https://wiki.geneontology.org/api.php?action=feedcontributions&user=Mlgwinn&feedformat=atomGO Wiki - User contributions [en]2024-03-29T04:59:10ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=October_2020_Remote_GOC_Meeting_Logistics&diff=78508October 2020 Remote GOC Meeting Logistics2020-07-30T20:37:54Z<p>Mlgwinn: </p>
<hr />
<div>=GOC Remote Meeting, October 6-8, 2020=<br />
<br />
<br />
This is the main Fall 2020 GOC meeting that will be held remotely due to the continued COVID pandemic.<br />
<br />
<br />
==Agenda==<br />
Please add the subjects you would like to be discussed, so that we can prioritize and schedule the meeting:<br />
* [https://docs.google.com/document/d/1-Ti2aplJWpGZX913Zr6w6i6oHoIOsnfj1SzbVBn_TMo/edit?usp=sharing Agenda topics google doc]<br />
<br />
<span style="color:green">The final agenda will be determined later based on proposals from attendees</span><br />
<br />
[[Category: GO Consortium Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=October_2020_Remote_GOC_Meeting_Logistics&diff=78507October 2020 Remote GOC Meeting Logistics2020-07-30T20:35:31Z<p>Mlgwinn: </p>
<hr />
<div>=GOC Remote Meeting, October 6-8, 2020=<br />
<br />
<br />
This is the main Fall 2020 GOC meeting that will be held remotely due to the continued COVID pandemic.<br />
<br />
<br />
==Agenda==<br />
Please add the subjects you would like to be discussed, so that we can prioritize and schedule the meeting:<br />
* [https://docs.google.com/document/d/1-Ti2aplJWpGZX913Zr6w6i6oHoIOsnfj1SzbVBn_TMo/edit?usp=sharing Agenda topics google doc]<br />
<br />
[[Category: GO Consortium Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=October_2020_Remote_GOC_Meeting_Logistics&diff=78506October 2020 Remote GOC Meeting Logistics2020-07-30T20:21:52Z<p>Mlgwinn: /* GOC Remote Meeting, October 6-8, 2020 */</p>
<hr />
<div>=GOC Remote Meeting, October 6-8, 2020=<br />
<br />
<br />
This is the main Fall 2020 GOC meeting that will be held remotely due to the continued COVID pandemic.<br />
<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=October_2020_Remote_GOC_Meeting_Logistics&diff=78505October 2020 Remote GOC Meeting Logistics2020-07-30T20:16:57Z<p>Mlgwinn: Created page with "=GOC Remote Meeting, October 6-8, 2020= This is the main Fall 2020 GOC meeting that will be done remotely due to the continued COVID pandemic. Category: GO Consortium..."</p>
<hr />
<div>=GOC Remote Meeting, October 6-8, 2020=<br />
<br />
<br />
This is the main Fall 2020 GOC meeting that will be done remotely due to the continued COVID pandemic.<br />
<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Consortium_Meetings_and_Workshops&diff=78504Consortium Meetings and Workshops2020-07-30T20:11:49Z<p>Mlgwinn: /* 2020 */</p>
<hr />
<div><br />
=2020=<br />
* GOC Meeting - Remote, October 6-8, 2020<br />
** [[October 2020 Remote GOC Meeting Logistics]]<br />
** [[October 2020 Remote GOC Meeting Agenda]]<br />
<br />
* GO Users Meeting - Remote, May 11<br />
** [[2020 Remote GO Users Meeting Logistics]]<br />
** [[2020 Remote GO Users Meeting Agenda]]<br />
<br />
* GOC Meeting - Remote, May 12 - 14<br />
** [[2020 Remote GOC Meeting Logistics]]<br />
** [[2020 Remote GOC Meeting Agenda]]<br />
<br />
*Imports and PIpeline Meeting - Caltech, February 24th - 28th<br />
** [[2020 Caltech Imports and PIpeline Meeting Logistics]]<br />
** [[2020 Caltech Imports and PIpeline Meeting Meeting Agenda]]<br />
<br />
=2019=<br />
<br />
*[https://docs.google.com/document/d/1b8oZYTEV6gdGMOcOH0j_NeWvKPw-c8d6RFuLhja6DK8/edit# GO-dev Berkeley hackathon]: Jan 28 - Feb 1<br />
*GOC meeting - Cambridge, UK April 11th - 12th (right after ISB meeting)<br />
** [[2019 Cambridge GOC Meeting Logistics]]<br />
** [[2019 Cambridge GOC Meeting Agenda]]<br />
* USC Face-2-face meeting, June 18-21<br />
** [[2019 USC Meeting Agenda]] and logistics<br />
* 2019 Oct GOC meeting - Berkeley, CA: October 7-10, 2019 (User Meeting Oct 7, GOC meeting Oct 8-10, SAB meeting Oct 11)<br />
** [[2019 Berkeley GOC User Meeting Logistics]]<br />
** [[2019 Berkeley GOC User Meeting Agenda]]<br />
** [[2019 Berkeley GOC Meeting Logistics]]<br />
** [[2019 Berkeley GOC Meeting Agenda]]<br />
** [[2019 Berkeley SAB Meeting Logistics]]<br />
** [[2019 Berkeley SAB Meeting Agenda]]<br />
* Pathways2GO in NYC: December 2,3,4<br />
** [https://drive.google.com/drive/folders/1K-ZqiJ8Oc27ircaAOZBoX0zGEKu6q1gq Meeting Folder]<br />
<br />
=2018=<br />
* [[2018 Ontology Editors' GH ticket Meeting]]<br />
* [[2018 USC Noctua developers meeting]]<br />
* [[2018 Berkeley GO Docathon]]<br />
* [[2018 Berkeley GO-Dev April Hackathon]]<br />
* [[2018 Berkeley GO-Dev July Hackathon]]<br />
*GOC meeting - New York (NYU) May 12-14<br />
** [[2018 NYU GOC Meeting Logistics]]<br />
** [[2018 NYU GOC Meeting Agenda]]<br />
** [[2018 NYU SAB Meeting Logistics]]<br />
** [[2018 NYU SAB Meeting Agenda]]<br />
*[[2018 August USC Developers Meeting]]<br />
*20th anniversary GOC meeting to be held in Montreal October 17-19, 2018<br />
** [[2018 Montreal GOC Meeting Logistics]]<br />
** [[2018 Montreal GOC Meeting Agenda]]<br />
** [[2018 Montreal GOC users workshop]]<br />
* [[Geneva ontology editors meeting- Dec 10-13, 2018 - Logistics]] <br />
