki.geneontology.org/index.php/Grant_Progress_Reports_December_2010 Return to 2010 Progress Reports]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Grant_Progress_Reports_December_2010&diff=32525Grant Progress Reports December 20102010-12-10T20:13:57Z<p>Adiehl: /* Supplements */</p>
<hr />
<div>=== Working Groups ===<br />
<br />
[[Ontology Development Progress Report December 2010]]<br />
<br />
[[Annotation Advocacy progress report for 2010]]<br />
<br />
[[Software Group progress report for 2010]]<br />
<br />
[[Reference Genome progress report for 2010]]<br />
<br />
=== MODs and Annotation Projects ===<br />
<br />
[http://wiki.geneontology.org/images/3/39/MODProgressReportTemplate_2008.doc MOD template]<br />
<br />
[[MGI]]<br />
<br />
[[WormBase]]<br />
<br />
[[EcoliWiki]]<br />
<br />
[[RGD December 2010]]<br />
<br />
[[dictyBase Progress Report December 2010]]<br />
<br />
[[FlyBase December 2010]]<br />
<br />
[[TAIR December 2010]]<br />
<br />
[[GOA December 2010]]<br />
<br />
[[SGD_December_2010]]<br />
<br />
[[BHF-UCL_December_2010]]<br />
<br />
[[ZFIN_December_2010]]<br />
<br />
=== Supplements ===<br />
<br />
<br />
[[Sequence_Ontology_2010]]<br><br />
[[Cell Ontology Progress Report 2010]]<br />
<br />
===Poster/Talks/Publications 2010===<br />
Please add information on Posters, talks or publications that you were part of for the year 2010- [http://gocwiki.geneontology.org/index.php/Publications,_Talks,_Posters_2010- GO 2010 Publications, Talks, Posters]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Grant_Progress_Reports_December_2010&diff=32524Grant Progress Reports December 20102010-12-10T20:13:37Z<p>Adiehl: /* Supplements */</p>
<hr />
<div>=== Working Groups ===<br />
<br />
[[Ontology Development Progress Report December 2010]]<br />
<br />
[[Annotation Advocacy progress report for 2010]]<br />
<br />
[[Software Group progress report for 2010]]<br />
<br />
[[Reference Genome progress report for 2010]]<br />
<br />
=== MODs and Annotation Projects ===<br />
<br />
[http://wiki.geneontology.org/images/3/39/MODProgressReportTemplate_2008.doc MOD template]<br />
<br />
[[MGI]]<br />
<br />
[[WormBase]]<br />
<br />
[[EcoliWiki]]<br />
<br />
[[RGD December 2010]]<br />
<br />
[[dictyBase Progress Report December 2010]]<br />
<br />
[[FlyBase December 2010]]<br />
<br />
[[TAIR December 2010]]<br />
<br />
[[GOA December 2010]]<br />
<br />
[[SGD_December_2010]]<br />
<br />
[[BHF-UCL_December_2010]]<br />
<br />
[[ZFIN_December_2010]]<br />
<br />
=== Supplements ===<br />
<br />
<br />
[[Sequence_Ontology_2010]]<br />
[[Cell Ontology Progress Report 2010]]<br />
<br />
===Poster/Talks/Publications 2010===<br />
Please add information on Posters, talks or publications that you were part of for the year 2010- [http://gocwiki.geneontology.org/index.php/Publications,_Talks,_Posters_2010- GO 2010 Publications, Talks, Posters]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2010_Bar_Harbor_Agenda&diff=312632010 Bar Harbor Agenda2010-09-23T17:10:47Z<p>Adiehl: /* Thursday September 9 */</p>
<hr />
<div>==Tuesday September 7==<br />
* 10:00-10:30: Welcome; Review of schedule and agenda (Judy)<br />
* 10:30 - Noon: Suzi, outline & discuss current draft of [[http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/doc/GO_2011_Specific%20Aims_v4.doc]] specific aims.<br />
* Noon-1: Lunch<br />
* 1:00-2:30: [[Annotation Advocacy and Coordination|Annotation]] Report (Rama & Rachael)- [[File: BHB2010.pdf]]<br />
*# recent projects - notes/accomplishments<br />
*#* 'binding" group report<br />
*#* 'response to' report<br />
*#* 'downstream effect' report<br />
*#* Reciprocal annotations (from binding group)<br />
*#* [[Annotations_to_Catalytic_activity_with_IPI| Annotating to catalytic terms with IPI (report from SGD)]]<br />
*# initial thoughts on grant renewal<br />
*# objectives for the next 4 & 12 months ([[Annotation Advocacy Roadmap|timeline and objectives]])<br />
*#* Reporting standards<br />
*2:30-3:00: break<br />
*3:00-4:30: [[Reference Genome Annotation Project|Ref. Genome]] Report (Pascale & Kara)<br />
Pascale's slides: http://gocwiki.geneontology.org/index.php/File:2010-09-BHB-RefG-progress-report-Pascale.pdf<br><br />
Kara slides: http://gocwiki.geneontology.org/index.php/File:GO_BarHarbor2010Kara.pdf<br />
*# recent projects - notes/accomplishments<br />
*#* PAINT (Mike L) Slides: http://gocwiki.geneontology.org/index.php/File:Livstone_Bar_Harbor_Sept_2010.pdf<br />
*#* Wnt (Varsha, Suzi and Mike L.)<br />
*#* Loading Panther files into MODs:initial reports (Harold)<br />
*#* Ref. genome project tracking (Sven & Chris)<br />
*#** Amigo slides: http://gocwiki.geneontology.org/index.php/File:Amigo.pdf<br />
*#** P-POD slides: http://gocwiki.geneontology.org/index.php/File:Ppod.pdf<br />
*#* Panther families/subfamilies annotation status report (Mary) Slides: http://gocwiki.geneontology.org/index.php/File:pantherGOreport.pdf<br />
*# initial thoughts on grant renewal (Pascale & Kara)<br />
*# objectives for the next 4 & 12 months ([[Reference Genome Timeline-June-Dec2010|timeline and objectives]])<br />
*<b>dinner on your own</b><br />
<br />
==Wednesday September 8==<br />
*8:30-10:00 [[Ontology Development]] Report (David and Jane)<br />
*# recent projects - notes/accomplishments<br />
*#* Aligning GO with ChEBI (David)<br />
*#* TermGenie demo (Jane)<br />
*#* Signaling group update (Becky)[[Media:Signaling.pdf.pdf]]<br />
*#* Transcription overhaul (Karen) [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/BarHarbor2010/TxnOverhaulKChristie.ppt TxnOverhaulKChristie.ppt]<br />
*# initial thoughts on grant renewal<br />
*# objectives for the next 4 & 12 months ([[2010 Timeline|2010]] and [[2011 Timeline|2011]] timelines and objectives)<br />
* 10:00-10:30 Break<br />
* 10:30-12:00 [[Software and Utilities|Software and Infrastructure]] Report (Chris, Suzi & Mike C)<br />
*# recent projects - notes/accomplishments<br />
*#* OBO-Edit update. isa-closure/MIREOT support (Amina) (5 mins)<br />
*#* AmiGO labs update (Chris and Seth) (5 mins)<br />
*#* Galaxy integration (Chris) (5 mins)<br />
*# objectives for the next 4 & 12 months & 5 years and renewal thoughts ([[SWUG Timeline 2010-2011|timeline and objectives]]) (1 hr). Presentation: [[Media:software-group-report-bar-harbor-2010.pdf]]<br />
* 12:00-1:00: Lunch (OBO-Edit Working Group Lunch Meeting)<br />
* 1:00-3:00 Inter-Operational issues <br>We will take this time to discuss solutions for infrastructure and best practices where the respective project teams must connect and communicate more effectively. <br />
*# Annotation group: <br />
*#* Annotation & reference genome groups communication (Pascale and Rama)<br />
*# Reference genome group: <br />
*#* What would be the best forum to discuss annotation and ontology issues ? wiki? SF? we've been doing a bit of both, plus email. It should be more formalized.( Pascale, Mike L)<br />
*# Ontology development: <br />
*#* Ontology and annotation (Jane & Rama) : how do ontology development get communicated to the annotation group? do we need to improve communication channels? <br />
*# Software and Infrastructure: <br />
*#* Delivery of GAFs to MODs (Suzi)<br />
* 3:00 Break for a Hike<br />
<br />
* <b>7:00 Dinner at HighSeas</b><br />
<br />
==Thursday September 9==<br />
* 8:30-10:00: Grant planning discussion<br />
*# Review of Timelines<br />
*# Refinement of aims and objectives (Judy: summary of discussions up to this point)<br />
*#* Overall statement of GOC accomplishments: progress report<br />
*#* Rolea and future of subcontracts to MODs supplemental grants to Princeton, ARRA funding to CL<br />
*#* Literature annotation (and ontology development)<br />
*#* Phylogenetic annotation (and ontology development)<br />
*#* Community annotation (and ontology development)<br />
*#* What new priorities, strategies, technology aspects are we proposing <br />
*#** Groups we might work more closely with (and perhaps additional funding opportunities): PRO, LAMHDI, ICGC, bacterial, Reactome,...<br />
*#** Expressivity of annotations: LEGO (Paul T), [[Media:Diehl_Enhanced_Annotation.pdf|Annotation IDs and Dependency]] (Alex)<br />
*#* Distribution channels and user support<br />
* 10:00-10:30 - break<br />
* 10:30-11:30 Refinement of aims and objectives cont.<br />
* 11:30-noon Review of action items<br />
* noon - 1 pm Lunch<br />
* <b> End of Meeting </b><br />
<br />
[[Category:Bar_Harbor_2010]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2010_Bar_Harbor_Agenda&diff=312622010 Bar Harbor Agenda2010-09-23T17:09:13Z<p>Adiehl: /* Thursday September 9 */</p>
<hr />
<div>==Tuesday September 7==<br />
* 10:00-10:30: Welcome; Review of schedule and agenda (Judy)<br />
* 10:30 - Noon: Suzi, outline & discuss current draft of [[http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/doc/GO_2011_Specific%20Aims_v4.doc]] specific aims.<br />
* Noon-1: Lunch<br />
* 1:00-2:30: [[Annotation Advocacy and Coordination|Annotation]] Report (Rama & Rachael)- [[File: BHB2010.pdf]]<br />
*# recent projects - notes/accomplishments<br />
*#* 'binding" group report<br />
*#* 'response to' report<br />
*#* 'downstream effect' report<br />
*#* Reciprocal annotations (from binding group)<br />
*#* [[Annotations_to_Catalytic_activity_with_IPI| Annotating to catalytic terms with IPI (report from SGD)]]<br />
*# initial thoughts on grant renewal<br />
*# objectives for the next 4 & 12 months ([[Annotation Advocacy Roadmap|timeline and objectives]])<br />
*#* Reporting standards<br />
*2:30-3:00: break<br />
*3:00-4:30: [[Reference Genome Annotation Project|Ref. Genome]] Report (Pascale & Kara)<br />
Pascale's slides: http://gocwiki.geneontology.org/index.php/File:2010-09-BHB-RefG-progress-report-Pascale.pdf<br><br />
Kara slides: http://gocwiki.geneontology.org/index.php/File:GO_BarHarbor2010Kara.pdf<br />
*# recent projects - notes/accomplishments<br />
*#* PAINT (Mike L) Slides: http://gocwiki.geneontology.org/index.php/File:Livstone_Bar_Harbor_Sept_2010.pdf<br />
*#* Wnt (Varsha, Suzi and Mike L.)<br />
*#* Loading Panther files into MODs:initial reports (Harold)<br />
*#* Ref. genome project tracking (Sven & Chris)<br />
*#** Amigo slides: http://gocwiki.geneontology.org/index.php/File:Amigo.pdf<br />
*#** P-POD slides: http://gocwiki.geneontology.org/index.php/File:Ppod.pdf<br />
*#* Panther families/subfamilies annotation status report (Mary) Slides: http://gocwiki.geneontology.org/index.php/File:pantherGOreport.pdf<br />
*# initial thoughts on grant renewal (Pascale & Kara)<br />
*# objectives for the next 4 & 12 months ([[Reference Genome Timeline-June-Dec2010|timeline and objectives]])<br />
*<b>dinner on your own</b><br />
<br />
==Wednesday September 8==<br />
*8:30-10:00 [[Ontology Development]] Report (David and Jane)<br />
*# recent projects - notes/accomplishments<br />
*#* Aligning GO with ChEBI (David)<br />
*#* TermGenie demo (Jane)<br />
*#* Signaling group update (Becky)[[Media:Signaling.pdf.pdf]]<br />
*#* Transcription overhaul (Karen) [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/BarHarbor2010/TxnOverhaulKChristie.ppt TxnOverhaulKChristie.ppt]<br />
*# initial thoughts on grant renewal<br />
*# objectives for the next 4 & 12 months ([[2010 Timeline|2010]] and [[2011 Timeline|2011]] timelines and objectives)<br />
* 10:00-10:30 Break<br />
* 10:30-12:00 [[Software and Utilities|Software and Infrastructure]] Report (Chris, Suzi & Mike C)<br />
*# recent projects - notes/accomplishments<br />
*#* OBO-Edit update. isa-closure/MIREOT support (Amina) (5 mins)<br />
*#* AmiGO labs update (Chris and Seth) (5 mins)<br />
*#* Galaxy integration (Chris) (5 mins)<br />
*# objectives for the next 4 & 12 months & 5 years and renewal thoughts ([[SWUG Timeline 2010-2011|timeline and objectives]]) (1 hr). Presentation: [[Media:software-group-report-bar-harbor-2010.pdf]]<br />
* 12:00-1:00: Lunch (OBO-Edit Working Group Lunch Meeting)<br />
* 1:00-3:00 Inter-Operational issues <br>We will take this time to discuss solutions for infrastructure and best practices where the respective project teams must connect and communicate more effectively. <br />
*# Annotation group: <br />
*#* Annotation & reference genome groups communication (Pascale and Rama)<br />
*# Reference genome group: <br />
*#* What would be the best forum to discuss annotation and ontology issues ? wiki? SF? we've been doing a bit of both, plus email. It should be more formalized.( Pascale, Mike L)<br />
*# Ontology development: <br />
*#* Ontology and annotation (Jane & Rama) : how do ontology development get communicated to the annotation group? do we need to improve communication channels? <br />
*# Software and Infrastructure: <br />
*#* Delivery of GAFs to MODs (Suzi)<br />
* 3:00 Break for a Hike<br />
<br />
* <b>7:00 Dinner at HighSeas</b><br />
<br />
==Thursday September 9==<br />
* 8:30-10:00: Grant planning discussion<br />
*# Review of Timelines<br />
*# Refinement of aims and objectives (Judy: summary of discussions up to this point)<br />
*#* Overall statement of GOC accomplishments: progress report<br />
*#* Rolea and future of subcontracts to MODs supplemental grants to Princeton, ARRA funding to CL<br />
*#* Literature annotation (and ontology development)<br />
*#* Phylogenetic annotation (and ontology development)<br />
*#* Community annotation (and ontology development)<br />
*#* What new priorities, strategies, technology aspects are we proposing <br />
*#** Groups we might work more closely with (and perhaps additional funding opportunities): PRO, LAMHDI, ICGC, bacterial, Reactome,...<br />
*#** Expressivity of annotations: LEGO (Paul T), Annotation IDs and Dependency (Alex)<br />
*#* Distribution channels and user support<br />
* 10:00-10:30 - break<br />
* 10:30-11:30 Refinement of aims and objectives cont.<br />
* 11:30-noon Review of action items<br />
* noon - 1 pm Lunch<br />
* <b> End of Meeting </b><br />
<br />
[[Category:Bar_Harbor_2010]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=File:Diehl_Enhanced_Annotation.pdf&diff=31261File:Diehl Enhanced Annotation.pdf2010-09-23T17:06:07Z<p>Adiehl: A few slides showing ideas for a enhanced GO annotation system incorporating IDs for individual annotations enabling one annotation to depend on others for support.</p>
<hr />
<div>A few slides showing ideas for a enhanced GO annotation system incorporating IDs for individual annotations enabling one annotation to depend on others for support.</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI&diff=31111MGI2010-09-20T19:40:11Z<p>Adiehl: /* Presentations and Publications */</p>
<hr />
<div>= Mouse Genome Informatics Summary, 2010 =<br />
lasted edited 9-14-10 by hjd<br />
<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake*<br />
<br />
Alexander Diehl*<br />
<br />
Mary Dolan*<br />
<br />
Harold J Drabkin*<br />
<br />
Midori Harris*<br />
<br />
David Hill*<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
<br />
<br />
* Funded entirely or partially by GO<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of December, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''09_Dec_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''09_Dec_09'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">34200*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">18207</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15993</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">87.84</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">32410</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">11668</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">20742</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">177.77</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4214</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">752</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">3462</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">460.37</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15667</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16050</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10514</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10749</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1414</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1510</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
<br />
The large changes in manual (non-IEA) curated genes are the result of the addition of 5 efforts.<br />
# Annotating genes with no literature annotation to one or more of the three roots. Quality control reports now alert curators for any genes annotated to one or more of the three roots when new literature is added to MGI and the literature is indexed to these genes.<br />
# We have added a pipeline to create annotations inferred by sequence orthology (ISO) to mouse genes that have rat orthologs where the rat orthologs have been annotated by experiment.<br />
# We have added a pipeline to load GOA annotations to mouse genes.<br />
# We have added a pipeline to add annotations based on intra-ontology relationships.<br />
# We have added a pipeline to add annotations by on sequence similarity (ISS)based on Panther family membership via the Reference Genome projet.<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We continue to explore natural language processing tools to aid in identifying the genes in papers selected for GO.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt keywords, InterPro domains, and EC numbers for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) <br />
# Genes with only IEA annotation but with literature (Li) <br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
*[[Publications,_Talks,_Posters_2010-]] (for all GOC)<br />
<br />
OR MGI should but following here. listing anything from Dec 2009 to now<br />
<br />
Publications<br />
<br />
Tutorials and Workshops<br />
<br />
Posters<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
<br />
*1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris and Jane Lomax to develop cross-products within and among the three GO namespaces.<br />
<br />
<br />
*2. David Hill continues to work with Chris Mungall and Tanya Berardini to inter-ontology links in GO.<br />
<br />
<br />
*3. David Hill has worked with Yasmin Alam-Faruque, Doug Howe, Midori Harris, Susan Tweedie, Becky Foulger and community experts to expand the kidney development portion of GO.<br />
<br />
<br />
*4. Alexander Diehl is active in the GO Signaling and Virus content development groups.<br />
<br />
<br />
*5. Alexander Diehl continues to act as the GOC liaison to the Infectious Disease Ontology and Vaccine Ontology groups and to act on term requests for the GO from those groups.<br />
<br />
<br />
*6. Alexander Diehl is project leader for the Cell Ontology (with Chris Mungall) and Terry Meehan is a full-time curator working on the Cell Ontology. Terry has finished implementing cross-products for hematopoietic cell ontology terms and is working on general improvements to the CL, and has moved on to import of FMA cell types, among others. Alex is focusing improvements to the representation of neurons in the CL, part of an ongoing collaboration with the International Neuroinformatics Framework (INCF). In May 2010 we held a very successful Cell Ontology Workshop at The Jackson Laboratory where many issues regarding the longterm development of the ontology were settled. We will hold another workshop on neurons in the first quarter of 2011. (See separate progress report for the Cell Ontology)<br />
<br />
<br />
*7. In summer 2010 Alexander Diehl mentored Morgan V. Hightshoe, a returned member of the Jackson Laboratory Summer Student Program, and Wade Valleau, a local high school intern in linked projects to revise the representation of nervous system cell types in the Cells Ontology. Wade received support from INCF for his work..<br />
<br />
<br />
*8. David Hill and Jane Lomax oversee the biological content development of GO. In particular, all new developmental biology-related terms submitted to SourceForge are handled by David Hill and all new 'regulation' terms are handled by David Hill and Tanya Berardini.<br><br><br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
* The Protein Ontology project continues to provide a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone.<br />
* Harold is mentoring to curators in Donna Slonim's group at Tufts, Heather Wick and Craig Fournier. They are focusing on genes involved in human fetal development.<br />
* David Hill continues to serve on the GO-help rota.<br />
<br />
= Other Highlights: =<br />
We are now suppling a GAF 2.0 format file to GOC with column 16 cell type and column 17 isoform data filled in. This file is also available directly from our own FTP site.<br />
<br />
*Dmitry Sitnikov continues collaboration with Larry Hunter's group (Dr. Mike Bada) to establish a large, high-quality, corpora of full-text publications, expertly annotated with expressive knowledge representations, to improve the performance of a wide variety of biochemical text mining systems and to create new approaches to text mining. This involves systematically training and evaluating a broad sample of information extraction methods for key tasks, including concept and relationship identification. This effort can also be useful in synonym improvements to the GO between GO terms and certain biological concepts and terminology used in the literature. So far, more then 80 artictles of the chosen 98 have been annotated for molecular function and process. Additionally, Dmitry is working to improve the usefulless of MGI internal GO QC reports. <br />