** Agenda: https://docs.google.com/document/d/1ixnmDZ75cFFdGN9H6CY5hyRkoPrCn6MvZVmERo_--Rw/edit<br />
<br />
=2017=<br />
<br />
* [[2017 November Berkeley Noctua Developers Meeting]]<br />
* GOC Meeting, Cambridge, UK, October 2-4, 2017<br />
** [[2017 Cambridge GOC Meeting Logistics]]<br />
** [[2017 Cambridge GOC Meeting Agenda]]<br />
** [[2017 Cambridge GOC Signalling Workshop]]<br />
* GOC GO Editors Workshop II, Berkeley, Aug 15-17<br />
**[[2017 Berkeley GO Editors Workshop II]]<br />
* GOC Meeting, Corvallis, Oregon, June 1-3 (plus workshops June 4-5), 2017<br />
** Logistics: https://sites.google.com/view/goc2017<br />
** [[2017 Corvallis GOC Meeting Agenda]]<br />
* GOC Protege Training Meeting Feb. 22, 23, and 24<br />
**[[Protege-OWL_Berkeley_Training_Logistics]]<br />
**Agenda: https://github.com/geneontology/protege-tutorial<br />
**Example tickets<br />
*** Adding a term: https://github.com/geneontology/go-ontology/issues/12996<br />
*** Obsoleting terms: https://github.com/geneontology/go-ontology/issues/12923<br />
*** Adding a term to a slim: https://github.com/geneontology/go-ontology/issues/13031<br />
*** Adding a taxon restriction:<br />
*** Merging terms https://github.com/geneontology/go-ontology/issues/12782<br />
<br />
=2016=<br />
* GOC Meeting, Los Angeles, November 4-6, 2016<br />
** [[2016 Los Angeles GOC Meeting Logistics]] <br />
** [[2016 Los Angeles GOC Meeting Agenda]]<br />
* Hinxton LEGO/Noctua Training, Hinxton, August 31 - September 02, 2016<br />
** [[2016 Hinxton LEGO/Noctua Training Logistics]] <br />
** [[2016 Hinxton LEGO/Noctua Training Agenda]]<br />
* GOC Meeting, Geneva, Switzerland, April 15-16, 2016<br />
** [[2016 Geneva GOC Meeting Logistics]] <br />
** [[2016 Geneva GOC Meeting Agenda]]<br />
<br />
=2015=<br />
* LEGO Jamboree, Geneva, Switzerland, December 8-10, 2015<br />
** [[2015 LEGO Jamboree Logistics]]<br />
* GOC Meeting, Washington, DC, August 30 - September 2, 2015<br />
** [[2015 Washington DC GOC Meeting Logistics]] <br />
** [[2015 Washington DC GOC Meeting Agenda]]<br />
** [[2015 Washington DC GOC Meeting Minutes]] <br />
** [[2015 Washington DC GOC Symposium Agenda]] <br />
** [[2015 Washington DC GOC Scientific Advisory Board Meeting Agenda]]<br />
* GOC All Hands Teleconference, April 1, 2015 <br />
** [[April 2015 GOC Teleconference Agenda and Logistics]]<br />
** [[April 2015 GOC Teleconference Minutes]]<br />
<br />
=2014=<br />
* GOC Meeting, Barcelona, October 13-15, 2014<br />
** [[2014 Barcelona Meeting Logistics]]<br />
** [[2014_Barcelona GOC Meeting_Agenda]]<br />
** [https://docs.google.com/document/d/1NonH97s8xEpDdx6DfonKPKI_RdHbbG-yft85UZtUmF0/edit#heading=h.2hxg96gzn5xe 2014 Barcelona Meeting Minutes]<br />
* PAINT Jamboree, Stanford CA, July 28-31, 2014<br />
** [[PAINT 2014 Summer Jamboree Kickoff Meeting Logistics]]<br />
* GOC Meeting, College Station, TX, March 16-17, 2014<br />
** [[2014 College Station Logistics]] <br />
** [[2014 College Station GOC Meeting Agenda]]<br />
<br />
=2013=<br />
* GOC Meeting, Bar Harbor, Maine, October (3), 4-6, 2013<br />
** [[2013 Bar Harbor Logistics]] <br />
** [[2013 Bar Harbor GOC Meeting Agenda]] <br />
** [[2013 GO Challenge]]<br />
* GOC Meeting, Cambridge, UK, April 11 - 13, 2013<br />
** [[2013 Cambridge Logistics]]<br />
** [[2013 Cambridge GOC Meeting Agenda]]<br />
** [[2013 Cambridge GOC Scientific Advisory Board Meeting Agenda]]<br />
* [http://www.ebi.ac.uk/biocuration2013/ BioCurator]<br />
* [[Ontology_workshop_Jan_2013]]<br />
<br />
=2012=<br />
*PAINT Training meeting, Stanford, Dec 10-13 2012<br />
** [[2012 PAINT workshop Logistics]] | [[2012 PAINT]] <br />
* GOC Meeting, Caltech, Pasadena, October 7 - 9, 2012<br />
** [[2012 Caltech GOC Meeting Logistics]] - [http://wiki.geneontology.org/index.php/2012_GOC_Meeting_Caltech 2012 Caltech GOC Meeting Agenda]<br />
* CAT Meeting, Caltech<br />
** [http://wiki.geneontology.org/index.php/Common_Annotation_Framework_Specification#Working_Meeting.2C_Caltech.2C_June_4th-8th.2C_2012 CAT meeting]<br />
* GOC Annotation Meeting, Stanford University, 26-28th February 2012<br />
** [[2012 Stanford Annotation Meeting Logistics]] - [http://wiki.geneontology.org/index.php/2012_Annotation_Meeting_Stanford 2012 Annotation Meeting Agenda] - [[Minutes_annotation_approaches_stanford_2012]]<br />
* [[Hinxton OBO-Edit/Protege 4 workshop Jan 2012 | Protege/OWL workshop]], Hinxton, UK, 30-31st Jan 2012<br />
<br />
=2011=<br />
* GOC meeting, University College London, 7-9th November 2011<br />
** [[2011 UCL Meeting Logistics]] - [[2011 UCL Meeting Agenda]]<br />
<br />
* GOC meeting, University of Southern California, 19-21st May 2011<br />
** [[2011 USC Meeting Logistics]] <br />
** [[2011 USC Meeting Agenda]]<br />
** [[2011 USC Meeting Action Items]]<br />
** [[File:minutes_LA2011.pdf]] <br />
<br />
* UCL GO [http://www.ucl.ac.uk/cardiovasculargeneontology/Outreach/Annotation_Workshops Annotation workshop] London, 6-7th April 2011<br />
<br />
=2010=<br />