<br />
*As the designated coordinator of the MGI/GO project with the GO Reference Genome project, Li Ni participates in annotations of genes assigned by the Reference Genome Project, maintain the mouse Reference Genome list on MGI GO wiki and Google spreadsheet, maintain the Reference Genome status table on GO wiki, oversees the curation of Reference Genome Genes for the mouse group. <br />
<br />
*Mary Dolan has been involved in a collaboration with Carol Bult at MGI on aligning gene ontology annotations for mouse genes assigned to MouseCyc pathways. See <br />
<br />
See http://www.informatics.jax.org/pathways.shtml</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI&diff=31110MGI2010-09-20T19:39:55Z<p>Adiehl: /* Presentations and Publications */</p>
<hr />
<div>= Mouse Genome Informatics Summary, 2010 =<br />
lasted edited 9-14-10 by hjd<br />
<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake*<br />
<br />
Alexander Diehl*<br />
<br />
Mary Dolan*<br />
<br />
Harold J Drabkin*<br />
<br />
Midori Harris*<br />
<br />
David Hill*<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
<br />
<br />
* Funded entirely or partially by GO<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of December, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''09_Dec_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''09_Dec_09'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">34200*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">18207</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15993</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">87.84</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">32410</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">11668</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">20742</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">177.77</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4214</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">752</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">3462</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">460.37</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15667</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16050</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10514</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10749</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1414</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1510</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
<br />
The large changes in manual (non-IEA) curated genes are the result of the addition of 5 efforts.<br />
# Annotating genes with no literature annotation to one or more of the three roots. Quality control reports now alert curators for any genes annotated to one or more of the three roots when new literature is added to MGI and the literature is indexed to these genes.<br />
# We have added a pipeline to create annotations inferred by sequence orthology (ISO) to mouse genes that have rat orthologs where the rat orthologs have been annotated by experiment.<br />
# We have added a pipeline to load GOA annotations to mouse genes.<br />
# We have added a pipeline to add annotations based on intra-ontology relationships.<br />
# We have added a pipeline to add annotations by on sequence similarity (ISS)based on Panther family membership via the Reference Genome projet.<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We continue to explore natural language processing tools to aid in identifying the genes in papers selected for GO.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt keywords, InterPro domains, and EC numbers for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) <br />
# Genes with only IEA annotation but with literature (Li) <br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
**[[Publications,_Talks,_Posters_2010-]] (for all GOC)<br />
<br />
OR MGI should but following here. listing anything from Dec 2009 to now<br />
<br />
Publications<br />
<br />
Tutorials and Workshops<br />
<br />
Posters<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
<br />
*1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris and Jane Lomax to develop cross-products within and among the three GO namespaces.<br />
<br />
<br />
*2. David Hill continues to work with Chris Mungall and Tanya Berardini to inter-ontology links in GO.<br />
<br />
<br />
*3. David Hill has worked with Yasmin Alam-Faruque, Doug Howe, Midori Harris, Susan Tweedie, Becky Foulger and community experts to expand the kidney development portion of GO.<br />
<br />
<br />
*4. Alexander Diehl is active in the GO Signaling and Virus content development groups.<br />
<br />
<br />
*5. Alexander Diehl continues to act as the GOC liaison to the Infectious Disease Ontology and Vaccine Ontology groups and to act on term requests for the GO from those groups.<br />
<br />
<br />
*6. Alexander Diehl is project leader for the Cell Ontology (with Chris Mungall) and Terry Meehan is a full-time curator working on the Cell Ontology. Terry has finished implementing cross-products for hematopoietic cell ontology terms and is working on general improvements to the CL, and has moved on to import of FMA cell types, among others. Alex is focusing improvements to the representation of neurons in the CL, part of an ongoing collaboration with the International Neuroinformatics Framework (INCF). In May 2010 we held a very successful Cell Ontology Workshop at The Jackson Laboratory where many issues regarding the longterm development of the ontology were settled. We will hold another workshop on neurons in the first quarter of 2011. (See separate progress report for the Cell Ontology)<br />
<br />
<br />
*7. In summer 2010 Alexander Diehl mentored Morgan V. Hightshoe, a returned member of the Jackson Laboratory Summer Student Program, and Wade Valleau, a local high school intern in linked projects to revise the representation of nervous system cell types in the Cells Ontology. Wade received support from INCF for his work..<br />
<br />
<br />
*8. David Hill and Jane Lomax oversee the biological content development of GO. In particular, all new developmental biology-related terms submitted to SourceForge are handled by David Hill and all new 'regulation' terms are handled by David Hill and Tanya Berardini.<br><br><br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
* The Protein Ontology project continues to provide a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone.<br />
* Harold is mentoring to curators in Donna Slonim's group at Tufts, Heather Wick and Craig Fournier. They are focusing on genes involved in human fetal development.<br />
* David Hill continues to serve on the GO-help rota.<br />
<br />
= Other Highlights: =<br />
We are now suppling a GAF 2.0 format file to GOC with column 16 cell type and column 17 isoform data filled in. This file is also available directly from our own FTP site.<br />
<br />
*Dmitry Sitnikov continues collaboration with Larry Hunter's group (Dr. Mike Bada) to establish a large, high-quality, corpora of full-text publications, expertly annotated with expressive knowledge representations, to improve the performance of a wide variety of biochemical text mining systems and to create new approaches to text mining. This involves systematically training and evaluating a broad sample of information extraction methods for key tasks, including concept and relationship identification. This effort can also be useful in synonym improvements to the GO between GO terms and certain biological concepts and terminology used in the literature. So far, more then 80 artictles of the chosen 98 have been annotated for molecular function and process. Additionally, Dmitry is working to improve the usefulless of MGI internal GO QC reports. <br />
<br />
*As the designated coordinator of the MGI/GO project with the GO Reference Genome project, Li Ni participates in annotations of genes assigned by the Reference Genome Project, maintain the mouse Reference Genome list on MGI GO wiki and Google spreadsheet, maintain the Reference Genome status table on GO wiki, oversees the curation of Reference Genome Genes for the mouse group. <br />
<br />
*Mary Dolan has been involved in a collaboration with Carol Bult at MGI on aligning gene ontology annotations for mouse genes assigned to MouseCyc pathways. See <br />
<br />
See http://www.informatics.jax.org/pathways.shtml</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI&diff=31106MGI2010-09-20T19:11:40Z<p>Adiehl: /* Other Highlights: */</p>
<hr />
<div>= Mouse Genome Informatics Summary, 2010 =<br />
lasted edited 9-14-10 by hjd<br />
<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake*<br />
<br />
Alexander Diehl*<br />
<br />
Mary Dolan*<br />
<br />
Harold J Drabkin*<br />
<br />
Midori Harris*<br />
<br />
David Hill*<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
<br />
<br />
* Funded entirely or partially by GO<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of December, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''09_Dec_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''09_Dec_09'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">34200*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">18207</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15993</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">87.84</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">32410</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">11668</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">20742</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">177.77</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4214</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">752</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">3462</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">460.37</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15667</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16050</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10514</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10749</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1414</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1510</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
<br />
The large changes in manual (non-IEA) curated genes are the result of the addition of 5 efforts.<br />
# Annotating genes with no literature annotation to one or more of the three roots. Quality control reports now alert curators for any genes annotated to one or more of the three roots when new literature is added to MGI and the literature is indexed to these genes.<br />
# We have added a pipeline to create annotations inferred by sequence orthology (ISO) to mouse genes that have rat orthologs where the rat orthologs have been annotated by experiment.<br />
# We have added a pipeline to load GOA annotations to mouse genes.<br />
# We have added a pipeline to add annotations based on intra-ontology relationships.<br />
# We have added a pipeline to add annotations by on sequence similarity (ISS)based on Panther family membership via the Reference Genome projet.<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We continue to explore natural language processing tools to aid in identifying the genes in papers selected for GO.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt keywords, InterPro domains, and EC numbers for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) <br />
# Genes with only IEA annotation but with literature (Li) <br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
**[[GO 2009 Publications, Tutorials & Workshops, Presentations, Posters, and Resources]] this is for 2009<br />
<br />
We either need a 2010 master (appears not to exist?). OR MGI should but following here. listing anything from Dec 2009 to now<br />
<br />
Publications<br />
<br />
<br />
Tutorials and Workshops<br />
<br />
Posters<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
<br />
*1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris and Jane Lomax to develop cross-products within and among the three GO namespaces.<br />
<br />
<br />
*2. David Hill continues to work with Chris Mungall and Tanya Berardini to inter-ontology links in GO.<br />
<br />
<br />
*3. David Hill has worked with Yasmin Alam-Faruque, Doug Howe, Midori Harris, Susan Tweedie, Becky Foulger and community experts to expand the kidney development portion of GO.<br />
<br />
<br />
*4. Alexander Diehl is active in the GO Signaling and Virus content development groups.<br />
<br />
<br />
*5. Alexander Diehl continues to act as the GOC liaison to the Infectious Disease Ontology and Vaccine Ontology groups and to act on term requests for the GO from those groups.<br />
<br />
<br />
*6. Alexander Diehl is project leader for the Cell Ontology (with Chris Mungall) and Terry Meehan is a full-time curator working on the Cell Ontology. Terry has finished implementing cross-products for hematopoietic cell ontology terms and is working on general improvements to the CL, and has moved on to import of FMA cell types, among others. Alex is focusing improvements to the representation of neurons in the CL, part of an ongoing collaboration with the International Neuroinformatics Framework (INCF). In May 2010 we held a very successful Cell Ontology Workshop at The Jackson Laboratory where many issues regarding the longterm development of the ontology were settled. We will hold another workshop on neurons in the first quarter of 2011. (See separate progress report for the Cell Ontology)<br />
<br />
<br />
*7. In summer 2010 Alexander Diehl mentored Morgan V. Hightshoe, a returned member of the Jackson Laboratory Summer Student Program, and Wade Valleau, a local high school intern in linked projects to revise the representation of nervous system cell types in the Cells Ontology. Wade received support from INCF for his work..<br />
<br />
<br />
*8. David Hill and Jane Lomax oversee the biological content development of GO. In particular, all new developmental biology-related terms submitted to SourceForge are handled by David Hill and all new 'regulation' terms are handled by David Hill and Tanya Berardini.<br><br><br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
* The Protein Ontology project continues to provide a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone.<br />
* Harold is mentoring to curators in Donna Slonim's group at Tufts, Heather Wick and Craig Fournier. They are focusing on genes involved in human fetal development.<br />
* David Hill continues to serve on the GO-help rota.<br />
<br />
= Other Highlights: =<br />
We are now suppling a GAF 2.0 format file to GOC with column 16 cell type and column 17 isoform data filled in. This file is also available directly from our own FTP site.<br />
<br />
*Dmitry Sitnikov continues collaboration with Larry Hunter's group (Dr. Mike Bada) to establish a large, high-quality, corpora of full-text publications, expertly annotated with expressive knowledge representations, to improve the performance of a wide variety of biochemical text mining systems and to create new approaches to text mining. This involves systematically training and evaluating a broad sample of information extraction methods for key tasks, including concept and relationship identification. This effort can also be useful in synonym improvements to the GO between GO terms and certain biological concepts and terminology used in the literature. So far, more then 80 artictles of the chosen 98 have been annotated for molecular function and process. Additionally, Dmitry is working to improve the usefulless of MGI internal GO QC reports. <br />
<br />
*As the designated coordinator of the MGI/GO project with the GO Reference Genome project, Li Ni participates in annotations of genes assigned by the Reference Genome Project, maintain the mouse Reference Genome list on MGI GO wiki and Google spreadsheet, maintain the Reference Genome status table on GO wiki, oversees the curation of Reference Genome Genes for the mouse group. <br />
<br />
*Mary Dolan has been involved in a collaboration with Carol Bult at MGI on aligning gene ontology annotations for mouse genes assigned to MouseCyc pathways. See <br />
<br />
See http://www.informatics.jax.org/pathways.shtml</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI&diff=31105MGI2010-09-20T19:10:51Z<p>Adiehl: /* A. Ontology Development Contributions: */</p>
<hr />
<div>= Mouse Genome Informatics Summary, 2010 =<br />
lasted edited 9-14-10 by hjd<br />
<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake*<br />
<br />
Alexander Diehl*<br />
<br />
Mary Dolan*<br />
<br />
Harold J Drabkin*<br />
<br />
Midori Harris*<br />
<br />
David Hill*<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
<br />
<br />
* Funded entirely or partially by GO<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of December, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''09_Dec_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''09_Dec_09'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">34200*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">18207</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15993</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">87.84</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">32410</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">11668</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">20742</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">177.77</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4214</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">752</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">3462</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">460.37</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15667</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16050</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10514</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10749</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1414</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1510</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
<br />
The large changes in manual (non-IEA) curated genes are the result of the addition of 5 efforts.<br />
# Annotating genes with no literature annotation to one or more of the three roots. Quality control reports now alert curators for any genes annotated to one or more of the three roots when new literature is added to MGI and the literature is indexed to these genes.<br />
# We have added a pipeline to create annotations inferred by sequence orthology (ISO) to mouse genes that have rat orthologs where the rat orthologs have been annotated by experiment.<br />
# We have added a pipeline to load GOA annotations to mouse genes.<br />
# We have added a pipeline to add annotations based on intra-ontology relationships.<br />
# We have added a pipeline to add annotations by on sequence similarity (ISS)based on Panther family membership via the Reference Genome projet.<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We continue to explore natural language processing tools to aid in identifying the genes in papers selected for GO.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt keywords, InterPro domains, and EC numbers for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) <br />
# Genes with only IEA annotation but with literature (Li) <br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
**[[GO 2009 Publications, Tutorials & Workshops, Presentations, Posters, and Resources]] this is for 2009<br />
<br />
We either need a 2010 master (appears not to exist?). OR MGI should but following here. listing anything from Dec 2009 to now<br />
<br />
Publications<br />
<br />
<br />
Tutorials and Workshops<br />
<br />
Posters<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
<br />
*1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris and Jane Lomax to develop cross-products within and among the three GO namespaces.<br />
<br />
<br />
*2. David Hill continues to work with Chris Mungall and Tanya Berardini to inter-ontology links in GO.<br />
<br />
<br />
*3. David Hill has worked with Yasmin Alam-Faruque, Doug Howe, Midori Harris, Susan Tweedie, Becky Foulger and community experts to expand the kidney development portion of GO.<br />
<br />
<br />
*4. Alexander Diehl is active in the GO Signaling and Virus content development groups.<br />
<br />
<br />
*5. Alexander Diehl continues to act as the GOC liaison to the Infectious Disease Ontology and Vaccine Ontology groups and to act on term requests for the GO from those groups.<br />
<br />
<br />
*6. Alexander Diehl is project leader for the Cell Ontology (with Chris Mungall) and Terry Meehan is a full-time curator working on the Cell Ontology. Terry has finished implementing cross-products for hematopoietic cell ontology terms and is working on general improvements to the CL, and has moved on to import of FMA cell types, among others. Alex is focusing improvements to the representation of neurons in the CL, part of an ongoing collaboration with the International Neuroinformatics Framework (INCF). In May 2010 we held a very successful Cell Ontology Workshop at The Jackson Laboratory where many issues regarding the longterm development of the ontology were settled. We will hold another workshop on neurons in the first quarter of 2011. (See separate progress report for the Cell Ontology)<br />
<br />
<br />
*7. In summer 2010 Alexander Diehl mentored Morgan V. Hightshoe, a returned member of the Jackson Laboratory Summer Student Program, and Wade Valleau, a local high school intern in linked projects to revise the representation of nervous system cell types in the Cells Ontology. Wade received support from INCF for his work..<br />
<br />
<br />
*8. David Hill and Jane Lomax oversee the biological content development of GO. In particular, all new developmental biology-related terms submitted to SourceForge are handled by David Hill and all new 'regulation' terms are handled by David Hill and Tanya Berardini.<br><br><br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
* The Protein Ontology project continues to provide a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone.<br />
* Harold is mentoring to curators in Donna Slonim's group at Tufts, Heather Wick and Craig Fournier. They are focusing on genes involved in human fetal development.<br />
* David Hill continues to serve on the GO-help rota.<br />
<br />
= Other Highlights: =<br />
We are now suppling a GAF 2.0 format file to GOC with column 16 cell type and column 17 isoform data filled in. This file is also available directly from our own FTP site.<br />
<br />
*Alexander Diehl co-wrote an ARRA Competitive Revision extension to the Gene Ontology Consortium grant HG000273, along with Chris Mungall and Judith Blake for the purpose of revising the Cell Ontology, and using the CL in conjunction with the GO in annotation and in cross-product term formation. This grant was funded on September 30, 2009.<br />
<br />
*Dmitry Sitnikov continues collaboration with Larry Hunter's group (Dr. Mike Bada) to establish a large, high-quality, corpora of full-text publications, expertly annotated with expressive knowledge representations, to improve the performance of a wide variety of biochemical text mining systems and to create new approaches to text mining. This involves systematically training and evaluating a broad sample of information extraction methods for key tasks, including concept and relationship identification. This effort can also be useful in synonym improvements to the GO between GO terms and certain biological concepts and terminology used in the literature. So far, more then 80 artictles of the chosen 98 have been annotated for molecular function and process. Additionally, Dmitry is working to improve the usefulless of MGI internal GO QC reports. <br />
<br />
*As the designated coordinator of the MGI/GO project with the GO Reference Genome project, Li Ni participates in annotations of genes assigned by the Reference Genome Project, maintain the mouse Reference Genome list on MGI GO wiki and Google spreadsheet, maintain the Reference Genome status table on GO wiki, oversees the curation of Reference Genome Genes for the mouse group. <br />
<br />
*Mary Dolan has been involved in a collaboration with Carol Bult at MGI on aligning gene ontology annotations for mouse genes assigned to MouseCyc pathways. See <br />
<br />
See http://www.informatics.jax.org/pathways.shtml</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI&diff=31104MGI2010-09-20T19:10:08Z<p>Adiehl: /* A. Ontology Development Contributions: */</p>
<hr />
<div>= Mouse Genome Informatics Summary, 2010 =<br />
lasted edited 9-14-10 by hjd<br />
<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake*<br />
<br />
Alexander Diehl*<br />
<br />
Mary Dolan*<br />
<br />
Harold J Drabkin*<br />
<br />
Midori Harris*<br />
<br />
David Hill*<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
<br />
<br />
* Funded entirely or partially by GO<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of December, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''09_Dec_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''09_Dec_09'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">34200*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">18207</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15993</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">87.84</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">32410</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">11668</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">20742</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">177.77</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4214</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">752</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">3462</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">460.37</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15667</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16050</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10514</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10749</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1414</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1510</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">tbc</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
<br />
The large changes in manual (non-IEA) curated genes are the result of the addition of 5 efforts.<br />
# Annotating genes with no literature annotation to one or more of the three roots. Quality control reports now alert curators for any genes annotated to one or more of the three roots when new literature is added to MGI and the literature is indexed to these genes.<br />
# We have added a pipeline to create annotations inferred by sequence orthology (ISO) to mouse genes that have rat orthologs where the rat orthologs have been annotated by experiment.<br />
# We have added a pipeline to load GOA annotations to mouse genes.<br />
# We have added a pipeline to add annotations based on intra-ontology relationships.<br />
# We have added a pipeline to add annotations by on sequence similarity (ISS)based on Panther family membership via the Reference Genome projet.<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We continue to explore natural language processing tools to aid in identifying the genes in papers selected for GO.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt keywords, InterPro domains, and EC numbers for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) <br />
# Genes with only IEA annotation but with literature (Li) <br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
**[[GO 2009 Publications, Tutorials & Workshops, Presentations, Posters, and Resources]] this is for 2009<br />
<br />
We either need a 2010 master (appears not to exist?). OR MGI should but following here. listing anything from Dec 2009 to now<br />
<br />
Publications<br />
<br />
<br />
Tutorials and Workshops<br />
<br />
Posters<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
<br />
*1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris and Jane Lomax to develop cross-products within and among the three GO namespaces.<br />
<br />
<br />
*2. David Hill continues to work with Chris Mungall and Tanya Berardini to inter-ontology links in GO.<br />
<br />
<br />
*3. David Hill has worked with Yasmin Alam-Faruque, Doug Howe, Midori Harris, Susan Tweedie, Becky Foulger and community experts to expand the kidney development portion of GO.<br />
<br />
<br />
*4. Alexander Diehl is active in the GO Signaling and Virus content development groups.<br />
<br />
<br />
*5. Alexander Diehl continues to act as the GOC liaison to the Infectious Disease Ontology and Vaccine Ontology groups and to act on term requests for the GO from those groups.<br />
<br />
<br />
*6. Alexander Diehl is project leader for the Cell Ontology (with Chris Mungall) and Terry Meehan is a full-time curator working on the Cell Ontology. Terry has finished implementing cross-products for hematopoietic cell ontology terms and is working on general improvements to the CL, and has moved on to import of FMA cell types, among others. Alex is focusing improvements to the representation of neurons in the CL, part of an ongoing collaboration with the International Neuroinformatics Framework (INCF). In May 2010 we held a very successful Cell Ontology Workshop at The Jackson Laboratory where many issues regarding the longterm development of the ontology were settled. We will hold another workshop on neurons in the first quarter of 2011. (See separate progress report for the Cell Ontology)<br />
<br />
<br />
*7. In summer 2010 Alexander Diehl mentored Morgan V. Hightshoe, a returned member of the Jackson Laboratory Summer Student Program, and Wade Valleau, a local high school intern in linked projects to revise the representation of nervous system cell types in the Cells Ontology. Wade received support from INCF for his work..<br />
<br />
<br />
*8. David Hill and Jane Lomax oversee the biological content development of GO. In particular, all new developmental biology-related terms submitted to SourceForge are handled by David Hill and all new 'regulation' terms are handled by David Hill and Tanya Berardini.<br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
* The Protein Ontology project continues to provide a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone.<br />
* Harold is mentoring to curators in Donna Slonim's group at Tufts, Heather Wick and Craig Fournier. They are focusing on genes involved in human fetal development.<br />
* David Hill continues to serve on the GO-help rota.<br />
<br />
= Other Highlights: =<br />
We are now suppling a GAF 2.0 format file to GOC with column 16 cell type and column 17 isoform data filled in. This file is also available directly from our own FTP site.<br />
<br />
*Alexander Diehl co-wrote an ARRA Competitive Revision extension to the Gene Ontology Consortium grant HG000273, along with Chris Mungall and Judith Blake for the purpose of revising the Cell Ontology, and using the CL in conjunction with the GO in annotation and in cross-product term formation. This grant was funded on September 30, 2009.<br />
<br />
*Dmitry Sitnikov continues collaboration with Larry Hunter's group (Dr. Mike Bada) to establish a large, high-quality, corpora of full-text publications, expertly annotated with expressive knowledge representations, to improve the performance of a wide variety of biochemical text mining systems and to create new approaches to text mining. This involves systematically training and evaluating a broad sample of information extraction methods for key tasks, including concept and relationship identification. This effort can also be useful in synonym improvements to the GO between GO terms and certain biological concepts and terminology used in the literature. So far, more then 80 artictles of the chosen 98 have been annotated for molecular function and process. Additionally, Dmitry is working to improve the usefulless of MGI internal GO QC reports. <br />
<br />
*As the designated coordinator of the MGI/GO project with the GO Reference Genome project, Li Ni participates in annotations of genes assigned by the Reference Genome Project, maintain the mouse Reference Genome list on MGI GO wiki and Google spreadsheet, maintain the Reference Genome status table on GO wiki, oversees the curation of Reference Genome Genes for the mouse group. <br />
<br />
*Mary Dolan has been involved in a collaboration with Carol Bult at MGI on aligning gene ontology annotations for mouse genes assigned to MouseCyc pathways. See <br />
<br />
See http://www.informatics.jax.org/pathways.shtml</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2010_Bar_Harbor_Logistics&diff=304442010 Bar Harbor Logistics2010-08-27T01:14:09Z<p>Adiehl: /* Attendees */</p>
<hr />
<div>==Attendees==<br />
(please use the Arrival and Departure info columns if you would like to try to carpool or share a shuttle to/from the airport)<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport (BHB=Bar Harbor or BGR=Bangor) <br />
! Departure Date/Time from Airport (BHB=Bar Harbor or BGR=Bangor)<br />
! Staying at HighSeas?<br />
! Food choice (Steak, Veggie,lobster)<br />
! Attending the GOC Dinner? <br />
|-<br />
| Suzi Lewis<br />
| BBOP<br />
| 6th Sept 20:35 (BHB)<br />
| 10th Sept 16:10 (BHB)<br />
| No<br />
| None<br />
| Yes<br />
|-<br />
| David Hill<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| lobster<br />
| yes<br />
|-<br />
| Judith Blake<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| none<br />
| yes<br />
|-<br />
|Harold Drabkin<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| steak<br />
| yes<br />
|-<br />
|Rachael Huntley<br />
| GOA<br />
| 6th Sept 20:45 (or if delayed 22:30) Bangor (Bus)<br />
| 9th Sept 11:10 (Bar Harbor)<br />
| Yes (with Susan Tweedie)<br />
| veggie/no fish<br />
| Yes<br />
|-|<br />
|Susan Tweedie<br />
| FlyBase<br />
| 6th Sept 20:35 (BHB)<br />
| 9th Sept 16:10 (BHB)<br />
| Yes (with Rachael Huntley)<br />
| lobster<br />
| Yes<br />
|-<br />
| Mary Shimoyama<br />
| RGD<br />
| 6th Sept Bar Harbor<br />
| 10th Sept Bar Harbor<br />
| no<br />
| none<br />
| yes<br />
|-<br />
| Donghui Li<br />
| TAIR<br />
| Sept 6 10:56 am Bangor<br />
| Sept 11 11:25 am Bangor<br />
| yes (single preferred, shared bath fine)<br />
| lobster<br />
| yes<br />
|-<br />
| Tanya Berardini<br />
| TAIR<br />
| 6th Sept pm BGR<br />
| staying on<br />
| no<br />
| lobstah<br />
| yes<br />
|-<br />
| Rebecca Foulger<br />
| UniProt/GO editorial<br />
| 6th Sept 16:50 (BHB)<br />
| 9th Sept 16:10 (BHB)<br />
| yes (ok to share: no roommate yet)<br />
| none<br />
| yes<br />
|-<br />
| Amelia Ireland<br />
| BBOP/GO Editorial Office<br />
| 6th Sept 16:50 (BHB)<br />
| 10th Sept 11:10 (BHB)<br />
| ? yes (no roommate yet)<br />
| veggie/no fish<br />
| yes<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
|I'll be in Bangor over the weekend so any time Monday I can go to BHB<br />
|9th Sept 3:19PM Bangor<br />
|Yes - shared bath fine, single preferred<br />
|None<br />
|Yes<br />
|-<br />
|Eva Huala<br />
|TAIR<br />
|6th Sept 20:35 (BHB)<br />
|9th Sept 16:10 (BHB)<br />
|yes, OK to share bath, prefer single<br />
|veggie<br />
|yes <br />
|-<br />
|Jane Lomax<br />
|GO-EBI<br />
| 6th Sept 16:50 (BHB)<br />
| 9th Sept 16:10 (BHB)<br />
| yes, prefer single if poss<br />
|lobster<br />
|yes <br />
|-<br />
|Sven Heinicke<br />
|Princeton<br />
| 6th Sept 1:05 (BHB)<br />
| 10th Sept 11:10 (BHB)<br />
| yes, roommate ok.<br />
|none<br />
|yes <br />
|-<br />
|Rama Balakrishnan<br />
|SGD, Stanford University<br />
|6th Sept, 8:35 PM BHB<br />
|9th Sept 4:10 PM BHB<br />
|yes, room mate ok.<br />
|veggie(prefer vegan food)<br />
|yes<br />
|-<br />
|Stan Laulederkind<br />
|RGD<br />
|6th Sept, 4:50 PM BHB<br />
|9th Sept 4:10 PM BHB<br />
|no<br />
|lobster<br />
|yes<br />
|-<br />
|Pascale Gaudet<br />
|dictybase<br />
| by car<br />
| by car<br />
| yes, room mate ok.<br />
|none<br />
|yes <br />
|-<br />
|Kimberly Van Auken<br />
|WormBase<br />
|USAir#3388 - 10:32pm, Bangor<br />
|USAir#3612 - 3:19pm, Bangor<br />
|yes, roommate ok<br />
|Veggie<br />
|Yes<br />
|-<br />
| Mindy Dwinell<br />
| RGD<br />
| 6th Sept Bar Harbor<br />
| 10th Sept Bar Harbor<br />
| no<br />
| none<br />
| yes<br />
|-<br />
| Mary Dolan<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| lobster<br />
| yes<br />
|-<br />
| Li Ni<br />
| GOC/MGI<br />
| 6th Sept Bar Harbor<br />
| 10th Sept Bar Harbor<br />
| yes<br />
| lobster<br />
| yes<br />
|-<br />
| Alexander Diehl<br />
| GOC/CL/MGI<br />
| local<br />
| local<br />
| no<br />
| lobster<br />
| yes<br />
|-<br />
| Amina Abdulla<br />
| GOC - LBL - BBOP<br />
| TBD<br />
| TBD<br />
| yes<br />
| lobster<br />
| yes<br />
|-<br />
| Karen Christie<br />
| SGD, Stanford University<br />
| 6th Sept, 8:35 PM BHB<br />
| 9th Sept 4:10 PM BHB<br />
| yes, room mate ok.<br />
| lobster<br />
| yes<br />
|-<br />
| Kara Dolinski<br />
| Princeton<br />
| 6th Sept <br />
| 10th Sept <br />
| no, staying in town<br />
| none<br />
| yes<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome, NYU<br />
| 6th Sept (by car?)<br />
| 10th Sept (by car?) <br />
| yes (prefer single but room-mate OK)<br />
| lobster<br />
| yes<br />
|-<br />
| Paul Thomas<br />
| PANTHER, EcoliHub, USC<br />
| 6th Sept<br />
| 9th Sept <br />
| yes<br />
| lobster<br />
| yes<br />
|-<br />
| Seth Carbon<br />
| Berkeley BOP<br />
| Mon 09/06/2010 at 8:35 PM<br />
| Fri 09/10/2010 at 4:10 PM <br />
| no<br />
| steak<br />
| yes<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport (BHB=Bar Harbor or BGR=Bangor) <br />
! Departure Date/Time from Airport (BHB=Bar Harbor or BGR=Bangor)<br />
! Staying at HighSeas with room-mate?<br />
! Food choice (Steak, Veggie,lobster)<br />
! Attending the GOC Dinner? <br />
|}<br />
<br />
==Remote Attendees==<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Email<br />
! Attending Tuesday 9/7<br />
! Attending Wednesday 9/8<br />
! Attending Thursday 9/9<br />
! Time zone<br />
|-<br />
| Mike Livstone<br />
| Princeton<br />
| livstone@genomics.princeton.edu<br />
| Yes<br />
| maybe (AM only)<br />
| No<br />
| EDT<br />
|-<br />
| Ruth Lovering<br />
| University College London (BHF-UCL)<br />
| r.lovering@ucl.ac.uk<br />
| Yes<br />
| Yes<br />
| Yes<br />
| BST<br />
|-<br />
|}<br />
<br />
==Travel to Bar Harbor==<br />
====Bar Harbor Airport to Bar Harbor====<br />
<br />
At Your Service Taxi Co. (207) 288-9222 (Due to heavy tourism, it is best to try to book in advance)<br />
<br />
Island Explorer: (Free Island Shuttle Bus from late June thru mid October)<br />
<br />
====Boston Airport to Bangor ME or Bar Harbor ME====<br />
<br />
=====Air=====<br />
<br />
It is possible for us to book round-trip airfare from Boston to Bar Harbor. We need to know in advance.<br />
<br />
=====Bus=====<br />
<br />
http://www.concordcoachlines.com/schedules-a-fares.html<br />
<br />
====Bangor ME to Bar Harbor ME====<br />
There are several ways to get to Bar Harbor from Bangor. As we learn more about who and when people are arriving and leaving from Bangor, we will try to arrange cabs, shuttles or have someone rent a car and drive to Bar Harbor and back. The laboratory also gets a special rate on the hotel at the airport in Bangor. If you are arriving on a late flight on Monday, there is an option to stay in Bangor on Monday night and come to Bar Harbor Tuesday morning. To get the special rate, we will have to book these rooms in advance.<br />
<br />
==Accommodations==<br />
====HighSeas (on site)====<br />
<br />
There are a limited number of rooms available at the HighSeas Conference Center here at The Jackson Laboratory. They are available until Friday morning. The rooms can be singles or doubles and two rooms share a bath. Please indicate if you would like to stay at HighSeas. If so, please indicate in the table above if you would be willing to share a room and if you have a room-mate. If you indicate that you will stay at HighSeas, we will assign you a room. If all the rooms fill, we will let you know. Low cost, charged to GOC grant; a good deal. Please consider.<br />
<br />
http://courses.jax.org/highseas.html<br />
<br />
====Harborside ($179-779 per night)====<br />
<br />
http://www.theharborsidehotel.com/<br />
<br />
====Cromwell Harbor Motel ($108-115)====<br />
<br />
http://www.cromwellharbor.com/<br />
<br />
<br />
==Meals==<br />
<br />
Lunches and break snacks will be served at the Conference center. For non-arranged dinners, there are many good restaurants in Bar Harbor.<br />
<br />
http://www.barharborinfo.com/dining/<br />
<br />
===Dinner===<br />
<br />
Monday Sept. 6 Dinner on your own<br />
<br />
Tuesday Sept.7 Dinner on your own (We could also organize something informal at the meeting)<br />
<br />
Wednesday Sept. 8 GOC Lobster Dinner at HighSeas (other choices will also be available)<br />
<br />
Thursday Sept. 9 Dinner on your own</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI,Sept_2010&diff=30215MGI,Sept 20102010-08-17T18:06:37Z<p>Adiehl: /* A. Ontology Development Contributions: */</p>
<hr />
<div>= Mouse Genome Informatics September, 2010 =<br />
<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake<br />
<br />
Alexander Diehl<br />
<br />
Mary Dolan<br />
<br />
Harold J Drabkin<br />
<br />
David Hill<br />
<br />
Terry Meehan<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of August 1, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''01_Aug_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''11_Mar_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">34271*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">35191</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">32488</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">33228</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4191</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4006</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15797</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15942</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10791</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10592</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1969</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1248</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right"> </div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