* The Jackson Laboratory, Bar Harbor, Maine, GOC Sept 7-9, 2010<br />
** [[2010 Bar Harbor Minutes]]<br />
<br />
* GO annotation camp, Centre Médical Universitaire (CMU) Geneva, Switzerland, June 16-18 2010<br />
** [[2010 GO camp Meeting Logistics]] <br />
** [[2010_GO_camp_Meeting_Agenda]]<br />
** [http://wiki.geneontology.org/index.php/Talk:2010_GO_camp_Meeting_Agenda GO camp Meeting Minutes]<br />
* GO Reference Genome Meeting Bar Harbor May 20-21, 2010 <br />
** Ref Genome May 2010 minutes [[RefG_Bar_Harbor_May_20-21_2010]]<br />
* GO Reference Genome Princeton April 12-13, 2010 <br />
** Ref Genome April 2010 minutes [[RefG_Princeton_April_12-13_2010]]<br />
* Leland Stanford Jr. University, Stanford, California, GOC March 30-31 & SAB April 1, 2010<br />
** [[2010 Stanford Meeting Minutes]]<br />
<br />
=2009=<br />
* [[Cambridge GO Consortium Meeting | Cambridge Combined GO Consortium and SAB Meeting]] Jesus College, Cambridge, UK, September 23-25, 2009<br />
** [[2009 Cambridge Meeting Logistics]] <br />
** [[GOC Meeting Minutes September 2009|GOC Meeting Minutes September 2009]]<br />
* [[Oregon GO Consortium Meeting]] Eugene, Oregon, March 30, 31, 2009 <br />
** [[2009_Oregon_Meeting_Logistics|2009 Oregon Meeting Logistics]]<br />
* [[Oregon Reference Genomes Meeting]] Eugene, Oregon, April 1, 2009<br />
** [[2009_Oregon_Meeting_Logistics|2009 Oregon Meeting Logistics]]<br />
* Heart development workshop : [[Heart_Development_workshop_(Archived)]]<br />
** [[Minutes_Heart_Development_workshop]]<br />
<br />
=2008=<br />
* [[20th GO Consortium Meeting]] Montreal, October 21-22, 2008 -- '''[[October 2008 Meeting Logistics]]'''<br />
** [[20th_GO_Consortium_Meeting_Minutes | 20th GO Consortium Meeting minutes]]<br />
* [[Oct 2008 SAB Meeting]] Montreal, October 23, 2008 -- '''[[October 2008 Meeting Logistics]]'''<br />
* [[Avian GO Workshop May 2008]]<br />
* [[SLC GO Reference Genome Project Meeting]], April 20-21, 2008 Univ. of Utah, Salt Lake City, Utah<br />
** [[Reference Genome Meeting Minutes April 2008|Reference Genome Meeting Minutes April 2008]]<br />
** [[April 2008 Meeting logistics summary]]<br />
* [[GO Field Trip]], Afternoon of April 21, 2008: Antelope Island<br />
** [[wildlife and birds seen]] - List of Birds and Mammals<br />
* [[SLC GO Consortium Meeting]], April 22-23, 2008 Univ of Utah, Salt Lake City, Utah Photo:[[http://www.geneontology.org/photo_GO_SaltLakeCity.shtml]]<br />
** [[SLC GO Consortium Meeting Minutes April 2008|SLC GO Consortium Meeting Meeting Minutes April 2008]]<br />
** [[April 2008 Meeting logistics summary]]<br />
* Please [[http://gocwiki.geneontology.org/index.php/Register#Registration_for_April_2008_GO_Meetings_at_University_of_Utah.2C_SLC Register]] for one or both meetings.<br />
<br />
=2007=<br />
*[[GO Reference Genome Meeting]], Sept 26-27th, 2007 Princeton, New Jersey<br />
** [[Reference Genome minutes|Reference Genome minutes]]<br />
** [[September 2007 Meeting logistics summary]]<br />
*[[GO 3rd Advisors Meeting]], September 25th, 2007 Princeton, New Jersey<br />
** [[2007-09_SAB_minutes|2007-09_SAB_minutes]]<br />
** [[September 2007 Meeting logistics summary]]<br />
* [[GO 18th Consortium Meeting]], September 23-24th, 2007 Princeton, New Jersey. Photo:[[http://www.geneontology.org/images/photo_GOC_20070923.jpg]]<br />
** [[GO 18th Consortium Meeting Minutes Day 1|Draft Minutes Day 1]]<br />
** [[GO 18th Consortium Meeting Minutes Day 2|Draft Minutes Day 2]]<br />
** [[GO 18th Consortium Meeting Action Items ]]<br />
** [[Outstanding Action Items from 17th GOC Meeting, Cambridge UK]]<br />
** [[September 2007 Meeting logistics summary]]<br />
*[[GO Consortium Meeting 2007]], January 7-10th, 2007 Cambridge UK Photo:[[http://www.geneontology.org/photo_GO_JesusCollege.shtml]], Minutes:[[http://www.geneontology.org/meeting/minutes/20070108_Cambridge.doc]]<br />
*[[GO Advisors Meeting]], September 7th, 2006 Seattle Washington<br />
*Third Annotation Camp, July 10-14th, 2006 Stanford University. Photo:[[http://www.geneontology.org/photo_GO_Annotation_Camp_20060714.shtml]], Minutes:[[http://www.geneontology.org/meeting/minutes/20060710_GOannotCamp_Stanford.pdf]]<br />
----<br />
<br />
=Progress Reports for GOC Meetings=<br />
#Meeting Progress Reports 2011<br />
## [[Meeting_Progress_Reports_November_2011]]<br />
## [[Meeting_Progress_Reports_May_2011]]<br />
#Meeting Progress Reports 2010<br />
## [[Meeting_Progress_Reports_September_2010]]<br />
## [[Meeting_Progress_Reports_March_2010]]<br />
#Meeting Progress Reports 2009<br />
##[[Meeting_Progress_Reports_September_2009]]<br />
##[[Meeting_Progress_Reports_March_2009]]<br />
##[[Meeting_Progress_Reports_September_2009]]<br />
#Meeting Progress Reports 2008<br />
##[[Meeting_Progress_Report_April_2008]]<br />
##[[Meeting Progress Reports October 2008]]<br />
#[[Converting .doc or .docx to Wiki]]<br />
<br />
=Progress Report Templates=<br />
# [https://docs.google.com/document/d/15HObk9-uPxYrgHaOK6RKKCbGJybnOrdoIr4JtkUTdjM/edit#heading=h.jtbq5nvboelc MOD template]<br />
# [[Ontology Development template]]<br />
# [https://docs.google.com/document/d/1zvL9o-tFFMwxOnp4jc7T4IEnA__LM7JmW9XjaJ-PJic/edit Overall progress report template]<br />
<br />