* Note: decreases in the number of genes annotated reflect effects of MGI Sequence Group reclassifying various markers as no longer type "gene", but pseudogene, complex/cluster, or "other genome feature". Previous annotation to these markers, even if to root, has been stricken. <br />
<br />
<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We are currently using ProMiner to improve associating incoming literature to genes in MGI (indexing). This association is used to drive various QC reports used for identifying annotation priorities.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt Keywords and InterPro domains for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) (see <nowiki>**</nowiki> above)<br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
Add new since March 2010:<br />
<br />
b. ''Presentations including Talks and Tutorials and Teaching''<br />
<br />
Add new since March 2010<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
Edit, adding new since March 2010:<br />
<br />
1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris, Jen Deegan and Jane Lomax to develop cross-products within the three GO namespaces. The regulation cross-products have been released in the extended GO. David and Tanya are now quality checking the internal biological process cross-products.<br />
<br />
2. David Hill has worked with Tanya Berardini to continuing to add interontology links between MF and BP.<br />
<br />
3. David Hill has worked with Varsha Khodiyar, Tanya Berardini, Doug Howe, Susan Tweedie, Ruth Lovering and community experts to expand the heart development portion of the ontology.<br />
<br />
4. David Hill has worked with Yasmin Alam-Faruque, Midori Harris, Becky Folger, Doug Howe, Emily Dimmer, Rachel Huntley and community experts to expand the kidney development portion of the ontology.<br />
<br />
5. David Hill and Tanya Berardini are maintaining the automated quality checks of the ontology on an ongoing basis.<br />
<br />
6. David Hill and Harold Drabkin are working with Jane Lomax, Midori Harris, Tanya Berardini and Jane Lomax to align the representation of biochemicals in GO. <br />
<br />
7. David Hill and Tanya Berardini added or modified 231 terms as a result of attending the American Society for Cell Biology Meeting in December.<br />
<br />
8. Alexander Diehl is part of the GO Signaling Working Group led by Becky Folger that continues to work on improvements in the representation of signaling in the GO.<br />
<br />
9. Alexander Diehl is project leader for the Cell Ontology (with Chris Mungall) and Terry Meehan is a full-time curator working on the Cell Ontology. Terry has finished implementing cross-products for hematopoietic cell ontology terms and is working on general improvements to the CL. Alex has recently worked with two summer students on improvements to the representation of neurons in the CL, part of an ongoing collaboration with the International Neuroinformatics Framework. In May 2010 we held a very successful Cell Ontology Workshop at The Jackson Laboratory where many issues regarding the longterm development of the ontology were settled. We will hold another workshop on neurons in the first quarter of 2011.<br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
The Protein Ontology project is providing a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro<br />
) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone. <br />
<br />
Harold and David, along with Emily Dimmer, are mentoring Heather Wick of Tufts University, for annotation of human fetal lung development<br />
<br />
= Other Highlights: =<br />
We have currently implemented a pipeline that adds "missing" annotations based on the function x process inter-ontology links being added to the GO.</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2010_Bar_Harbor_Logistics&diff=301582010 Bar Harbor Logistics2010-08-16T18:20:15Z<p>Adiehl: /* Attendees */</p>
<hr />
<div>==Attendees==<br />
(please use the Arrival and Departure info columns if you would like to try to carpool or share a shuttle to/from the airport)<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport (BHB=Bar Harbor or BGR=Bangor) <br />
! Departure Date/Time from Airport (BHB=Bar Harbor or BGR=Bangor)<br />
! Staying at HighSeas?<br />
! Food requirement (None, Veggie, Vegan)<br />
! Attending the GOC Dinner?<br />
! Will you dine at HighSeas Thursday? <br />
|-<br />
| David Hill<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| none<br />
| yes<br />
| no<br />
|-<br />
| Judith Blake<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| none<br />
| yes<br />
| no<br />
|-<br />
|Harold Drabkin<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| none<br />
| yes<br />
| no<br />
|<br />
|-|<br />
|Rachael Huntley<br />
| GOA<br />
| 6th Sept 20:45 (or if delayed 22:30) Bangor (Bus)<br />
| 9th Sept 11:10 (Bar Harbor)<br />
| Yes (with Susan Tweedie)<br />
| veggie/no fish<br />
| Yes<br />
| No<br />
|-|<br />
|Susan Tweedie<br />
| FlyBase<br />
| 6th Sept 20:35 (BHB)<br />
| 9th Sept 16:10 (BHB)<br />
| Yes (with Rachael Huntley)<br />
| none<br />
| Yes<br />
| No<br />
|-<br />
| Mary Shimoyama<br />
| RGD<br />
| 6th Sept Bar Harbor<br />
| 10th Sept Bar Harbor<br />
| no<br />
| none<br />
| yes<br />
| not sure<br />
|-<br />
| Donghui Li<br />
| TAIR<br />
| Sept 6 10:56 am Bangor<br />
| Sept 11 11:25 am Bangor<br />
| yes<br />
| none<br />
| yes<br />
| yes<br />
|-<br />
| Tanya Berardini<br />
| TAIR<br />
| <br />
|<br />
| no<br />
| none<br />
| yes<br />
| no<br />
|-<br />
| Rebecca Foulger<br />
| UniProt/GO editorial<br />
| 6th Sept 16:50 (BHB)<br />
| 9th Sept 16:10 (BHB)<br />
| yes (ok to share: no roommate yet)<br />
| none<br />
| yes<br />
| yes<br />
|-<br />
| Amelia Ireland<br />
| BBOP/GO Editorial Office<br />
| 6th Sept 16:50 (BHB)<br />
| 10th Sept 11:10 (BHB)<br />
| ? yes (no roommate yet)<br />
| veggie/no fish<br />
| yes<br />
| maybe<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
|I'll be in Bangor over the weekend so any time Monday I can go to BHB<br />
|9th Sept 3:19PM Bangor<br />
|Yes - shared bath fine, single preferred<br />
|None<br />
|Yes<br />
|No<br />
|-<br />
|Eva Huala<br />
|TAIR<br />
|6th Sept 20:35 (BHB)<br />
|9th Sept 16:10 (BHB)<br />
|yes, OK to share bath, prefer single<br />
|none<br />
|yes <br />
|no<br />
|-<br />
|Jane Lomax<br />
|GO-EBI<br />
| 6th Sept 16:50 (BHB)<br />
| 9th Sept 16:10 (BHB)<br />
| yes, prefer single if poss<br />
|none<br />
|yes <br />
|no<br />
|-<br />
|Sven Heinicke<br />
|Princeton<br />
| 6th Sept 1:05 (BHB)<br />
| 10th Sept 11:10 (BHB)<br />
| yes, roommate ok.<br />
|none<br />
|yes <br />
|no<br />
|-<br />
|Rama Balakrishnan<br />
|SGD, Stanford University<br />
|6th Sept, 8:35 PM BHB<br />
|9th Sept 4:10 PM BHB<br />
|yes, room mate ok.<br />
|veggie(prefer vegan food)<br />
|yes<br />
|yes<br />
|-<br />
|Stan Laulederkind<br />
|RGD<br />
|6th Sept, 4:50 PM BHB<br />
|9th Sept 4:10 PM BHB<br />
|no<br />
|none<br />
|yes<br />
|no<br />
|-<br />
|Pascale Gaudet<br />
|dictybase<br />
| by car<br />
| by car<br />
| yes, room mate ok.<br />
|none<br />
|yes <br />
|no<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase<br />
|USAir#3388 - 10:32pm, Bangor<br />
|USAir#3612 - 3:19pm, Bangor<br />
|yes, roommate ok<br />
|Veggie<br />
|Yes<br />
|No<br />
|-<br />
| Mindy Dwinell<br />
| RGD<br />
| 6th Sept Bar Harbor<br />
| 10th Sept Bar Harbor<br />
| no<br />
| none<br />
| yes<br />
| not sure<br />
|-<br />
| Mary Dolan<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| none<br />
| yes<br />
| no<br />
|-<br />
| Alexander Diehl<br />
| GOC/CL/MGI<br />
| local<br />
| local<br />
| no<br />
| none<br />
| yes<br />
| no<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport (BHB=Bar Harbor or BGR=Bangor) <br />
! Departure Date/Time from Airport (BHB=Bar Harbor or BGR=Bangor)<br />
! Staying at HighSeas with room-mate?<br />
! Food requirement (None, Veggie, Vegan)<br />
! Attending the GOC Dinner?<br />
! Will you dine at HighSeas Thursday? <br />
|}<br />
<br />
==Remote Attendees==<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Email<br />
! Attending Tuesday 9/7<br />
! Attending Wednesday 9/8<br />
! Attending Thursday 9/9<br />
! Time zone<br />
|-<br />
| Mike Livstone<br />
| Princeton<br />
| livstone@genomics.princeton.edu<br />
| Yes<br />
| maybe (AM only)<br />
| No<br />
| EDT<br />
|-<br />
| Ruth Lovering<br />
| University College London (BHF-UCL)<br />
| r.lovering@ucl.ac.uk<br />
| Yes<br />
| Yes<br />
| Yes<br />
| BST<br />
|-<br />
|}<br />
<br />
==Travel to Bar Harbor==<br />
====Bar Harbor Airport to Bar Harbor====<br />
<br />
At Your Service Taxi Co. (207) 288-9222 (Due to heavy tourism, it is best to try to book in advance)<br />
<br />
Island Explorer: (Free Island Shuttle Bus from late June thru mid October)<br />
<br />
====Boston Airport to Bangor ME or Bar Harbor ME====<br />
<br />
=====Air=====<br />
<br />
It is possible for us to book round-trip airfare from Boston to Bar Harbor. We need to know in advance.<br />
<br />
=====Bus=====<br />
<br />
http://www.concordcoachlines.com/schedules-a-fares.html<br />
<br />
====Bangor ME to Bar Harbor ME====<br />
There are several ways to get to Bar Harbor from Bangor. As we learn more about who and when people are arriving and leaving from Bangor, we will try to arrange cabs, shuttles or have someone rent a car and drive to Bar Harbor and back. The laboratory also gets a special rate on the hotel at the airport in Bangor. If you are arriving on a late flight on Monday, there is an option to stay in Bangor on Monday night and come to Bar Harbor Tuesday morning. To get the special rate, we will have to book these rooms in advance.<br />
<br />
==Accommodations==<br />
====HighSeas (on site)====<br />
<br />
There are a limited number of rooms available at the HighSeas Conference Center here at The Jackson Laboratory. The rooms can be singles or doubles and two rooms share a bath. Please indicate if you would like to stay at HighSeas. If so, please indicate in the table below if you would be willing to share a room and if you have a room-mate. Low cost, charged to GOC grant; a good deal. Please consider.<br />
<br />
http://courses.jax.org/highseas.html<br />
<br />
====Harborside ($179-779 per night)====<br />
<br />
http://www.theharborsidehotel.com/<br />
<br />
====Cromwell Harbor Motel ($108-115)====<br />
<br />
http://www.cromwellharbor.com/<br />
<br />
<br />
==Meals==<br />
<br />
Lunches and break snacks will be served at the Conference center. For non-arranged dinners, there are many good restaurants in Bar Harbor.<br />
<br />
http://www.barharborinfo.com/dining/<br />
<br />
===Dinner===<br />
<br />
Monday Sept. 6 Dinner on your own<br />
<br />
Tuesday Sept.7 Dinner on your own (We could also organize something informal at the meeting)<br />
<br />
Wednesday Sept. 8 GOC Lobster Dinner at HighSeas (other choices will also be available)<br />
<br />
Thursday Sept. 9 An informal Dinner can be arranged at HighSeas with enough advance notice. See the table below.</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2010_Bar_Harbor_Logistics&diff=301572010 Bar Harbor Logistics2010-08-16T18:19:01Z<p>Adiehl: /* Attendees */</p>
<hr />
<div>==Attendees==<br />
(please use the Arrival and Departure info columns if you would like to try to carpool or share a shuttle to/from the airport)<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport (BHB=Bar Harbor or BGR=Bangor) <br />
! Departure Date/Time from Airport (BHB=Bar Harbor or BGR=Bangor)<br />
! Staying at HighSeas?<br />
! Food requirement (None, Veggie, Vegan)<br />
! Attending the GOC Dinner?<br />
! Will you dine at HighSeas Thursday? <br />
|-<br />
| David Hill<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| none<br />
| yes<br />
| no<br />
|-<br />
| Judith Blake<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| none<br />
| yes<br />
| no<br />
|-<br />
|Harold Drabkin<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| none<br />
| yes<br />
| no<br />
|<br />
|-|<br />
|Rachael Huntley<br />
| GOA<br />
| 6th Sept 20:45 (or if delayed 22:30) Bangor (Bus)<br />
| 9th Sept 11:10 (Bar Harbor)<br />
| Yes (with Susan Tweedie)<br />
| veggie/no fish<br />
| Yes<br />
| No<br />
|-|<br />
|Susan Tweedie<br />
| FlyBase<br />
| 6th Sept 20:35 (BHB)<br />
| 9th Sept 16:10 (BHB)<br />
| Yes (with Rachael Huntley)<br />
| none<br />
| Yes<br />
| No<br />
|-<br />
| Mary Shimoyama<br />
| RGD<br />
| 6th Sept Bar Harbor<br />
| 10th Sept Bar Harbor<br />
| no<br />
| none<br />
| yes<br />
| not sure<br />
|-<br />
| Donghui Li<br />
| TAIR<br />
| Sept 6 10:56 am Bangor<br />
| Sept 11 11:25 am Bangor<br />
| yes<br />
| none<br />
| yes<br />
| yes<br />
|-<br />
| Tanya Berardini<br />
| TAIR<br />
| <br />
|<br />
| no<br />
| none<br />
| yes<br />
| no<br />
|-<br />
| Rebecca Foulger<br />
| UniProt/GO editorial<br />
| 6th Sept 16:50 (BHB)<br />
| 9th Sept 16:10 (BHB)<br />
| yes (ok to share: no roommate yet)<br />
| none<br />
| yes<br />
| yes<br />
|-<br />
| Amelia Ireland<br />
| BBOP/GO Editorial Office<br />
| 6th Sept 16:50 (BHB)<br />
| 10th Sept 11:10 (BHB)<br />
| ? yes (no roommate yet)<br />
| veggie/no fish<br />
| yes<br />
| maybe<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
|I'll be in Bangor over the weekend so any time Monday I can go to BHB<br />
|9th Sept 3:19PM Bangor<br />
|Yes - shared bath fine, single preferred<br />
|None<br />
|Yes<br />
|No<br />
|-<br />
|Eva Huala<br />
|TAIR<br />
|6th Sept 20:35 (BHB)<br />
|9th Sept 16:10 (BHB)<br />
|yes, OK to share bath, prefer single<br />
|none<br />
|yes <br />
|no<br />
|-<br />
|Jane Lomax<br />
|GO-EBI<br />
| 6th Sept 16:50 (BHB)<br />
| 9th Sept 16:10 (BHB)<br />
| yes, prefer single if poss<br />
|none<br />
|yes <br />
|no<br />
|-<br />
|Sven Heinicke<br />
|Princeton<br />
| 6th Sept 1:05 (BHB)<br />
| 10th Sept 11:10 (BHB)<br />
| yes, roommate ok.<br />
|none<br />
|yes <br />
|no<br />
|-<br />
|Rama Balakrishnan<br />
|SGD, Stanford University<br />
|6th Sept, 8:35 PM BHB<br />
|9th Sept 4:10 PM BHB<br />
|yes, room mate ok.<br />
|veggie(prefer vegan food)<br />
|yes<br />
|yes<br />
|-<br />
|Stan Laulederkind<br />
|RGD<br />
|6th Sept, 4:50 PM BHB<br />
|9th Sept 4:10 PM BHB<br />
|no<br />
|none<br />
|yes<br />
|no<br />
|-<br />
|Pascale Gaudet<br />
|dictybase<br />
| by car<br />
| by car<br />
| yes, room mate ok.<br />
|none<br />
|yes <br />
|no<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase<br />
|USAir#3388 - 10:32pm, Bangor<br />
|USAir#3612 - 3:19pm, Bangor<br />
|yes, roommate ok<br />
|Veggie<br />
|Yes<br />
|No<br />
|-<br />
| Mindy Dwinell<br />
| RGD<br />
| 6th Sept Bar Harbor<br />
| 10th Sept Bar Harbor<br />
| no<br />
| none<br />
| yes<br />
| not sure<br />
|-<br />
| Mary Dolan<br />
| GOC/MGI<br />
| local<br />
| local<br />
| no<br />
| none<br />
| yes<br />
| no<br />
|-<br />
| Alexander Diehl<br />
| GOC/CL/MGI<br />
| local<br />
| local<br />
| no<br />
| none<br />
| yes<br />
| yes<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport (BHB=Bar Harbor or BGR=Bangor) <br />
! Departure Date/Time from Airport (BHB=Bar Harbor or BGR=Bangor)<br />
! Staying at HighSeas with room-mate?<br />
! Food requirement (None, Veggie, Vegan)<br />
! Attending the GOC Dinner?<br />
! Will you dine at HighSeas Thursday? <br />
|}<br />
<br />
==Remote Attendees==<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Email<br />
! Attending Tuesday 9/7<br />
! Attending Wednesday 9/8<br />
! Attending Thursday 9/9<br />
! Time zone<br />
|-<br />
| Mike Livstone<br />
| Princeton<br />
| livstone@genomics.princeton.edu<br />
| Yes<br />
| maybe (AM only)<br />
| No<br />
| EDT<br />
|-<br />
| Ruth Lovering<br />
| University College London (BHF-UCL)<br />
| r.lovering@ucl.ac.uk<br />
| Yes<br />
| Yes<br />
| Yes<br />
| BST<br />
|-<br />
|}<br />
<br />
==Travel to Bar Harbor==<br />
====Bar Harbor Airport to Bar Harbor====<br />
<br />
At Your Service Taxi Co. (207) 288-9222 (Due to heavy tourism, it is best to try to book in advance)<br />
<br />
Island Explorer: (Free Island Shuttle Bus from late June thru mid October)<br />
<br />
====Boston Airport to Bangor ME or Bar Harbor ME====<br />
<br />
=====Air=====<br />
<br />
It is possible for us to book round-trip airfare from Boston to Bar Harbor. We need to know in advance.<br />
<br />
=====Bus=====<br />
<br />
http://www.concordcoachlines.com/schedules-a-fares.html<br />
<br />
====Bangor ME to Bar Harbor ME====<br />
There are several ways to get to Bar Harbor from Bangor. As we learn more about who and when people are arriving and leaving from Bangor, we will try to arrange cabs, shuttles or have someone rent a car and drive to Bar Harbor and back. The laboratory also gets a special rate on the hotel at the airport in Bangor. If you are arriving on a late flight on Monday, there is an option to stay in Bangor on Monday night and come to Bar Harbor Tuesday morning. To get the special rate, we will have to book these rooms in advance.<br />
<br />
==Accommodations==<br />
====HighSeas (on site)====<br />
<br />
There are a limited number of rooms available at the HighSeas Conference Center here at The Jackson Laboratory. The rooms can be singles or doubles and two rooms share a bath. Please indicate if you would like to stay at HighSeas. If so, please indicate in the table below if you would be willing to share a room and if you have a room-mate. Low cost, charged to GOC grant; a good deal. Please consider.<br />
<br />
http://courses.jax.org/highseas.html<br />
<br />
====Harborside ($179-779 per night)====<br />
<br />
http://www.theharborsidehotel.com/<br />
<br />
====Cromwell Harbor Motel ($108-115)====<br />
<br />
http://www.cromwellharbor.com/<br />
<br />
<br />
==Meals==<br />
<br />
Lunches and break snacks will be served at the Conference center. For non-arranged dinners, there are many good restaurants in Bar Harbor.<br />
<br />
http://www.barharborinfo.com/dining/<br />
<br />
===Dinner===<br />
<br />
Monday Sept. 6 Dinner on your own<br />
<br />
Tuesday Sept.7 Dinner on your own (We could also organize something informal at the meeting)<br />
<br />
Wednesday Sept. 8 GOC Lobster Dinner at HighSeas (other choices will also be available)<br />
<br />
Thursday Sept. 9 An informal Dinner can be arranged at HighSeas with enough advance notice. See the table below.</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Main_Page&diff=28904Main Page2010-07-05T12:16:50Z<p>Adiehl: Undo revision 28903 by DerrickBark (Talk)</p>
<hr />
<div><big>'''Welcome to the Gene Ontology Consortium Wiki'''</big><br />
<br />
== GOC Public Resources ==<br />
<br />
[[:Category:FAQ|GO Frequently Asked Questions]]<br />
<br />
=== Community Annotation Pages ===<br />
[[Cardiovascular|Cardiovascular Genes]]<br />
<br />
[[Immunology]]<br />
<br />
[[Muscle Biology|Muscle Biology]]<br />
<br />
[[Reference Genome Genes]]<br />
<br />
[[Lung Development]]<br />
<br />
=== Web Pages ===<br />
<br />
* [http://www.geneontology.org/ GO Home]<br />
* [http://www.geneontology.org/GO.contents.doc.shtml GO Documentation]<br />
* [http://www.geneontology.org/GO.downloads.shtml GO Downloads]<br />
<br />
=== Database Query Pages ===<br />
* [http://amigo.geneontology.org AmiGO]<br />
<br />
== GO Working Group Wiki ==<br />
<br />
These pages are limited to use by members of the GOC.<br />
<br />
*[[User Advocacy]]<br />
*[[Annotation Outreach]]<br />
*[[Ontology Development]]<br />
*[[Reference Genome Annotation Project]]<br />
*[[Software and Utilities]]<br />
*[[GO Leadership]]<br />
*[[GO Managers]]<br />
*[[Consortium Meetings]]<br />
*[[Working Groups]]<br />
**[[AmiGO Hub]]<br />
**[[:Category:OBO-Edit working group|OBO-Edit working group]]<br />
**[[:Category:Web Presence Working Group|Web Presence Working Group]]<br />
**[[:Category:Immunology Annotation working group|Immunology Annotation working group]]<br />
**[[Web Presence Working Group]]<br />
*[[GO Content Checklist]]<br />
*[[GO Timeline]]<br />
*[[Progress Reports]]<br />
*[[Publications%2C_tutorials%2C_talks%2C_posters|Publication list]]<br />
<br />
== Useful Links ==<br />
<br />
Help pages for using wikis: http://meta.wikimedia.org/wiki/Help:Help<br />
<br />
Quick guide to formatting wiki text: http://meta.wikimedia.org/wiki/Help:Wikitext<br />
<br />
[[Wiki_best_practice|Guidelines for using this wiki]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Main_Page&diff=28831Main Page2010-07-01T19:57:16Z<p>Adiehl: Undo revision 28830 by SophiaGreen (Talk)</p>
<hr />
<div><big>'''Welcome to the Gene Ontology Consortium Wiki'''</big><br />
<br />
== GOC Public Resources ==<br />
<br />
[[:Category:FAQ|GO Frequently Asked Questions]]<br />
<br />
=== Community Annotation Pages ===<br />
[[Cardiovascular|Cardiovascular Genes]]<br />
<br />
[[Immunology]]<br />
<br />
[[Muscle Biology|Muscle Biology]]<br />
<br />
[[Reference Genome Genes]]<br />
<br />
[[Lung Development]]<br />
<br />
=== Web Pages ===<br />
<br />
* [http://www.geneontology.org/ GO Home]<br />
* [http://www.geneontology.org/GO.contents.doc.shtml GO Documentation]<br />
* [http://www.geneontology.org/GO.downloads.shtml GO Downloads]<br />
<br />
=== Database Query Pages ===<br />
* [http://amigo.geneontology.org AmiGO]<br />
<br />
== GO Working Group Wiki ==<br />
<br />
These pages are limited to use by members of the GOC.<br />
<br />
*[[User Advocacy]]<br />
*[[Annotation Outreach]]<br />
*[[Ontology Development]]<br />
*[[Reference Genome Annotation Project]]<br />
*[[Software and Utilities]]<br />
*[[GO Leadership]]<br />
*[[GO Managers]]<br />
*[[Consortium Meetings]]<br />
*[[Working Groups]]<br />
**[[AmiGO Hub]]<br />
**[[:Category:OBO-Edit working group|OBO-Edit working group]]<br />
**[[:Category:Web Presence Working Group|Web Presence Working Group]]<br />
**[[:Category:Immunology Annotation working group|Immunology Annotation working group]]<br />
**[[Web Presence Working Group]]<br />
*[[GO Content Checklist]]<br />
*[[GO Timeline]]<br />
*[[Progress Reports]]<br />
*[[Publications%2C_tutorials%2C_talks%2C_posters|Publication list]]<br />
<br />
== Useful Links ==<br />
<br />
Help pages for using wikis: http://meta.wikimedia.org/wiki/Help:Help<br />
<br />
Quick guide to formatting wiki text: http://meta.wikimedia.org/wiki/Help:Wikitext<br />
<br />
[[Wiki_best_practice|Guidelines for using this wiki]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Main_Page&diff=28794Main Page2010-06-30T00:48:54Z<p>Adiehl: Undo revision 28762 by Laura Ashby (Talk)</p>
<hr />
<div><big>'''Welcome to the Gene Ontology Consortium Wiki'''</big><br />
<br />
== GOC Public Resources ==<br />
<br />
[[:Category:FAQ|GO Frequently Asked Questions]]<br />
<br />
=== Community Annotation Pages ===<br />
[[Cardiovascular|Cardiovascular Genes]]<br />
<br />
[[Immunology]]<br />
<br />
[[Muscle Biology|Muscle Biology]]<br />
<br />
[[Reference Genome Genes]]<br />
<br />
[[Lung Development]]<br />
<br />
=== Web Pages ===<br />
<br />
* [http://www.geneontology.org/ GO Home]<br />
* [http://www.geneontology.org/GO.contents.doc.shtml GO Documentation]<br />
* [http://www.geneontology.org/GO.downloads.shtml GO Downloads]<br />
<br />
=== Database Query Pages ===<br />
* [http://amigo.geneontology.org AmiGO]<br />
<br />
== GO Working Group Wiki ==<br />
<br />
These pages are limited to use by members of the GOC.<br />
<br />
*[[User Advocacy]]<br />
*[[Annotation Outreach]]<br />
*[[Ontology Development]]<br />
*[[Reference Genome Annotation Project]]<br />
*[[Software and Utilities]]<br />
*[[GO Leadership]]<br />
*[[GO Managers]]<br />
*[[Consortium Meetings]]<br />
*[[Working Groups]]<br />
**[[AmiGO Hub]]<br />
**[[:Category:OBO-Edit working group|OBO-Edit working group]]<br />
**[[:Category:Web Presence Working Group|Web Presence Working Group]]<br />
**[[:Category:Immunology Annotation working group|Immunology Annotation working group]]<br />
**[[Web Presence Working Group]]<br />
*[[GO Content Checklist]]<br />
*[[GO Timeline]]<br />
*[[Progress Reports]]<br />
*[[Publications%2C_tutorials%2C_talks%2C_posters|Publication list]]<br />
<br />
== Useful Links ==<br />
<br />
Help pages for using wikis: http://meta.wikimedia.org/wiki/Help:Help<br />
<br />
Quick guide to formatting wiki text: http://meta.wikimedia.org/wiki/Help:Wikitext<br />
<br />
[[Wiki_best_practice|Guidelines for using this wiki]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2010_Stanford_Meeting_Logistics&diff=261582010 Stanford Meeting Logistics2010-03-29T01:31:21Z<p>Adiehl: /* Cell Type Ontology (Terry) */</p>
<hr />
<div>=Dates=<br />
GO consortium & SAB meetings March 30-31, April 1, 2010<br />
<br />
# We wish all attendees to attend from the morning of March 30 through the morning of April 1st. The afternoon of April 1st will be for all GO subcontract PIs, GOC PIs and our SAB. We suggest you arrive the evening of March 29th and leave after noon on the 1st, unless you are a PI or SAB member.<br />
<br />
=Venue=<br />
Meetings will be at the [http://www.stanford.edu Stanford University], Stanford, CA, USA.<br />
<br />
The GOC and SAB meeting will take place at the [http://www.stanfordalumni.org/aboutsaa/alumni_center/conference/home.html Arrillaga Alumni Center].<br />
<br />
Lunches will be at the Arrillaga Center.<br />
<br />
There will be a group dinner on March 31st for the GOC and SAB.<br />
<br />
We will also facilitate dinners on March 29th and 30th. There are a large variety of restaurants in the area.<br />
<br />
=Maps=<br />
[http://maps.stanford.edu/ Stanford University maps]<br />
<br />
Meeting will be held at the Arrillaga Alumni Center, 341 Galvez Street, Stanford, CA<br />
[http://tinyurl.com/ycxtzbk]<br />
<br />
=Registration=<br />
Registration will open in early 2010. <br />
<br />
#Registration Fee. We anticipate a minimal registration fee to cover lunch and a light breakfast. The meeting will be sponsored by the Cherry Lab.<br />
<br />
=Lodging Information=<br />
Four hotels are within a 15-20 minute walk to the Alumni Center. Ordered below by price per night, lowest to highest.<br />
<br />
#[http://www.hotelcalifornia.com/ Hotel California] $<br />
#[http://www.cardinalhotel.com/ Cardinal Hotel] $<br />
#[http://www.stanfordterraceinn.com/ Stanford Terrace Inn] $$<br />
#[http://specialoffers.starwoodhotels.com/SheratonPaloAlto/so.htm?PS=PS_aa_Western_Google_sheraton_palo_alto_california_011209_NAD_FM Sheraton Palo Alto Hotel] $$$$<br />
#[http://specialoffers.starwoodhotels.com/WestinPaloAlto/so.htm?PS=PS_aa_Western_Google_westin_palo_alto_ca_011209_NAD_FM Westin Palo Alto] $$$$<br />
<br />
=Agenda for GOC meeting March 30 and March 31=<br />
==Tuesday, March 30 – Morning [Start - Break]==<br />
#Review Agenda; intro new people<br />
#who is taking minutes? <br />
#who is tracking the teleconferencers?<br />
===Communication and Process for the GOC [Suzi]=== <br />
# Changes in Managers structure<br />
# Description of integrated team approach to annotation<br />
# Increasing our efficiency in completing projects (using MF-BP and RefGenome as examples)<br />
## Clear problem statement, what will the end result look like: Fuzziness = Failure<br />
## Identify -a- project manager to oversee progress<br />
## Establish project priority with respect to all other GOC projects<br />
## Talk to all affected parties, revisit these groups as each new milestone is reached<br />
##* Effective use of wiki and mailing lists<br />
## Establish milestones and dependencies<br />
<br />
==Tuesday, March 30 – Morning [Break – Lunch]==<br />
===Ref Genome Project and PAINT [Pascale and Kara]===<br />
# Current focus on process sets<br />
#Update on Annotation<br />
#* Curation: About eleven protein families have been done with beta version of PAINT, primarily by Mike Livstone in Kara's group at Princeton. [http://genomics.princeton.edu/~kara/PAINTupdate slides].<br />
#* References for PAINT annotations: One reference is available for each family's annotation.<br />
# PAINT Software [Ed]<br />
# Inferences from MF-BP links<br />
# Need for MOD incorporation<br />
<br />
==Tuesday, March 30 Afternoon [After lunch - Break]==<br />
===AMIGO updates/report (Seth)===<br />
# New search features<br />
# PAINT-style displays in AmiGO<br />
# Improved tree view<br />
<br />
===Ontology Updates===<br />
#Term additions from the ASCB and SDB meeting (6 slides, Tanya)<br />
# Additions from the kidney and heart development meeting (14 slides, David)<br />
# PAMGO (Jane)<br />
# Cross products (18 slides, David)<br />
#* Internal cross products<br />
#* Cross-products already in place<br />
#* Cross-products "in production"<br />
#* External cross-products<br />
# Aligning chemicals (11 slides, David)<br />
<br />
==Tuesday, March 30 Afternoon [Break – Dinner] ==<br />
===Cell Ontology (Terry)===<br />
# Content update (Terry)<br />
# Improved support for OBO/OWL/Protégé intersections (Chris)<br />
# OBO_EDIT updates/report (Amina)<br />
# streamlining addition of compositional terms [Chris]<br />
<br />
===Ontology Content Projects=== <br />
# Bringing the NIF ontologies into GO (Chris)<br />
# GO-Pathway database integration (Chris)<br />
# PRO, MouseCyc, Reactome and GO: Complexes in PRO and GO (Harold)<br />
<br />
==Wednesday, March 31 Morning – Break ==<br />
===Action Items Review (Judy)===<br />
#from last GOC<br />
#from yesterday, Tuesday, March 30<br />
<br />
===Impact of recent ontology changes from an annotator/ontology developer perspective [David]===<br />
# MF-BP links, what they are and how they impact annotation<br />
# Scope of regulation relationship<br />
# Scope of has_part relationship<br />
<br />
===Evidence Codes===<br />
# NOT evidence codes<br />
## "IMR" -> "Inferred from missing residues“ lacking domains, etc <br />
##"IRD" -> "Inferred from rapid divergence“ sequences have rapidly diverged (e.g., paralogs) <br />
##"IDS" -> "Inferred from descendant sequence(s)“ lack of function is annotated due to existing protein that have been previously annotated with lacking this function <br />
<br />
# Proposal from CJM to extend Evidence codes to support chains of evidence<br />
# Position of ISM<br />
# RCA usage and documentation<br />
# Notice of ISMB workshop on Assays, ECO and OBI [Judy]<br />
<br />
== Wednesday, March 31 Morning [Break – Lunch] ==<br />
===Annotation (Rama, Emily) ===<br />
# Guidelines for 'binding' terms'''<br />
#* [http://wiki.geneontology.org/index.php/Binding_terms_working_group#2010_discussion proposed guidelines]<br />
#* What, if any, binding term annotations can be transferred via ISS/ISO?<br />
# Discuss guideline documentation, progress and unresolved issues (Emily and Ruth; 12 slides).<br />
#* Should we include transporters in these guidelines? <br />
#* Should we capture drug information?<br />
#* Should the guidelines include a statement suggesting that the specific substrate for an enzyme with 'GO:0032451 demethylase activity' can be included in column 16?<br />
#* Should we create terms like ‘ATP binding involved in kinase activity'?<br />
# Discussion of taxon IDs and subspecies [Jim Hu]<br />
# Requirements and QC for contributed annotations [Rama]<br />
#* M. tuberculosis example<br />
# Ideas for incorporating IMEX data into GOC? [Emily]<br />
# Plans for Geneva GO Annotation Workshop [Pascal]<br />
<br />
== Wednesday, March 31 Afternoon [Lunch - Break] ==<br />
=== File Issues ===<br />
#A suggestion from the OBO Foundry meeting: we make GO ext the main GO file, the one that new users see. The other files continue to exist in the same place, but make it clear they are legacy files. That way anyone new coming to GO will build tools using GO ext. <br />
# Ease of file dissemination<br />
=== GAF file ===<br />
# GAF2 update<br />
# Proposal to add a new column to the GAF to indicate if an annotation was reviewed by a curator or not.<br />
<br />
== Wednesday, March 31 Afternoon [Break - end of day] ==<br />
# OBO-Foundry Report (Jane)<br />
# Parking lot item discussions or catch-up reports<br />
# Open forum on thoughts regarding upcoming competitive renewal applications<br />
# Preparation for SAB next day<br />
<br />
=Agenda GO SAB Meeting April 1 2010=<br />
==Morning==<br />
:8:30: Welcome, Agenda Review<br />
:9:00am - 9:20 Grant news: 5 year Aims, Structure with Subcontracts, Metrics of Ontology and Annotation Success [Judy]<br />
:9:20 – 10:00 Management structure and Project process (Suzi)<br />
:10:00- 10:20 AmiGO and GO usage stats (Mike)<br />
<br />
:10:20 – 10:45 Break<br />
<br />
:10:45 – 11:00 Vision and Questions for Competitive Renewal/Future of GO (Michael)<br />
:11:00 – 12:00 Discussion of Aims and Objectives for Competitive Renewal (Suzi: Judy and others note-taking)<br />
:12:00 – 1:00 pm working lunch, open discussion<br />
<br />
==Afternoon==<br />
:1:00 – 2:00 SAB executive session<br />
:2:00 – 3:00 SAB and PIs<br />
:3:00 – 3:30 Break<br />
:3:30 – 4:30 Summary [open to all GOC still round]<br />
<br />
=Attendees=<br />
Airport codes: SFO = San Francisco International; SJC = San Jose International Airport<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport (see codes above)<br />
! Departure Date/Time from Airport<br />
|-<br />
| Mike Cherry<br />
| GO / SGD<br />
| walking<br />
| <br />
|-<br />
| Judy Blake<br />
| GO / MGI<br />
| March 29 SFO<br />
| April 2 SFO<br />
|-<br />
| Suzi Lewis<br />
| GO / BBOP<br />
| Driving<br />
|-<br />
| Mary Shimoyama<br />
| RGD<br />
| March 29 SFO<br />
| April 2 SFO<br />
|-<br />
| Chris Mungall<br />
| GO / BBOP<br />
| CalTrain<br />
|<br />
|-<br />
| Seth Carbon<br />
| GO / BBOP<br />
| Driving<br />
|<br />
|-<br />
| Amina Abdulla<br />
| GO / BBOP<br />
| Driving<br />
|<br />
|-<br />
| Amelia Ireland<br />
| GO / BBOP<br />
| Hitching a ride<br />
|<br />
|-<br />
| Kara Dolinski<br />
| GO / PPOD<br />
| TBA<br />
| TBA<br />
|-<br />
| Eva Huala<br />
| TAIR<br />
| March 29<br />
| April 2<br />
|-<br />
| Karen Eilbeck<br />
| SO (U of Utah)<br />
| San Jose 29th March<br />
| San Jose April 1 - evening<br />
|-<br />
| Barry Smith<br />
| SAB (U at Buffalo)<br />
| March 31 SFO<br />
| April 1 SFO<br />
|-<br />
| Richard Scheuermann<br />
| SAB (UT Southwestern)<br />
| March 31 SJC 9:30 am<br />
| April 1 SJC 6:15 pm<br />
|-<br />
| Tanya Berardini<br />
| TAIR<br />
| on site<br />
| on site<br />
|-<br />
| Donghui li<br />
| TAIR<br />
| on site<br />
| on site<br />
|-<br />
| Larry Hunter<br />
| SAB (U Colorado)<br />
| March 31 SFO<br />
| April 2 SFO<br />
|- <br />
|Paul Sternberg<br />
|WormBase and Caltech<br />
|San Jose<br />
|San Jose<br />
|-<br />
|Doug Howe<br />
|ZFIN<br />
|SFO March 29<br />
| <br />
|-<br />
|Dianna Fisk<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Ben Hitz<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Jane Lomax<br />
|GO-EBI<br />
|March 29 SFO<br />
|April 2 SFO<br />
|-<br />
|Pascale Gaudet<br />
|dictyBase<br />
| <br />
| <br />
|-<br />
|Harold Drabkin<br />
|MGI<br />
|March 29th SFO<br />
|April TBA<br />
|-<br />
|Terry Meehan<br />
|MGI<br />
|March 28th SFO<br />
|April 2<br />
|-<br />
|Jim Hu<br />
|EcoliWiki<br />
|March 29 SFO 8PM<br />
|April 2 SFO 1:40PM<br />
|-<br />
|David Hill<br />
|GO/MGI<br />
|<br />
|<br />
|-<br />
|Stan Laulederkind<br />
|RGD<br />
|March 28 SFO 7:47PM<br />
|April 1 SJC 2:20PM<br />
|-<br />
|Monte Westerfield<br />
|ZFIN<br />
|April 1 SFO<br />
|<br />
|-<br />
|Selina Dwight<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Kate Dreher<br />
|TAIR<br />
|on site<br />
|on site<br />
|-<br />
|Rama Balakrishnan<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Stacia Engel<br />
|SGD<br />
|N/A<br />
|N/A<br />
|-<br />
|Ranjana Kishore<br />
|WormBase<br />
|SJC 3/29 5.50 PM<br />
|SJC 4/01 3.00 PM<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase<br />
|TBD<br />
|TBD<br />
|-<br />
|Petra Fey<br />
|dictyBase<br />
|N/A<br />
|SFO 4/01 1:55 PM<br />
|-<br />
|Peter D'Eustachio<br />
|Reactome / NYUMC<br />
|SJC 3/29 7:02 PM<br />
|SJC 4/1 10:25 PM<br />
|-<br />
|Serenella Ferro Rojas<br />
|UniProtKB/Swiss-Prot<br />
|March 29 SFO<br />
|April 4 SFO<br />
|-<br />
|Eurie Hong<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Emily Dimmer<br />
|GOA<br />
|March 29 SFO<br />
|April 2 SFO<br />
|-<br />
|-<br />
|Tony Sawford<br />
|GOA<br />
|March 29 SFO<br />
|April 2 SFO<br />
|-<br />
|Karen Christie<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Julie Park<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Ingrid Keseler<br />
|EcoCyc<br />
|N/A<br />
|N/A<br />
|-<br />
| Paul Thomas<br />
| PANTHER/EcoliHub<br />
| driving<br />
| <br />
|-<br />
|}<br />
<br />
=Remote Attendees=<br />
Webex and Telephone Conferencing will be provided<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! email (needed to set up your remote access)<br />
! Attending GOC (March 30-31)<br />
! Attending SAB (April 1)<br />
! Calling in alone or in a group (with whom and from where, if known)<br />
|-<br />
|Midori Harris<br />
|EBI GO<br />
|midori at ebi dot ac dot uk<br />
|yes<br />
|yes<br />
|TBD<br />
|-<br />
| Jennifer Deegan<br />
| GO Editorial Office<br />
| jdeegan at ebi.ac.uk<br />
| Yes<br />
| Yes<br />
| Probably alone from home.<br />
|-<br />
| Ruth Lovering<br />
| BHF-UCL annotator<br />
| r.lovering at ucl.ac.uk<br />
| Yes<br />
| Yes<br />
| From home, Tuesday, and wed afternoon session only<br />
|-<br />
| Rachael Huntley<br />
| GOA Curator<br />
| huntley at ebi.ac.uk<br />
| Yes<br />
| Yes<br />
| From home.<br />
|-<br />
| Michelle Giglio<br />
| IGS, UMD<br />
| mgiglio at som.umaryland.edu<br />
| Yes<br />
| No<br />
| alone from work/home<br />
|-<br />
| Marcus Chibucos<br />
| IGS, UMD<br />
| mchibucos at som dot umaryland dot edu<br />
| Yes<br />
| No<br />
| alone from work/home<br />
|-<br />
| Alexander Diehl<br />
| MGI<br />
| adiehl@informatics.jax.org<br />
| Yes<br />
| Yes<br />
| alone from work/home<br />
|-<br />
| Michael Livstone<br />
| Princeton<br />
| livstone@genomics.princeton.edu<br />
| No<br />
| Yes<br />
| alone from work/home, can present PAINT families that have been curated via webex if that is on the agenda for the SAB. Available 9AM-5PM EDT, 6AM-2PM PDT.<br />
|-<br />
| Lakshmi Pillai<br />
| AgBase <br />
| pillai@cvm.msstate.edu<br />
| Yes<br />
| No<br />
| TBD<br />
|-<br />
| Susan Tweedie<br />
| FlyBase<br />
| sart2 at gen dot cam dot ac dot uk<br />
| Yes<br />
| Yes<br />
| alone from home<br />
|-<br />
| Yasmin Alam-Faruque<br />
| EBI GOA<br />
| yalam at ebi.ac.uk<br />
| Yes<br />
| Yes<br />
| alone from home<br />
|-<br />
| Varsha Khodiyar<br />
| BHF-UCL annotator<br />
| v.khodiyar at ucl.ac.uk<br />
| Yes<br />
| No<br />
| alone from home<br />
|}<br />
<br />
<br />
----<br />
Return to [[Consortium_Meetings]] page</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI,_March_2010&diff=25857MGI, March 20102010-03-23T18:14:31Z<p>Adiehl: /* A. Ontology Development Contributions: */</p>
<hr />
<div>= Mouse Genome Informatics March, 2010 =<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake<br />
<br />
Alexander Diehl<br />
<br />
Harold J Drabkin<br />
<br />
David Hill<br />
<br />
Terry Meehan<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
Mary Dolan<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of March 22, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''01_Sept_09'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''22_Mar_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">18188</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">35191*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16993</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">93.43</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">11177</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">33228**</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">22051</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">197.29</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">708</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4006</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">3298***</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">465.82</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16145</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15942</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">62</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.39</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10533</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10592</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-3</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-0.03</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1491</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1248</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">13</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.89</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
<nowiki>** We have now tagged all genes in MGI that have no annotation or only IEA annotation with annotation to one or more of the three Gene Ontology root terms as needed. These genes were also then marked as “annotation complete.” This now allows for notification when GO-appropriate literature becomes indexed to these genes as it comes in through our normal triage process.</nowiki><br />
<br />
<nowiki>*** We have added a curator-monitored pipeline whereby annotations based on experimental evidence made to rat genes by RGD curators are added to MGI as annotations to mouse genes based on sequence orthology. This has helped fill in annotation to certain under-represented metabolic processes not normally studied in mouse due to their small size. </nowiki><br />
<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We are currently using ProMiner to improve associating incoming literature to genes in MGI (indexing). This association is used to drive various QC reports used for identifying annotation priorities.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt Keywords and InterPro domains for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) (see <nowiki>**</nowiki> above)<br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. (2010). Ontology Engineering. Nature Biotechnol. Feb;28(2):128-30.<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. (2010) Hematopoietic cell types: Prototype for a revised cell ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Dowell, KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA. (2009). Integrating Text Mining into the MGI Biocuration Workflow Database. Bap019.<br />
<br />
Hill DP, Berardini TZ, Howe DG, Van Auken KM. (2009). Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology. Mol Reprod. Dev. 77(4):314-29.<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. (2010). Cross-Product Extensions of the Gene Ontology. J. Biomed. Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002]<br />