=Publications, tutorials, talks, posters=<br />
# [[Publications, tutorials, talks, posters]]<br />
<br />
<br />
[[Category:GOC Overview]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=762122019 Berkeley GOC Meeting Logistics2019-09-18T22:11:45Z<p>Mlgwinn: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Berkeley, October 7-10, 2019=<br />
<br />
* Location: [https://goo.gl/maps/cfabKMyCSPZmFkFf7| 717 Potter Street, Berkeley, CA]<br />
<br />
==Registration==<br />
* Via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351| Eventbrite]--pay online with credit or debit card or Paypal<br />
** $130 registration fee covers coffee & snacks for the 2.5-day GOC meeting, as well as 2 lunches and the Consortium dinner on Oct 9 (not including alcoholic beverages). It does NOT cover any expenses for the User Meeting or the SAB meeting.<br />
* Please also fill in the fields in the [[#Attendees | Attendees list]] at the bottom of this page.<br />
<br />
==Overall schedule== <br />
*Monday, October 7: User Meeting (8:30am-5pm)<br />
*Tuesday-Thursday October 8-10: GOC Meeting (8:30am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11 (time TBA): [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics SAB Meeting], UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley).<br />
* Note that food and beverages at the User Meeting are not covered by the GOC meeting registration fee--you are responsible for paying for your own food and beverages during the User Meeting.<br />
<br />
=SAB Meeting=<br />
* SAB Meeting: Friday, October 11 (time TBA) in [https://goo.gl/maps/kFG8EPBBjWJnuy6EA Stanley Hall] on the UC Berkeley campus. Logistics [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| here].<br />
* SAB dinner: Thursday, October 10, 7pm: place TBD<br />
<br />
=Arriving=<br />
<br />
The closest airports are San Francisco (SFO) and Oakland (OAK). From either of those, you can take BART to Berkeley and get a taxi/Lyft/Uber from the Ashby BART station.<br />
<br />
Scroll down to the "Getting around" section for more info.<br />
<br />
=Hotels=<br />
These are listed in increasing order by price. The Four Points by Sheraton is the only one that's walking distance (1.4 miles) from the meeting location; the others are downtown, a short drive away. [https://docs.google.com/document/d/1DaSiBXlW6gjH840h9kdC3FVbuVuetqglcsgrDvB7maE/edit| This map] shows the relative locations of the hotels.<br />
<br />
For travel to our building, we will arrange for attendees to have access to the LBNL Potter St. shuttle to our building from downtown Berkeley.<br />
<br />
===[http://downtownberkeleyinn.com/| Downtown Berkeley Inn]===<br />
* '''Address''': 2001 Bancroft Way, Berkeley (2.4 miles from the Potter Street meeting location)<br />
* '''Phone''': (510) 843-4043<br />
* '''Rate''': LBNL rate is $129/night (normal rate $139/night).<br />
* '''How to book''': Phone (don't book online) and ask for “LBL” or “Gene Ontology” room block.<br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': Very basic, but adequate.<br />
* '''Advantages''': Cheapest option. Fairly close to downtown Berkeley.<br />
<br />
===[https://www.marriott.com/event-reservations/reservation-link.mi?id=1563407776453&key=GRP&app=resvlink| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the Potter Street meeting location),<br />
* '''Phone''': 1-800-325-3535<br />
* '''Rate''': $175/night (single or double) block rate for “Gene Ontology / GO meeting”.<br />
* '''How to book''': Book using this link: https://www.marriott.com/events/start.mi?id=1563407776453&key=GRP or call 1-800-325-3535 and ask for the “Gene Ontology” room block. <br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': A normal hotel. Has an outdoor pool and a fitness center.<br />
* '''Advantages''': Closest hotel to meeting location.<br />
<br />
===[https://www.graduatehotels.com/berkeley/| The Graduate] (formerly the Hotel Durant)===<br />
* '''Address''': 2600 Durant Ave, Berkeley (2.9 miles from the Potter Street meeting location)<br />
* '''Phone''': 510-845-8981<br />
* '''Rate''': Average of $210/night for a room with one queen.<br />
* '''How to book''': No special rates; you can book [https://www.graduatehotels.com/berkeley| online]<br />
* '''Description''': No pool or fitness center. More distinctive than the similarly-priced Hotel Shattuck Plaza. A recent article about The Graduate noted, "Berkeley's quirky counterculture is represented by bong-shaped lamps in the guestrooms and a restroom urinal painted with the logo and colors of Stanford, Cal-Berkeley’s arch-rival." Known for having made a brief appearance in the movie of the same name.<br />
* '''Advantages''': Near UC Campus and Telegraph Avenue, a colorful if slightly sketchy part of Berkeley.<br />
<br />
===[http://www.hotelshattuckplaza.com| Hotel Shattuck Plaza]===<br />
* '''Address''': 2086 Allston Way, Berkeley (2.5 miles from the Potter Street meeting location)<br />
* '''Phone''': 866-466-9199<br />
* '''Rate''': UC Berkeley rate: $215/night. Same price for double or single. <br />