<br />
The Gene Ontology Consortium. (2010). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38:D331-5. <br />
<br />
<br />
<br />
b. ''Presentations including Talks and Tutorials and Teaching''<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
<br />
1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris, Jen Deegan and Jane Lomax to develop cross-products within the three GO namespaces. The regulation cross-products have been released in the extended GO. David and Tanya are now quality checking the internal biological process cross-products.<br />
<br />
2. David Hill has worked with Tanya Berardini to continuing to add interontology links between MF and BP.<br />
<br />
3. David Hill has worked with Varsha Khodiyar, Tanya Berardini, Doug Howe, Susan Tweedie, Ruth Lovering and community experts to expand the heart development portion of the ontology.<br />
<br />
4. David Hill has worked with Yasmin Alam-Faruque, Midori Harris, Becky Folger, Doug Howe, Emily Dimmer, Rachel Huntley and community experts to expand the kidney development portion of the ontology.<br />
<br />
5. David Hill and Tanya Berardini are maintaining the automated quality checks of the ontology on an ongoing basis.<br />
<br />
6. David Hill and Harold Drabkin are working with Jane Lomax, Midori Harris, Tanya Berardini and Jane Lomax to align the representation of biochemicals in GO. <br />
<br />
7. David Hill and Tanya Berardini added or modified 231 terms as a result of attending the American Society for Cell Biology Meeting in December.<br />
<br />
8. Alexander Diehl is part of the GO Signaling Working Group led by Jen Deegan that has recently implemented improvements in the representation of signaling in the GO.<br />
<br />
9. Alexander Diehl is project leader for the Cell Ontology (with Chris Mungall) and Terry Meehan is a full-time curator working on the Cell Ontology. Terry is currently focusing on implementing cross-products for hematopoietic cell ontology terms, while Alex is working on general improvements to the CL and organization a Cell Ontology Workshop in May 2010.<br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
The Protein Ontology project is providing a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro<br />
) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone. <br />
<br />
Harold and David, along with Emily Dimmer, are mentoring Heather Wick of Tufts University, for annotation of human fetal lung development<br />
<br />
= Other Highlights: =<br />
We are now suppling a GAF 2.0 format file to GOC with column 16 and 17 data filled in. This file is also available directly from our own FTP site. Currently, the data in column 16 refers to the cell type that the experiment supporting the annotation was carried out in, by use of cell ontology terms.</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI,_March_2010&diff=25856MGI, March 20102010-03-23T18:09:46Z<p>Adiehl: /* Staff: */</p>
<hr />
<div>= Mouse Genome Informatics March, 2010 =<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake<br />
<br />
Alexander Diehl<br />
<br />
Harold J Drabkin<br />
<br />
David Hill<br />
<br />
Terry Meehan<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
Mary Dolan<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of March 22, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''01_Sept_09'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''22_Mar_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">18188</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">35191*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16993</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">93.43</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">11177</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">33228**</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">22051</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">197.29</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">708</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4006</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">3298***</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">465.82</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16145</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15942</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">62</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.39</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10533</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10592</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-3</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-0.03</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1491</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1248</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">13</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.89</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
<nowiki>** We have now tagged all genes in MGI that have no annotation or only IEA annotation with annotation to one or more of the three Gene Ontology root terms as needed. These genes were also then marked as “annotation complete.” This now allows for notification when GO-appropriate literature becomes indexed to these genes as it comes in through our normal triage process.</nowiki><br />
<br />
<nowiki>*** We have added a curator-monitored pipeline whereby annotations based on experimental evidence made to rat genes by RGD curators are added to MGI as annotations to mouse genes based on sequence orthology. This has helped fill in annotation to certain under-represented metabolic processes not normally studied in mouse due to their small size. </nowiki><br />
<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We are currently using ProMiner to improve associating incoming literature to genes in MGI (indexing). This association is used to drive various QC reports used for identifying annotation priorities.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt Keywords and InterPro domains for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) (see <nowiki>**</nowiki> above)<br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. (2010). Ontology Engineering. Nature Biotechnol. Feb;28(2):128-30.<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. (2010) Hematopoietic cell types: Prototype for a revised cell ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Dowell, KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA. (2009). Integrating Text Mining into the MGI Biocuration Workflow Database. Bap019.<br />
<br />
Hill DP, Berardini TZ, Howe DG, Van Auken KM. (2009). Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology. Mol Reprod. Dev. 77(4):314-29.<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. (2010). Cross-Product Extensions of the Gene Ontology. J. Biomed. Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002]<br />
<br />
The Gene Ontology Consortium. (2010). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38:D331-5. <br />
<br />
<br />
<br />
b. ''Presentations including Talks and Tutorials and Teaching''<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
<br />
1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris, Jen Deegan and Jane Lomax to develop cross-products within the three GO namespaces. The regulation cross-products have been released in the extended GO. David and Tanya are now quality checking the internal biological process cross-products.<br />
<br />
2. David Hill has worked with Tanya Berardini to continuing to add interontology links between MF and BP.<br />
<br />
3. David Hill has worked with Varsha Khodiyar, Tanya Berardini, Doug Howe, Susan Tweedie, Ruth Lovering and community experts to expand the heart development portion of the ontology.<br />
<br />
4. David Hill has worked with Yasmin Alam-Faruque, Midori Harris, Becky Folger, Doug Howe, Emily Dimmer, Rachel Huntley and community experts to expand the kidney development portion of the ontology.<br />
<br />
5. David Hill and Tanya Berardini are maintaining the automated quality checks of the ontology on an ongoing basis.<br />
<br />
6. David Hill and Harold Drabkin are working with Jane Lomax, Midori Harris, Tanya Berardini and Jane Lomax to align the representation of biochemicals in GO. <br />
<br />
7. David Hill and Tanya Berardini added or modified 231 terms as a result of attending the American Society for Cell Biology Meeting in December.<br />
<br />
8. Alexander Diehl is part of the GO Signaling Working Group led by Jen Deegan that has recently implemented improvements in the representation of signaling in the GO.<br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
The Protein Ontology project is providing a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro<br />
) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone. <br />
<br />
Harold and David, along with Emily Dimmer, are mentoring Heather Wick of Tufts University, for annotation of human fetal lung development<br />
<br />
= Other Highlights: =<br />
We are now suppling a GAF 2.0 format file to GOC with column 16 and 17 data filled in. This file is also available directly from our own FTP site. Currently, the data in column 16 refers to the cell type that the experiment supporting the annotation was carried out in, by use of cell ontology terms.</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI,_March_2010&diff=25855MGI, March 20102010-03-23T18:09:24Z<p>Adiehl: /* A. Ontology Development Contributions: */</p>
<hr />
<div>= Mouse Genome Informatics March, 2010 =<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake<br />
<br />
Alexander Diehl<br />
<br />
Harold J Drabkin<br />
<br />
David Hill<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
Mary Dolan <br />
<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of March 22, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''01_Sept_09'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''22_Mar_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">18188</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">35191*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16993</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">93.43</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">11177</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">33228**</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">22051</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">197.29</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">708</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4006</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">3298***</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">465.82</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16145</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15942</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">62</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.39</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10533</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10592</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-3</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-0.03</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1491</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1248</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">13</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.89</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
<nowiki>** We have now tagged all genes in MGI that have no annotation or only IEA annotation with annotation to one or more of the three Gene Ontology root terms as needed. These genes were also then marked as “annotation complete.” This now allows for notification when GO-appropriate literature becomes indexed to these genes as it comes in through our normal triage process.</nowiki><br />
<br />
<nowiki>*** We have added a curator-monitored pipeline whereby annotations based on experimental evidence made to rat genes by RGD curators are added to MGI as annotations to mouse genes based on sequence orthology. This has helped fill in annotation to certain under-represented metabolic processes not normally studied in mouse due to their small size. </nowiki><br />
<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We are currently using ProMiner to improve associating incoming literature to genes in MGI (indexing). This association is used to drive various QC reports used for identifying annotation priorities.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt Keywords and InterPro domains for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) (see <nowiki>**</nowiki> above)<br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. (2010). Ontology Engineering. Nature Biotechnol. Feb;28(2):128-30.<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. (2010) Hematopoietic cell types: Prototype for a revised cell ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Dowell, KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA. (2009). Integrating Text Mining into the MGI Biocuration Workflow Database. Bap019.<br />
<br />
Hill DP, Berardini TZ, Howe DG, Van Auken KM. (2009). Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology. Mol Reprod. Dev. 77(4):314-29.<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. (2010). Cross-Product Extensions of the Gene Ontology. J. Biomed. Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002]<br />
<br />
The Gene Ontology Consortium. (2010). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38:D331-5. <br />
<br />
<br />
<br />
b. ''Presentations including Talks and Tutorials and Teaching''<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
<br />
1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris, Jen Deegan and Jane Lomax to develop cross-products within the three GO namespaces. The regulation cross-products have been released in the extended GO. David and Tanya are now quality checking the internal biological process cross-products.<br />
<br />
2. David Hill has worked with Tanya Berardini to continuing to add interontology links between MF and BP.<br />
<br />
3. David Hill has worked with Varsha Khodiyar, Tanya Berardini, Doug Howe, Susan Tweedie, Ruth Lovering and community experts to expand the heart development portion of the ontology.<br />
<br />
4. David Hill has worked with Yasmin Alam-Faruque, Midori Harris, Becky Folger, Doug Howe, Emily Dimmer, Rachel Huntley and community experts to expand the kidney development portion of the ontology.<br />
<br />
5. David Hill and Tanya Berardini are maintaining the automated quality checks of the ontology on an ongoing basis.<br />
<br />
6. David Hill and Harold Drabkin are working with Jane Lomax, Midori Harris, Tanya Berardini and Jane Lomax to align the representation of biochemicals in GO. <br />
<br />
7. David Hill and Tanya Berardini added or modified 231 terms as a result of attending the American Society for Cell Biology Meeting in December.<br />
<br />
8. Alexander Diehl is part of the GO Signaling Working Group led by Jen Deegan that has recently implemented improvements in the representation of signaling in the GO.<br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
The Protein Ontology project is providing a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro<br />
) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone. <br />
<br />
Harold and David, along with Emily Dimmer, are mentoring Heather Wick of Tufts University, for annotation of human fetal lung development<br />
<br />
= Other Highlights: =<br />
We are now suppling a GAF 2.0 format file to GOC with column 16 and 17 data filled in. This file is also available directly from our own FTP site. Currently, the data in column 16 refers to the cell type that the experiment supporting the annotation was carried out in, by use of cell ontology terms.</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI,_March_2010&diff=25854MGI, March 20102010-03-23T18:06:57Z<p>Adiehl: /* Presentations and Publications */</p>
<hr />
<div>= Mouse Genome Informatics March, 2010 =<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake<br />
<br />
Alexander Diehl<br />
<br />
Harold J Drabkin<br />
<br />
David Hill<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
Mary Dolan <br />
<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of March 22, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''01_Sept_09'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''22_Mar_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">18188</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">35191*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16993</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">93.43</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">11177</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">33228**</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">22051</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">197.29</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">708</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4006</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">3298***</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">465.82</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16145</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15942</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">62</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.39</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10533</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10592</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-3</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-0.03</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1491</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1248</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">13</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.89</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
<nowiki>** We have now tagged all genes in MGI that have no annotation or only IEA annotation with annotation to one or more of the three Gene Ontology root terms as needed. These genes were also then marked as “annotation complete.” This now allows for notification when GO-appropriate literature becomes indexed to these genes as it comes in through our normal triage process.</nowiki><br />
<br />
<nowiki>*** We have added a curator-monitored pipeline whereby annotations based on experimental evidence made to rat genes by RGD curators are added to MGI as annotations to mouse genes based on sequence orthology. This has helped fill in annotation to certain under-represented metabolic processes not normally studied in mouse due to their small size. </nowiki><br />
<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We are currently using ProMiner to improve associating incoming literature to genes in MGI (indexing). This association is used to drive various QC reports used for identifying annotation priorities.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt Keywords and InterPro domains for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) (see <nowiki>**</nowiki> above)<br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. (2010). Ontology Engineering. Nature Biotechnol. Feb;28(2):128-30.<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. (2010) Hematopoietic cell types: Prototype for a revised cell ontology. J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Dowell, KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA. (2009). Integrating Text Mining into the MGI Biocuration Workflow Database. Bap019.<br />
<br />
Hill DP, Berardini TZ, Howe DG, Van Auken KM. (2009). Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology. Mol Reprod. Dev. 77(4):314-29.<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. (2010). Cross-Product Extensions of the Gene Ontology. J. Biomed. Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002]<br />
<br />
The Gene Ontology Consortium. (2010). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38:D331-5. <br />
<br />
<br />
<br />
b. ''Presentations including Talks and Tutorials and Teaching''<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
<br />
1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris, Jen Deegan and Jane Lomax to develop cross-products within the three GO namespaces. The regulation cross-products have been released in the extended GO. David and Tanya are now quality checking the internal biological process cross-products.<br />
<br />
2. David Hill has worked with Tanya Berardini to continuing to add interontology links between MF and BP.<br />
<br />
3. David Hill has worked with Varsha Khodiyar, Tanya Berardini, Doug Howe, Susan Tweedie, Ruth Lovering and community experts to expand the heart development portion of the ontology.<br />
<br />
4. David Hill has worked with Yasmin Alam-Faruque, Midori Harris, Becky Folger, Doug Howe, Emily Dimmer, Rachel Huntley and community experts to expand the kidney development portion of the ontology.<br />
<br />
5. David Hill and Tanya Berardini are maintaining the automated quality checks of the ontology on an ongoing basis.<br />
<br />
6. David Hill and Harold Drabkin are working with Jane Lomax, Midori Harris, Tanya Berardini and Jane Lomax to align the representation of biochemicals in GO. <br />
<br />
7. David Hill and Tanya Berardini added or modified 231 terms as a result of attending the American Society for Cell Biology Meeting in December.<br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
The Protein Ontology project is providing a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro<br />
) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone. <br />
<br />
Harold and David, along with Emily Dimmer, are mentoring Heather Wick of Tufts University, for annotation of human fetal lung development<br />
<br />
= Other Highlights: =<br />
We are now suppling a GAF 2.0 format file to GOC with column 16 and 17 data filled in. This file is also available directly from our own FTP site. Currently, the data in column 16 refers to the cell type that the experiment supporting the annotation was carried out in, by use of cell ontology terms.</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI,_March_2010&diff=25853MGI, March 20102010-03-23T18:06:21Z<p>Adiehl: /* Presentations and Publications */</p>
<hr />
<div>= Mouse Genome Informatics March, 2010 =<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake<br />
<br />
Alexander Diehl<br />
<br />
Harold J Drabkin<br />
<br />
David Hill<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
Mary Dolan <br />
<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of March 22, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''01_Sept_09'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''22_Mar_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">18188</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">35191*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16993</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">93.43</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">11177</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">33228**</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">22051</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">197.29</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">708</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4006</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">3298***</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">465.82</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16145</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15942</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">62</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.39</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10533</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10592</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-3</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-0.03</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1491</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1248</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">13</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.89</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
<nowiki>** We have now tagged all genes in MGI that have no annotation or only IEA annotation with annotation to one or more of the three Gene Ontology root terms as needed. These genes were also then marked as “annotation complete.” This now allows for notification when GO-appropriate literature becomes indexed to these genes as it comes in through our normal triage process.</nowiki><br />
<br />
<nowiki>*** We have added a curator-monitored pipeline whereby annotations based on experimental evidence made to rat genes by RGD curators are added to MGI as annotations to mouse genes based on sequence orthology. This has helped fill in annotation to certain under-represented metabolic processes not normally studied in mouse due to their small size. </nowiki><br />
<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We are currently using ProMiner to improve associating incoming literature to genes in MGI (indexing). This association is used to drive various QC reports used for identifying annotation priorities.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt Keywords and InterPro domains for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) (see <nowiki>**</nowiki> above)<br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. (2010). Ontology Engineering. Nature Biotechnol. Feb;28(2):128-30.<br />
<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. Hematopoietic cell types: Prototype for a revised cell ontology. (2010) J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Dowell, KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA. (2009). Integrating Text Mining into the MGI Biocuration Workflow Database. Bap019.<br />
<br />
Hill DP, Berardini TZ, Howe DG, Van Auken KM. (2009). Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology. Mol Reprod. Dev. 77(4):314-29.<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. (2010). Cross-Product Extensions of the Gene Ontology. J. Biomed. Inform. [http://dx.doi.org/10.1016/j.jbi.2010.02.002 doi:10.1016/j.jbi.2010.02.002]<br />
<br />
The Gene Ontology Consortium. (2010). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38:D331-5. <br />
<br />
<br />
<br />
b. ''Presentations including Talks and Tutorials and Teaching''<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
<br />
1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris, Jen Deegan and Jane Lomax to develop cross-products within the three GO namespaces. The regulation cross-products have been released in the extended GO. David and Tanya are now quality checking the internal biological process cross-products.<br />
<br />
2. David Hill has worked with Tanya Berardini to continuing to add interontology links between MF and BP.<br />
<br />
3. David Hill has worked with Varsha Khodiyar, Tanya Berardini, Doug Howe, Susan Tweedie, Ruth Lovering and community experts to expand the heart development portion of the ontology.<br />
<br />
4. David Hill has worked with Yasmin Alam-Faruque, Midori Harris, Becky Folger, Doug Howe, Emily Dimmer, Rachel Huntley and community experts to expand the kidney development portion of the ontology.<br />
<br />
5. David Hill and Tanya Berardini are maintaining the automated quality checks of the ontology on an ongoing basis.<br />
<br />
6. David Hill and Harold Drabkin are working with Jane Lomax, Midori Harris, Tanya Berardini and Jane Lomax to align the representation of biochemicals in GO. <br />
<br />
7. David Hill and Tanya Berardini added or modified 231 terms as a result of attending the American Society for Cell Biology Meeting in December.<br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
The Protein Ontology project is providing a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro<br />
) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone. <br />
<br />
Harold and David, along with Emily Dimmer, are mentoring Heather Wick of Tufts University, for annotation of human fetal lung development<br />
<br />
= Other Highlights: =<br />
We are now suppling a GAF 2.0 format file to GOC with column 16 and 17 data filled in. This file is also available directly from our own FTP site. Currently, the data in column 16 refers to the cell type that the experiment supporting the annotation was carried out in, by use of cell ontology terms.</div>Adiehlhttps://wiki.geneontology.org/index.php?title=MGI,_March_2010&diff=25852MGI, March 20102010-03-23T18:03:45Z<p>Adiehl: /* Presentations and Publications */</p>
<hr />
<div>= Mouse Genome Informatics March, 2010 =<br />
= Overview =<br />
<br />
= Staff: =<br />
Judith Blake<br />
<br />
Alexander Diehl<br />
<br />
Harold J Drabkin<br />
<br />
David Hill<br />
<br />
Li Ni<br />
<br />
Dmitry Sitnikov<br />
<br />
Mary Dolan <br />
<br />
<br />
= Annotation Progress =<br />
We continue to put emphasis on those genes selected for the Reference Genome Project. Additional emphasis has been placed on certain genes associated with lung development.<br />
<br />
<br />
<center>'''MGI GO STATS as of March 22, 2010'''</center><br />
<br />
<br />
<br />
{| style="border-spacing:0;"<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Annotation Type'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''01_Sept_09'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''22_Mar_10'''<br />
| style="border-top:0.0007in solid #000000;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Change'''<br />
| style="border:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Genes annotated (with at least one GO term of any kind):<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">18188</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">35191*</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16993</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">93.43</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total Manual Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Number of Genes<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">11177</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">33228**</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">22051</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">197.29</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Orthology:<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">708</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">4006</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">3298***</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">465.82</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| colspan="5" style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| IEA Annotation<br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| SwissProt to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">16145</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">15942</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">62</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.39</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Interpro to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10533</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">10592</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-3</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">-0.03</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| EC to GO<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1491</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">1248</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">13</div><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <div align="right">0.89</div><br />
<br />
|-<br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <nowiki>* 100% of current gene models</nowiki><br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
| style="border-top:none;border-bottom:0.0007in solid #000000;border-left:0.0007in solid #000000;border-right:0.0007in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| <br />
<br />
|}<br />
<br />
<nowiki>** We have now tagged all genes in MGI that have no annotation or only IEA annotation with annotation to one or more of the three Gene Ontology root terms as needed. These genes were also then marked as “annotation complete.” This now allows for notification when GO-appropriate literature becomes indexed to these genes as it comes in through our normal triage process.</nowiki><br />
<br />
<nowiki>*** We have added a curator-monitored pipeline whereby annotations based on experimental evidence made to rat genes by RGD curators are added to MGI as annotations to mouse genes based on sequence orthology. This has helped fill in annotation to certain under-represented metabolic processes not normally studied in mouse due to their small size. </nowiki><br />
<br />
<br />
==Methods and strategies for annotation==<br />
<br />
<br />
''Literature curation:''<br />
<br />
Literature curation continues to be the major focus of our annotation efforts. We are currently using ProMiner to improve associating incoming literature to genes in MGI (indexing). This association is used to drive various QC reports used for identifying annotation priorities.<br />
<br />
<br />
''Computational annotation strategies:'' <br />
<br />
As always current strategies involve use of translation table to mine SwissProt Keywords and InterPro domains for IEA annotation. These are performed automatically on a nightly basis and require little human intervention.<br />
<br />
<br />
''Priorities for annotation''<br />
<br />
# Genes assigned by Reference Genome Project (everyone)<br />
# Isoform curation (Harold, Protein Ontology project); now co-ordinating with 1 by focusing on reference genes that have isoforms.<br />
# Genes with no GO annotation but with literature (Li and Dmitry) (see <nowiki>**</nowiki> above)<br />
# Genes identified as being important in lung development (Dmitry)<br />
# Genes marked as having GO annotation completed, but now having new literature (Dmitry)<br />
<br />
= Presentations and Publications =<br />
Diehl AD, Augustine AD, Blake JA, Cowell LG, Gold ES, Gondré-Lewis TA, Masci AM, Meehan TF, Morel PA, Nijnik A, Peters B, Pulendran B, Scheuermann RH, Yao QA, Zand MS, Mungall CJ. Hematopoietic cell types: Prototype for a revised cell ontology. (2010) J Biomed Inform. [http://dx.doi.org/10.1016/j.jbi.2010.01.006 doi:10.1016/j.jbi.2010.01.006].<br />
<br />
Mungall CJ, Bada M, Berardini TZ, Deegan J, Ireland A, Harris MA, Hill DP, Lomax J. (2010). Cross-Product Extensions of the Gene Ontology. J. Biomed. Inform. Feb. 9 [Epub ahead of print]<br />
<br />
Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. (2010). Ontology Engineering. Nature Biotechnol. Feb;28(2):128-30.<br />
<br />
The Gene Ontology Consortium. (2010). The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 38:D331-5. <br />
<br />
Hill DP, Berardini TZ, Howe DG, Van Auken KM. (2009). Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology. Mol Reprod. Dev. 77(4):314-29.<br />
<br />
Dowell, KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA. (2009). Integrating Text Mining into the MGI Biocuration Workflow Database. Bap019.<br />
<br />
<br />
<br />
b. ''Presentations including Talks and Tutorials and Teaching''<br />
<br />
= A. Ontology Development Contributions:=<br />
<br />
<br />
1. David Hill has worked on a team with Tanya Berardini, Chris Mungall, Midori Harris, Jen Deegan and Jane Lomax to develop cross-products within the three GO namespaces. The regulation cross-products have been released in the extended GO. David and Tanya are now quality checking the internal biological process cross-products.<br />
<br />
2. David Hill has worked with Tanya Berardini to continuing to add interontology links between MF and BP.<br />
<br />
3. David Hill has worked with Varsha Khodiyar, Tanya Berardini, Doug Howe, Susan Tweedie, Ruth Lovering and community experts to expand the heart development portion of the ontology.<br />
<br />
4. David Hill has worked with Yasmin Alam-Faruque, Midori Harris, Becky Folger, Doug Howe, Emily Dimmer, Rachel Huntley and community experts to expand the kidney development portion of the ontology.<br />
<br />
5. David Hill and Tanya Berardini are maintaining the automated quality checks of the ontology on an ongoing basis.<br />
<br />
6. David Hill and Harold Drabkin are working with Jane Lomax, Midori Harris, Tanya Berardini and Jane Lomax to align the representation of biochemicals in GO. <br />
<br />
7. David Hill and Tanya Berardini added or modified 231 terms as a result of attending the American Society for Cell Biology Meeting in December.<br />
<br />
= Annotation Outreach and User Advocacy Efforts: =<br />
The Protein Ontology project is providing a web interface (http/pir.georgetown.edu/cgi-bin/pro/race_pro<br />
) whereby functional annotation using the GO can be applied to PRO submissions. These are reviewed by Cecilia Arighi of Georgetown. At present, only the PRO curators (Georgetown and MGI) are using the tool, but it is available to anyone. <br />
<br />
Harold and David, along with Emily Dimmer, are mentoring Heather Wick of Tufts University, for annotation of human fetal lung development<br />
<br />
= Other Highlights: =<br />
We are now suppling a GAF 2.0 format file to GOC with column 16 and 17 data filled in. This file is also available directly from our own FTP site. Currently, the data in column 16 refers to the cell type that the experiment supporting the annotation was carried out in, by use of cell ontology terms.</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2010_Stanford_Meeting_Logistics&diff=256262010 Stanford Meeting Logistics2010-03-16T19:00:24Z<p>Adiehl: /* Remote Attendees */</p>
<hr />
<div>=Dates=<br />
GO consortium & SAB meetings March 30-31, April 1, 2010<br />
<br />
# We wish all attendees to attend from the morning of March 30 through the morning of April 1st. The afternoon of April 1st will be for all GO subcontract PIs, GOC PIs and our SAB. We suggest you arrive the evening of March 29th and leave after noon on the 1st, unless you are a PI or SAB member.<br />
<br />
=Venue=<br />
Meetings will be at the [http://www.stanford.edu Stanford University], Stanford, CA, USA.<br />
<br />
The GOC and SAB meeting will take place at the [http://www.stanfordalumni.org/aboutsaa/alumni_center/conference/home.html Arrillaga Alumni Center].<br />
<br />
Lunches will be at the Arrillaga Center.<br />
<br />
There will be a group dinner on March 31st for the GOC and SAB.<br />
<br />
We will also facilitate dinners on March 29th and 30th. There are a large variety of restaurants in the area.<br />
<br />
=Maps=<br />
[http://maps.stanford.edu/ Stanford University maps]<br />
<br />
=Registration=<br />
Registration will open in early 2010. <br />
<br />
#Registration Fee. We anticipate a minimal registration fee to cover lunch and a light breakfast. The meeting will be sponsored by the Cherry Lab.<br />
<br />
=Lodging Information=<br />
Four hotels are within a 15-20 minute walk to the Alumni Center. Ordered below by price per night, lowest to highest.<br />
<br />
#[http://www.hotelcalifornia.com/ Hotel California] $<br />
#[http://www.cardinalhotel.com/ Cardinal Hotel] $<br />
#[http://www.stanfordterraceinn.com/ Stanford Terrace Inn] $$<br />
#[http://specialoffers.starwoodhotels.com/SheratonPaloAlto/so.htm?PS=PS_aa_Western_Google_sheraton_palo_alto_california_011209_NAD_FM Sheraton Palo Alto Hotel] $$$$<br />
#[http://specialoffers.starwoodhotels.com/WestinPaloAlto/so.htm?PS=PS_aa_Western_Google_westin_palo_alto_ca_011209_NAD_FM Westin Palo Alto] $$$$<br />
<br />
=Agenda=<br />
<br />
==Workshop/Tutorial-Curators meet developers (content and software)==<br />
A workshop/tutorial on how to use all the utilities and content that GO has to offer. <br />
*AmiGO has lot of cool features now and many curators may or may not know how to incorporate these features in everyday curation. <br />
*how to interpret relationships in the ontology, how the annotations can mean something else if the relationships are overlooked etc.<br />
<br />
== Taxon IDs ==<br />
I'd like a discussion of taxon IDs and subspecies. --[[User:JimHu|JimHu]] 17:28, 4 February 2010 (UTC)<br />
<br />
==Making ext GO 'main'==<br />
A suggestion from the OBO Foundry meeting: we make GO ext the main GO file, the one that new users see. The other files continue to exist in the same place, but make it clear they are legacy files. That way anyone new coming to GO will build tools using GO ext. [Jane]<br />
<br />
==Guidelines for 'binding' terms==<br />
<br />
Discuss guideline documentation, progess and unresolved issues [Ruth].<br />
<br />
[http://wiki.geneontology.org/index.php/Binding_terms_working_group#2010_discussion proposed guidelines]<br />
<br />
'''Unresolved issues:'''<br />
* Should we include transporters in these guidelines? <br />
* Should we capture drug information?<br />
* Should the guidelines include a statement suggesting that the specific substrate for an enzyme with 'GO:0032451 demethylase activity' can be included in column 16?<br />
* Should we create terms like ‘ATP binding involved in kinase activity'?<br />
* What, if any, binding term annotations can be transferred via ISS/ISO?<br />
<br />
=Attendees=<br />
Airport codes: SFO = San Francisco International; SJC = San Jose International Airport<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport (see codes above)<br />
! Departure Date/Time from Airport<br />
|-<br />
| Mike Cherry<br />
| GO / SGD<br />
| walking<br />
| <br />
|-<br />
| Judy Blake<br />
| GO / MGI<br />
| March 29 SFO<br />
| April 2 SFO<br />
|-<br />
| Suzi Lewis<br />
| GO / BBOP<br />
| Driving<br />
|<br />
|-<br />
| Chris Mungall<br />
| GO / BBOP<br />
| CalTrain<br />
|<br />
|-<br />
| Seth Carbon<br />
| GO / BBOP<br />
| Driving<br />
|<br />
|-<br />
| Amina Abdulla<br />
| GO / BBOP<br />
| Driving<br />
|<br />
|-<br />
| Amelia Ireland<br />
| GO / BBOP<br />
| Hitching a ride<br />
|<br />
|-<br />
| Kara Dolinski<br />
| GO / PPOD<br />
| TBA<br />
| TBA<br />
|-<br />
| Eva Huala<br />
| TAIR<br />
| March 29<br />
| April 2<br />
|-<br />
| Karen Eilbeck<br />
| SO (U of Utah)<br />
| San Jose 29th March<br />
| San Jose April 1 - evening<br />
|-<br />
| Barry Smith<br />
| SAB (U at Buffalo)<br />
| March 31 SFO<br />
| April 1 SFO<br />
|-<br />
| Tanya Berardini<br />
| TAIR<br />
| on site<br />
| on site<br />
|-<br />
| Donghui li<br />
| TAIR<br />
| on site<br />
| on site<br />
|-<br />
| Larry Hunter<br />
| SAB (U Colorado)<br />
| March 31 SFO<br />