* '''How to book''': You will need to phone and ask for the UC Berkeley rate--not available online.<br />
* '''Description''': A more upscale hotel than the previous three, it was completely remodeled a few years ago. Has a fitness center but no pool.<br />
* '''Advantages''': Right in the heart of downtown Berkeley, near BART, Potter St. shuttle, and many world-class restaurants<br />
<br />
= Getting around / To do / Local activities =<br />
<br />
The organizers have lived in the area for a very long time. If you have *any* questions, do not hesitate to reach out to us and let us make your stay in the Bay Area more more pleasant.<br />
<br />
== Getting around ==<br />
<br />
The LBL Potter Street site is located near a highway in a mixed business park and light industrial area.<br />
<br />
=== Walking ===<br />
<br />
Walking from the Emeryville hotel (Four Points Sheraton) to the meeting site is doable, but not necessarily a "pleasant" walk. It takes about half an hour.<br />
<br />
Walking from downtown is not advised and would take about an hour.<br />
<br />
=== By car (inc. "rideshare") ===<br />
<br />
If you are driving to the GO meeting, parking should not be an issue--while there will be no on-site parking, there is usually plenty of on-street parking in the surrounding area if you can walk a little. If you intend on driving, contact Seth or Nomi for details and fill out the [http://bit.ly/2019GOCBerkeleyTransportation form] so we can submit for site access in the week before the meeting.<br />
<br />
The are usually plenty of Lyfts and Ubers in the area. The downtown area is about 10-12 minutes away.<br />
<br />
=== By public transportation ===<br />
<br />
==== From downtown ====<br />
<br />
===== LBL shuttle =====<br />
<br />
There is a fairly frequent LBL shuttle that directly connects downtown Berkeley area and the Potter Street site:<br />
<br />
https://commute.lbl.gov/resource/shuttle-buses/maps-routes-schedules/potter-st-jbei-route/<br />
<br />
You will need to show an LBL guest pass to board this shuttle. We can provide these on request--contact Seth or Nomi and fill out the [http://bit.ly/2019GOCBerkeleyTransportation form] so we can submit for site access in the week before the meeting. The shuttle is often a 15-person van, so large groups may need to split up at peak times.<br />
<br />
===== Bus (AC Transit) =====<br />
<br />
There is also a bus that departs from near downtown and the Durant hotel and has a stop quite near the Potter Street site:<br />
<br />
http://www.actransit.org/maps/schedule_results.php?quick_line=36&Go=Go<br />
<br />
==== From Emeryville ====<br />
<br />
While it does not run directly by the hotel, one would need to walk a little and cross a bridge over the tracks, there is a free public shuttle that runs from near the hotel to near the Potter Street site: The Emery Go-round ():<br />
<br />
https://www.emerygoround.com/standard-service.html<br />
<br />
=== Biking and scootering ===<br />
<br />
The are is fairly well served by various "last mile" solutions.<br />
<br />
Rental bikes (now Lyft, previously Ford GoBikes) are available at various locations (https://member.baywheels.com/map/), including downtown Berkeley and near the meeting site (next to the Berkeley Bowl grocery store).<br />
<br />
==Food and drinks==<br />
<br />
=== Overview ===<br />
<br />
Downtown Berkeley has lots of places to eat. The LBL Potter Street location is much more limited for cafes and restaurants, but there is a large supermarket with a cafe (Berkeley Bowl) a few blocks away. Ubereats and the like are always an option for people wanting more variety and many of the organizers will have vehicles and may be doing various errands about town anyways, if there is something in particular you want or need.<br />
<br />
Seth will be happy to talk nearly endlessly about local restaurant, bar, and tea/cafe opportunities.<br />
<br />
==== Official and unofficial GOC dinners ====<br />
<br />
Tuesday, October 8, 5:30pm: [http://www.rottencitypizza.com/#board Rotten City Pizza], located walking distance between Potter Street and Emeryville. Beer, wine, cider, pizza, pool & darts. Pay your own way.<br />
<br />
Wednesday, October 9, 6pm: GOC meeting dinner, Stella Nonna Restaurant. Covered by registration fee.<br />
<br />
==Exercise==<br />
<br />
For people interested in hitting the gym or swimming, the UC Berkeley recreational facilities are open to the general public with day passes:<br />
<br />
https://recsports.berkeley.edu/day-passes/<br />
<br />
The main rec facility and pool location is a short walk from downtown Berkeley. Several of the satellite pools have reduced day pass rates.<br />
<br />
==Things to do in the Berkeley area==<br />
The popular [http://www.hardlystrictlybluegrass.com/2019/ "Hardly Strictly Bluegrass" festival] (which leans more towards alternative rock than bluegrass) will take place in San Francisco, Fri-Sun October 4-6.<br />
<br />
On Wednesday, Oct 9, we will break early for an optional hike in Tilden Park.<br />
<br />
On Thursday, Oct 10, there will be an optional outing to the Exploratorium in San Francisco. The Exploratorium is open [https://www.exploratorium.edu/visit/calendar/after-dark Thursday evenings until 10pm for adults only (18+)]. To add to the fun, we'll take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] and then get dinner near there.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
If you're staying around until Friday, there's an optional expedition on Thursday evening (see above).<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend! (If you don't have edit permission, you can instead fill out [https://bit.ly/2019GOBerkeley this signup form].)<br />
Don't forget to register and pay via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351%7C| Eventbrite].<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
|Judy Blake<br />
|JAX<br />
|Yes<br />
|Yes<br />
|Yes<br />
|Four Points<br />
|Yes<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| yes<br />
| yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
|<br />
|-<br />
| Adam Wright<br />
| OICR<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hilton Garden Inn<br />
| Yes<br />
|-<br />
| Justin Reese<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase, Northwestern<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Berkeley Inn<br />
| Yes<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Oakland airbnb<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| not yet<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Berkeley Inn <br />
| Yes<br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hotel Shattuck Plaza<br />
| not yet<br />
|-<br />
| Suvarna Nadendla<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hotel Shattuck Plaza<br />
| not yet<br />
|-<br />
| Alex Ignatchenko<br />
| EBI<br />
| Yes<br />
| Yes<br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Jeff De Pons<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| George Georghiou<br />
| EBI<br />
| Yes<br />
| Yes<br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| Anushya Muruganujan<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Valerie Wood<br />
| Cambridge<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airb&b<br />
| Yes<br />
|-<br />
| Felix Gondwe<br />
| SGD, Stanford<br />
| Yes<br />
| Yes <br />
| No<br />
| N/A<br />
| <br />
|-<br />
| Patrick Masson<br />
| SIB<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| <br />
| <br />
| <br />
| <br />
| <br />
| <br />
| <br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Malcolm Fisher (Xenbase) will attend remotely.<br />
<br />
Li Ni (MGI) will attend remotely.<br />
<br />
Birgit Meldal (EBI Complex Portal) - remotely if required (need to see schedule) / manageable (I'm +8 hours)<br />
<br />
Stacia Engel (SGD) not attending - son on Fall Break so we're doing family stuff<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=760792019 Berkeley GOC Meeting Logistics2019-08-31T15:21:00Z<p>Mlgwinn: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Berkeley, October 7-10, 2019=<br />
<br />
* Location: [https://goo.gl/maps/cfabKMyCSPZmFkFf7| 717 Potter Street, Berkeley, CA]<br />
<br />
==Registration==<br />
* Via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351| Eventbrite]--pay online with credit or debit card or Paypal<br />
* $130 registration fee covers coffee & snacks for the 2.5-day GOC meeting, as well as 2 lunches and the Consortium dinner on Oct 9 (not including alcoholic beverages)<br />
* Please also fill in the fields in the Attendees list at the bottom of this page. If you don't have edit permission, you can instead fill out [https://bit.ly/2019GOBerkeley this signup form].<br />
<br />
==Overall schedule== <br />
*Monday, October 7: User Meeting (8:30am-5pm)<br />
*Tuesday-Thursday October 8-10: GOC Meeting (8:30am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11 (time TBA): [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| SAB Meeting], UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley). More details soon.<br />
<br />
=SAB Meeting=<br />
* SAB Meeting: Friday, October 11 (time TBA) in Stanley Hall on the UC Berkeley campus. Logistics [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| here].<br />
* SAB dinner: Thursday, October 10, 7pm: place TBD<br />
<br />
=Arriving=<br />
<br />
The closest airports are San Francisco (SFO) and Oakland (OAK). From either of those, you can take BART to Berkeley and get a taxi/Lyft/Uber from the Ashby BART station.<br />
<br />
Scroll down to the "Getting around" section for more info.<br />
<br />
=Hotels=<br />
These are listed in increasing order by price. The Four Points by Sheraton is the only one that's walking distance (1.4 miles) from the meeting location; the others are downtown, a short drive away. [https://docs.google.com/document/d/1DaSiBXlW6gjH840h9kdC3FVbuVuetqglcsgrDvB7maE/edit| This map] shows the relative locations of the hotels.<br />
<br />
For travel to our building, we will arrange for attendees to have access to the LBNL Potter St. shuttle to our building from downtown Berkeley.<br />
<br />
===[http://downtownberkeleyinn.com/| Downtown Berkeley Inn]===<br />