| April 2 SFO<br />
|- <br />
|Paul Sternberg<br />
|WormBase and Caltech<br />
|San Jose<br />
|San Jose<br />
|-<br />
|Doug Howe<br />
|ZFIN<br />
|SFO March 29<br />
| <br />
|-<br />
|Dianna Fisk<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Ben Hitz<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Susan Tweedie<br />
|FlyBase<br />
|March 27 SFO<br />
|April 1 16:55 SFO<br />
|-<br />
|Jane Lomax<br />
|GO-EBI<br />
|March 29 SFO<br />
|April 2 SFO<br />
|-<br />
|Pascale Gaudet<br />
|dictyBase<br />
| <br />
| <br />
|-<br />
|Harold Drabkin<br />
|MGI<br />
|March 29th SFO<br />
|April TBA<br />
|-<br />
|Jim Hu<br />
|EcoliWiki<br />
|<br />
|<br />
|-<br />
|David Hill<br />
|GO/MGI<br />
|<br />
|<br />
|-<br />
|Stan Laulederkind<br />
|RGD<br />
|<br />
|<br />
|-<br />
|Monte Westerfield<br />
|ZFIN<br />
|April 1 SFO<br />
|<br />
|-<br />
|Selina Dwight<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Kate Dreher<br />
|TAIR<br />
|on site<br />
|on site<br />
|-<br />
|Rama Balakrishnan<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Stacia Engel<br />
|SGD<br />
|N/A<br />
|N/A<br />
|-<br />
|Ranjana Kishore<br />
|WormBase<br />
|SJC 3/29 5.50 PM<br />
|SJC 4/01 3.00 PM<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase<br />
|TBD<br />
|TBD<br />
|-<br />
|Petra Fey<br />
|dictyBase<br />
|TBD<br />
|TBD<br />
|-<br />
|Peter D'Eustachio<br />
|Reactome / NYUMC<br />
|SJC 3/29 7:02 PM<br />
|SJC 4/1 10:25 PM<br />
|-<br />
|Serenella Ferro Rojas<br />
|UniProtKB/Swiss-Prot<br />
|March 29 SFO<br />
|April 4 SFO<br />
|-<br />
|Eurie Hong<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Emily Dimmer<br />
|GOA<br />
|March 29 SFO<br />
|April 2 SFO<br />
|-<br />
|-<br />
|Tony Sawford<br />
|GOA<br />
|March 29 SFO<br />
|April 2 SFO<br />
|-<br />
|Karen Christie<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Julie Park<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|}<br />
<br />
=Remote Attendees=<br />
Webex and Telephone Conferencing will be provided<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! email (needed to set up your remote access)<br />
! Attending GOC (March 30-31)<br />
! Attending SAB (April 1)<br />
! Calling in alone or in a group (with whom and from where, if known)<br />
|-<br />
|Midori Harris<br />
|EBI GO<br />
|midori at ebi dot ac dot uk<br />
|yes<br />
|yes<br />
|TBD<br />
|-<br />
| Jennifer Deegan<br />
| GO Editorial Office<br />
| jdeegan at ebi.ac.uk<br />
| Yes<br />
| Yes<br />
| Probably alone from home.<br />
|-<br />
| Ruth Lovering<br />
| BHF-UCL annotator<br />
| r.lovering at ucl.ac.uk<br />
| Yes<br />
| Yes<br />
| From home<br />
|-<br />
| Rachael Huntley<br />
| GOA Curator<br />
| huntley at ebi.ac.uk<br />
| Yes<br />
| Yes<br />
| From home.<br />
|-<br />
| Michelle Giglio<br />
| IGS, UMD<br />
| mgiglio at som.umaryland.edu<br />
| Yes<br />
| No<br />
| alone from work/home<br />
|-<br />
| Marcus Chibucos<br />
| IGS, UMD<br />
| mchibucos at som dot umaryland dot edu<br />
| Yes<br />
| No<br />
| alone from work/home<br />
|-<br />
| Alexander Diehl<br />
| MGI<br />
| adiehl@informatics.jax.org<br />
| Yes<br />
| Yes<br />
| alone from work/home<br />
|}<br />
<br />
<br />
----<br />
Return to [[Consortium_Meetings]] page</div>Adiehlhttps://wiki.geneontology.org/index.php?title=2010_Stanford_Meeting_Logistics&diff=256252010 Stanford Meeting Logistics2010-03-16T19:00:01Z<p>Adiehl: /* Remote Attendees */</p>
<hr />
<div>=Dates=<br />
GO consortium & SAB meetings March 30-31, April 1, 2010<br />
<br />
# We wish all attendees to attend from the morning of March 30 through the morning of April 1st. The afternoon of April 1st will be for all GO subcontract PIs, GOC PIs and our SAB. We suggest you arrive the evening of March 29th and leave after noon on the 1st, unless you are a PI or SAB member.<br />
<br />
=Venue=<br />
Meetings will be at the [http://www.stanford.edu Stanford University], Stanford, CA, USA.<br />
<br />
The GOC and SAB meeting will take place at the [http://www.stanfordalumni.org/aboutsaa/alumni_center/conference/home.html Arrillaga Alumni Center].<br />
<br />
Lunches will be at the Arrillaga Center.<br />
<br />
There will be a group dinner on March 31st for the GOC and SAB.<br />
<br />
We will also facilitate dinners on March 29th and 30th. There are a large variety of restaurants in the area.<br />
<br />
=Maps=<br />
[http://maps.stanford.edu/ Stanford University maps]<br />
<br />
=Registration=<br />
Registration will open in early 2010. <br />
<br />
#Registration Fee. We anticipate a minimal registration fee to cover lunch and a light breakfast. The meeting will be sponsored by the Cherry Lab.<br />
<br />
=Lodging Information=<br />
Four hotels are within a 15-20 minute walk to the Alumni Center. Ordered below by price per night, lowest to highest.<br />
<br />
#[http://www.hotelcalifornia.com/ Hotel California] $<br />
#[http://www.cardinalhotel.com/ Cardinal Hotel] $<br />
#[http://www.stanfordterraceinn.com/ Stanford Terrace Inn] $$<br />
#[http://specialoffers.starwoodhotels.com/SheratonPaloAlto/so.htm?PS=PS_aa_Western_Google_sheraton_palo_alto_california_011209_NAD_FM Sheraton Palo Alto Hotel] $$$$<br />
#[http://specialoffers.starwoodhotels.com/WestinPaloAlto/so.htm?PS=PS_aa_Western_Google_westin_palo_alto_ca_011209_NAD_FM Westin Palo Alto] $$$$<br />
<br />
=Agenda=<br />
<br />
==Workshop/Tutorial-Curators meet developers (content and software)==<br />
A workshop/tutorial on how to use all the utilities and content that GO has to offer. <br />
*AmiGO has lot of cool features now and many curators may or may not know how to incorporate these features in everyday curation. <br />
*how to interpret relationships in the ontology, how the annotations can mean something else if the relationships are overlooked etc.<br />
<br />
== Taxon IDs ==<br />
I'd like a discussion of taxon IDs and subspecies. --[[User:JimHu|JimHu]] 17:28, 4 February 2010 (UTC)<br />
<br />
==Making ext GO 'main'==<br />
A suggestion from the OBO Foundry meeting: we make GO ext the main GO file, the one that new users see. The other files continue to exist in the same place, but make it clear they are legacy files. That way anyone new coming to GO will build tools using GO ext. [Jane]<br />
<br />
==Guidelines for 'binding' terms==<br />
<br />
Discuss guideline documentation, progess and unresolved issues [Ruth].<br />
<br />
[http://wiki.geneontology.org/index.php/Binding_terms_working_group#2010_discussion proposed guidelines]<br />
<br />
'''Unresolved issues:'''<br />
* Should we include transporters in these guidelines? <br />
* Should we capture drug information?<br />
* Should the guidelines include a statement suggesting that the specific substrate for an enzyme with 'GO:0032451 demethylase activity' can be included in column 16?<br />
* Should we create terms like ‘ATP binding involved in kinase activity'?<br />
* What, if any, binding term annotations can be transferred via ISS/ISO?<br />
<br />
=Attendees=<br />
Airport codes: SFO = San Francisco International; SJC = San Jose International Airport<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport (see codes above)<br />
! Departure Date/Time from Airport<br />
|-<br />
| Mike Cherry<br />
| GO / SGD<br />
| walking<br />
| <br />
|-<br />
| Judy Blake<br />
| GO / MGI<br />
| March 29 SFO<br />
| April 2 SFO<br />
|-<br />
| Suzi Lewis<br />
| GO / BBOP<br />
| Driving<br />
|<br />
|-<br />
| Chris Mungall<br />
| GO / BBOP<br />
| CalTrain<br />
|<br />
|-<br />
| Seth Carbon<br />
| GO / BBOP<br />
| Driving<br />
|<br />
|-<br />
| Amina Abdulla<br />
| GO / BBOP<br />
| Driving<br />
|<br />
|-<br />
| Amelia Ireland<br />
| GO / BBOP<br />
| Hitching a ride<br />
|<br />
|-<br />
| Kara Dolinski<br />
| GO / PPOD<br />
| TBA<br />
| TBA<br />
|-<br />
| Eva Huala<br />
| TAIR<br />
| March 29<br />
| April 2<br />
|-<br />
| Karen Eilbeck<br />
| SO (U of Utah)<br />
| San Jose 29th March<br />
| San Jose April 1 - evening<br />
|-<br />
| Barry Smith<br />
| SAB (U at Buffalo)<br />
| March 31 SFO<br />
| April 1 SFO<br />
|-<br />
| Tanya Berardini<br />
| TAIR<br />
| on site<br />
| on site<br />
|-<br />
| Donghui li<br />
| TAIR<br />
| on site<br />
| on site<br />
|-<br />
| Larry Hunter<br />
| SAB (U Colorado)<br />
| March 31 SFO<br />
| April 2 SFO<br />
|- <br />
|Paul Sternberg<br />
|WormBase and Caltech<br />
|San Jose<br />
|San Jose<br />
|-<br />
|Doug Howe<br />
|ZFIN<br />
|SFO March 29<br />
| <br />
|-<br />
|Dianna Fisk<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Ben Hitz<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Susan Tweedie<br />
|FlyBase<br />
|March 27 SFO<br />
|April 1 16:55 SFO<br />
|-<br />
|Jane Lomax<br />
|GO-EBI<br />
|March 29 SFO<br />
|April 2 SFO<br />
|-<br />
|Pascale Gaudet<br />
|dictyBase<br />
| <br />
| <br />
|-<br />
|Harold Drabkin<br />
|MGI<br />
|March 29th SFO<br />
|April TBA<br />
|-<br />
|Jim Hu<br />
|EcoliWiki<br />
|<br />
|<br />
|-<br />
|David Hill<br />
|GO/MGI<br />
|<br />
|<br />
|-<br />
|Stan Laulederkind<br />
|RGD<br />
|<br />
|<br />
|-<br />
|Monte Westerfield<br />
|ZFIN<br />
|April 1 SFO<br />
|<br />
|-<br />
|Selina Dwight<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Kate Dreher<br />
|TAIR<br />
|on site<br />
|on site<br />
|-<br />
|Rama Balakrishnan<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Stacia Engel<br />
|SGD<br />
|N/A<br />
|N/A<br />
|-<br />
|Ranjana Kishore<br />
|WormBase<br />
|SJC 3/29 5.50 PM<br />
|SJC 4/01 3.00 PM<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase<br />
|TBD<br />
|TBD<br />
|-<br />
|Petra Fey<br />
|dictyBase<br />
|TBD<br />
|TBD<br />
|-<br />
|Peter D'Eustachio<br />
|Reactome / NYUMC<br />
|SJC 3/29 7:02 PM<br />
|SJC 4/1 10:25 PM<br />
|-<br />
|Serenella Ferro Rojas<br />
|UniProtKB/Swiss-Prot<br />
|March 29 SFO<br />
|April 4 SFO<br />
|-<br />
|Eurie Hong<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Emily Dimmer<br />
|GOA<br />
|March 29 SFO<br />
|April 2 SFO<br />
|-<br />
|-<br />
|Tony Sawford<br />
|GOA<br />
|March 29 SFO<br />
|April 2 SFO<br />
|-<br />
|Karen Christie<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|Julie Park<br />
|SGD<br />
|on site<br />
|on site<br />
|-<br />
|}<br />
<br />
=Remote Attendees=<br />
Webex and Telephone Conferencing will be provided<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! email (needed to set up your remote access)<br />
! Attending GOC (March 30-31)<br />
! Attending SAB (April 1)<br />
! Calling in alone or in a group (with whom and from where, if known)<br />
|-<br />
|Midori Harris<br />
|EBI GO<br />
|midori at ebi dot ac dot uk<br />
|yes<br />
|yes<br />
|TBD<br />
|-<br />
| Jennifer Deegan<br />
| GO Editorial Office<br />
| jdeegan at ebi.ac.uk<br />
| Yes<br />
| Yes<br />
| Probably alone from home.<br />
|-<br />
| Ruth Lovering<br />
| BHF-UCL annotator<br />
| r.lovering at ucl.ac.uk<br />
| Yes<br />
| Yes<br />
| From home<br />
|-<br />
| Rachael Huntley<br />
| GOA Curator<br />
| huntley at ebi.ac.uk<br />
| Yes<br />
| Yes<br />
| From home.<br />
|-<br />
| Michelle Giglio<br />
| IGS, UMD<br />
| mgiglio at som.umaryland.edu<br />
| Yes<br />
| No<br />
| alone from work/home<br />
|-<br />
| Marcus Chibucos<br />
| IGS, UMD<br />
| mchibucos at som dot umaryland dot edu<br />
| Yes<br />
| No<br />
| alone from work/home<br />
|-<br />
| Alexander Diehl<br />
| MGI<br />
| adiehl@informatics.jax.org<br />
| Yes<br />
| Yes<br />
| alone from work/home|}<br />
<br />
<br />
----<br />
Return to [[Consortium_Meetings]] page</div>Adiehlhttps://wiki.geneontology.org/index.php?title=Ontology_Development&diff=24079Ontology Development2010-01-08T19:17:17Z<p>Adiehl: /* Other Ontology Development Group Activities */</p>
<hr />
<div>This group's purpose is to ensure that the Gene Ontology represents biology in a way that is useful for gene product annotation of reference genomes and other MODs using the GO for annotation. The group serves as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO. Members of the group are responsible for reporting areas of the GO that need development and for suggesting changes and additions to the GO as needs arise. Members of the group serve as biological experts in domains that are covered by their organism. They are responsible for reviewing changes to be sure that they accurately reflect our current understanding of biology.<br />
<br />
==Administrative==<br />
*[[Ontology Development group summary]]<br />
*[[Meeting_minutes:_general_topics|Miscellaneous meeting minutes]]<br />
<br />
==Content Development ==<br />
===Priority ranking===<br />
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)<br />
*High Priority<br />
**Cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]<br />
***[[Cell cross-products]] (David, Jane, Tanya, Alex, Chris, others?)<br />
***[[XP:biological_process_xp_chebi |Chebi cross-products]] (David, Jane, Tanya, Chris, others?)<br />
**[[Cellular component processes]] (Jane, David, Midori, Val, ad hoc others)<br />
**[[Taxon and sensu|Taxon data]] (Note: sensu revamp complete) (Jen)<br />
**[[Function-Process Links]]<br />
***part_of links between function and process (David, Tanya)<br />
***has_part links between function and process (Harold, Jen)<br />
**[[Transporters]](Jen and community experts)<br />
**[[Metabolism |Filling in metabolism terms]] (Jane, David, Chris, Midori)<br />
**Generic [[GO slim overhaul]] (Jane, Val, others?)<br />
*Medium Priority<br />
**[[:Category:Content PAMGO|PAMGO collaboration]] (Jane)<br />
**[[Virus terms|Virus-related term overhaul]] (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl & others)<br />
**IMG mapping (Jane)<br />
**[[Signaling |Signaling overhaul]] (Jen, Alex Diehl)<br />
**[[Transcription |Transcription & transcription factor activity overhaul]] (Karen)<br />
**[[Kidney Development]] (David, Midori, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)<br />
*Low priority<br />
**[[Response to drug]] (Jen)<br />
**Ion homeostasis ([https://sourceforge.net/tracker/func=detail&atid=440764&aid=1751898&group_id=36855| SF 1751898])<br />
**Cytokine receptor binding ([https://sourceforge.net/tracker/ufnc=detail&atid=440764&aid=1751924&group_id=36855| SF 1751924])<br />
**Peripheral nervous system development<br />
**Formation/assembly/biogenesis/etc. rationalization ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1733770&group_id=36855| SF 1733770])<br />
**[[Polyketide synthases]]<br />
<br />
===Timeline===<br />
====Current content work====<br />
*[[Virus terms|Virus-related term overhaul]] (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh & others)<br />
*[[Signaling |Signaling overhaul]]<br />
*[[Cellular component processes]] (Jane, David, Midori, Val, ad hoc others) - started summer 2008<br />
*[[Transcription |Transcription & transcription factor activity overhaul]] - started June 2008<br />
*[[Taxon and sensu|Taxon data]] <br />
*[[Transporters]] - Started Feb. 2007<br />
*[[Electron transport]]<br />
*IMG mapping<br />
*[[Function-Process Links]] - pilot projects begun Feb. 2008; first links added May 2009<br />
**kinases, phosphatases, transporters, and other 1:1- May/June 2009<br />
*[[Cell cross-products]] - TBD<br />
*[[Plant terms]]<br />
* Filling in [[metabolism]] terms - face-to-face meeting July 9, 2008<br />
* [[Notes on Sourceforge items in progress]]<br />
<br />
====Future content work====<br />
*Generic [[GO slim overhaul]] - summer 2009<br />
*Ion homeostasis ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1751898&group_id=36855| SF 1751898])<br />
*Cytokine receptor binding ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1751924&group_id=36855| SF 1751924])<br />
*[[Response to drug]]<br />
*Peripheral nervous system development<br />
*Formation/assembly/biogenesis/etc. rationalization ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1733770&group_id=36855| SF 1733770])<br />
*[[Polyketide synthases]]<br />
<br />
===[[Selected SourceForge links]]===<br />
<br />
===Completed content work===<br />
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 2 (as of Jan. 2007)<br />
*[[Immunology Revisions]]<br />
*[[Central Nervous System Development]]<br />
*[[Isa-complete_BP|is_a complete biological process]]<br />
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 1<br />
*Correct disjointness violations<br />
*[[RNA processing]]<br />
*[[Collaboration with MIT GO-Engineering]] - Manuscript written<br />
*[[Muscle Development]] - Started Feb. 2007; meeting July 2007; Done Oct 2007<br />
*[[Cardiovascular physiology/development]] - implemented Oct 2007<br />
*Make cc part_of tree complete (i.e. find homes for the children of 'unlocalized protein complex')<br />
*[[Sensu Main Page|Sensu revamp]]<br />
*[[Regulation Main Page]] live March 2008<br />
*Gene expression ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1418820&group_id=36855| SF 1418820])<br />
*[[Electron transport]]<br />
*[[Proteases |Peptidase & protease activity overhaul]] begun June 2008; essentially completed August 2008<br />
*[[SDB 2009]]<br />
*[[Function-Process Links]]<br />
**[[FP-regulates| regulates links between function and process]] (David, Tanya)<br />
*[[Morphogenesis]] (David, Tanya)<br />
*regulates links- Dec 2008 (David, Tanya)<br />
*[[Regulators |Regulator, activator and inhibitor MF terms]] (David, Tanya)<br />
*[[Chaperones]](completed by working group at Cambridge GOC meeting Sept. 2009)<br />
**[http://wiki.geneontology.org/index.php/Lung_Development Lung Development] (David, Jen, community experts)<br />
**[[Binding_terms_working_group|Binding]] discussion - mainly annotation issues, but with some ontology content points<br />
<br />
==Other Ontology Development Group Activities==<br />
*[[GO Timeline|Ontology development timeline]] and [[Ontology_publishing_pipeline_2009|release pipeline]]<br />
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)<br />
*[[Tracker wishlist]]<br />
*[[Webinar Software Investigation]]<br />
*[[Content Meeting Documentation]]<br />
**[http://wiki.geneontology.org/index.php/Content_Meeting_Participants_Information| Content meeting participants' information]<br />
*[[Editor Guide]]<br />
*[[Ontology Documentation Drafts]] - for working on documentation of ontology content that will become part of the web-based documentation<br />
<br />
==Agenda Items==<br />
*[[Agenda items for next content conference call]]<br />
<br />
==Reports==<br />
Beginning with the November 2006 document, reports include two sections: the first focuses on ontology development work, and the second gives an overview of the rest of the GO Editorial Office staff activities (to avoid redundancy, the latter may cross-reference other management group reports). Reports issued earlier are not so divided, and have a GO Editorial Office-centric perspective, but do cover a substantial portion of the GOC's ontology development work.<br />
<br />
*November 2006-present [[Ontology_Development_reports|Combined Ontology Development and GO Editorial Office reports]]<br />
*July 2005-October 2006 [[GO Editorial Office reports]]<br />
<br />
==GO Clinics==<br />
<br />
*[[GO clinic late 2009|Items for the next GO clinic]]<br />
<br />
[[Category:Ontology]]</div>Adiehlhttps://wiki.geneontology.org/index.php?title=User_Advocacy&diff=24078User Advocacy2010-01-08T19:13:41Z<p>Adiehl: /* Sections: */</p>
<hr />
<div>The purpose of the User Advocacy group is to establish lines of communication between the scientific community and the GO Consortium. The goal is to ensure that the GOC does not become insular and remains receptive to the needs of the scientific community. In addition, open lines of communication will increase the awareness and usefulness of GO in the scientific community.<br />
<br />
This purpose includes:<br />
#ensuring that changes in the GO are publicized and communicated to the community<br />
#acting as a broker between the community and the GOC so that the GOC does not become insular<br />
#providing user support for the products produced by GO<br />
#providing documentation for the products produced by GO.<br />
<br />
This group will ensure that GO remains useful, relevant, and accessible to the scientific community. This [[Media:Advocacy_diagram_v4.jpg|figure]] outlines this group's aims and organisation.<br />
<br />
==Sections:==<br />
<br />
*[[gohelp|GO helpdesk]]<br />
*[[news feed|News pages]]<br />
*[[Annotation_Outreach_group_reports|Monthly Reports]]<br />
<br />
'''Overview:'''<br />
*[[User Advocacy group summary]]<br />
*[[Media:Advocacy_diagram_v4.jpg|User Advocacy group figure]] ([[Media:TasksSimple.jpg|GOC-2007]])<br />
*[[User Advocacy group aims 2006]]<br />
<br />
'''Working Groups:'''<br />
*[[:Category:Web_presence_working_group|Web presence working group]]<br />
*[[AmiGO_Hub|AmiGO Hub]]<br />
*[[News group]]<br />
<br />
'''Other:'''<br />
*[[newsletter]] - discontinued as of Oct 2008. See [[news feed]].<br />
*[[GO survey 2009/10]]<br />
*[[users_meetings|Future Users Meetings]]<br />
*[[tools_standards|Standards for GO tools]]<br />
*[[journals_advice|RSC journals: marking up text]]<br />
*[[Documentation needed]]<br />
*[[Future outreach/advocacy at specific meetings]]<br />
<br />
<br />
[[Outreach and Advocacy]]<br />
<br />
[[Individual Meeting Plans]]<br />
<br />
[[Category:Advocacy and Outreach]]</div>Adiehl