* '''Address''': 2001 Bancroft Way, Berkeley (2.4 miles from the meeting location)<br />
* '''Phone''': (510) 843-4043<br />
* '''Rate''': LBNL rate is $129/night (normal rate $139/night).<br />
* '''How to book''': Phone (don't book online) and ask for “LBL” or “Gene Ontology” room block.<br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': Very basic, but adequate.<br />
* '''Advantages''': Cheapest option. Fairly close to downtown Berkeley.<br />
<br />
===[https://www.marriott.com/hotels/travel/sfofp-four-points-san-francisco-bay-bridge/| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the meeting location),<br />
* '''Phone''': 1-800-325-3535<br />
* '''Rate''': $175/night (single or double) block rate for “Gene Ontology / GO meeting”.<br />
* '''How to book''': Book using this link: https://www.marriott.com/events/start.mi?id=1563407776453&key=GRP or call 1-800-325-3535 and ask for the “Gene Ontology” room block. <br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': A normal hotel. Has an outdoor pool and a fitness center.<br />
* '''Advantages''': Closest hotel to meeting location.<br />
<br />
===[https://www.graduatehotels.com/berkeley/| The Graduate] (formerly the Hotel Durant)===<br />
* '''Address''': 2600 Durant Ave, Berkeley (2.9 miles from the meeting location)<br />
* '''Phone''': 510-845-8981<br />
* '''Rate''': Average of $210/night for a room with one queen.<br />
* '''How to book''': No special rates; you can book [https://www.graduatehotels.com/berkeley| online]<br />
* '''Description''': No pool or fitness center. More distinctive than the similarly-priced Hotel Shattuck Plaza. A recent article about The Graduate noted, "Berkeley's quirky counterculture is represented by bong-shaped lamps in the guestrooms and a restroom urinal painted with the logo and colors of Stanford, Cal-Berkeley’s arch-rival." Known for having made a brief appearance in the movie of the same name.<br />
* '''Advantages''': Near UC Campus and Telegraph Avenue, a colorful if slightly sketchy part of Berkeley.<br />
<br />
===[http://www.hotelshattuckplaza.com| Hotel Shattuck Plaza]===<br />
* '''Address''': 2086 Allston Way, Berkeley (2.5 miles from the meeting location)<br />
* '''Phone''': 866-466-9199<br />
* '''Rate''': UC Berkeley rate: $215/night. Same price for double or single. <br />
* '''How to book''': You will need to phone and ask for the UC Berkeley rate--not available online.<br />
* '''Description''': A more upscale hotel than the previous three, it was completely remodeled a few years ago. Has a fitness center but no pool.<br />
* '''Advantages''': Right in the heart of downtown Berkeley, near BART, Potter St. shuttle, and many world-class restaurants<br />
<br />
= Getting around / To do / Local activities =<br />
<br />
The organizers have lived in the area for a very long time. If you have *any* questions, do not hesitate to reach out to us and let us make your stay in the Bay Area more more pleasant.<br />
<br />
== Getting around ==<br />
<br />
The LBL Potter Street site is located near a highway in a mixed business park and light industrial area.<br />
<br />
=== Walking ===<br />
<br />
Walking from the Emeryville hotel (Four Points Sheraton) to the meeting site is doable, but not necessarily a "pleasant" walk. It takes about half an hour.<br />
<br />
Walking from downtown is not advised and would take about an hour.<br />
<br />
=== By car (inc. "rideshare") ===<br />
<br />
If you are driving to the GO meeting, parking should not be an issue--while there will be no on-site parking, there is usually plenty of on-street parking in the surrounding area if you can walk a little. If you intend on driving, contact Seth or Nomi for details.<br />
<br />
The are usually plenty of Lyfts and Ubers in the area. The downtown area is about 10-12 minutes away.<br />
<br />
=== By public transportation ===<br />
<br />
==== From downtown ====<br />
<br />
===== LBL shuttle =====<br />
<br />
There is a fairly frequent LBL shuttle that directly connects downtown Berkeley area and the Potter Street site:<br />
<br />
https://commute.lbl.gov/resource/shuttle-buses/maps-routes-schedules/potter-st-jbei-route/<br />
<br />
You will need to show an LBL guest pass to board this shuttle. We can provide these on request--contact Seth or Nomi. The shuttle is often a 15-person van, so large groups may need to split up at peak times.<br />
<br />
===== Bus (AC Transit) =====<br />
<br />
There is also a bus that departs from near downtown and the Durant hotel and has a stop quite near the Potter Street site:<br />
<br />
http://www.actransit.org/maps/schedule_results.php?quick_line=36&Go=Go<br />
<br />
==== From Emeryville ====<br />
<br />
While it does not run directly by the hotel, one would need to walk a little and cross a bridge over the tracks, there is a free public shuttle that runs from near the hotel to near the Potter Street site: The Emery Go-round ():<br />
<br />
https://www.emerygoround.com/standard-service.html<br />
<br />
=== Biking and scootering ===<br />
<br />
The are is fairly well served by various "last mile" solutions.<br />
<br />
Rental bikes (now Lyft, previously Ford GoBikes) are available at various locations (https://member.baywheels.com/map/), including downtown Berkeley and near the meeting site (next to the Berkeley Bowl grocery store).<br />
<br />
==Food and drinks==<br />
<br />
=== Overview ===<br />
<br />
Downtown Berkeley has lots of places to eat. The LBL Potter Street location is much more limited for cafes and restaurants, but there is a large supermarket with a cafe (Berkeley Bowl) a few blocks away. Ubereats and the like are always an option for people wanting more variety and many of the organizers will have vehicles and may be doing various errands about town anyways, if there is something in particular you want or need.<br />
<br />
Seth will be happy to talk nearly endlessly about local restaurant, bar, and tea/cafe opportunities.<br />
<br />
==Exercise==<br />
<br />
For people interested in hitting the gym or swimming, the UC Berkeley recreational facilities are open to the general public with day passes:<br />
<br />
https://recsports.berkeley.edu/day-passes/<br />
<br />
The main rec facility and pool location is a short walk from downtown Berkeley. Several of the satellite pools have reduced day pass rates.<br />
<br />
==Things to do in the Berkeley area==<br />
The popular [http://www.hardlystrictlybluegrass.com/2019/ "Hardly Strictly Bluegrass" festival] (which leans more towards alternative rock than bluegrass) will take place in San Francisco, Fri-Sun October 4-6.<br />
<br />
On Wednesday, Oct 8, we will break early for an optional hike in Tilden Park.<br />
<br />
On Thursday, Oct 9, there will be an optional outing to the Exploratorium in San Francisco. The Exploratorium is open [https://www.exploratorium.edu/visit/calendar/after-dark Thursday evenings until 10pm for adults only (18+)]. To add to the fun, we'll take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] and then get dinner near there.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
If you're staying around until Friday, there's an optional expedition on Thursday evening (see above).<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend! Don't forget to register and pay via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351%7C| Eventbrite].<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
|Judy Blake<br />
|JAX<br />
|Yes<br />
|Yes<br />
|Yes<br />
|Four Points<br />
|Yes<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| TBD<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| yes<br />
| yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Nash Hotel<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not booked yet<br />
| not yet<br />
|-<br />
| Adam Wright<br />
| OICR<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hilton Garden Inn<br />
| Yes<br />
|-<br />
| Justin Reese<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase, Northwestern<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not yet booked<br />
|<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Oakland airbnb<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| not yet<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| <br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| <br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
| Suvarna Nadendla<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Malcolm Fisher (Xenbase) will attend remotely.<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=760682019 Berkeley GOC Meeting Logistics2019-08-28T17:10:55Z<p>Mlgwinn: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Berkeley, October 7-10, 2019=<br />
<br />
* Location: [https://goo.gl/maps/cfabKMyCSPZmFkFf7| 717 Potter Street, Berkeley, CA]<br />
<br />
==Registration==<br />
* Via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351| Eventbrite]--pay online with credit or debit card or Paypal<br />
* $130 registration fee covers coffee & snacks for the 2.5-day GOC meeting, as well as 2 lunches and the Consortium dinner on Oct 9 (not including alcoholic beverages)<br />
* Please also fill in the fields in the Attendees list at the bottom of this page. If you don't have edit permission, you can instead fill out [https://bit.ly/2019GOBerkeley this signup form].<br />
<br />
==Overall schedule== <br />
*Monday, October 7: User Meeting (8:30am-5pm)<br />
*Tuesday-Thursday October 8-10: GOC Meeting (8:30am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11 (time TBA): SAB Meeting, UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley). More details soon.<br />
<br />
=SAB Meeting=<br />
* Meeting: Friday, October 11 (time TBA) in Stanley Hall on the UC Berkeley campus. Logistics [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| here].<br />
* SAB dinner: Thursday, October 10, 7pm: place TBD<br />
<br />
=Arriving=<br />
<br />
The closest airports are San Francisco (SFO) and Oakland (OAK). From either of those, you can take BART to Berkeley and get a taxi/Lyft/Uber from the Ashby BART station.<br />
<br />
Scroll down to the "Getting around" section for more info.<br />
<br />
=Hotels=<br />
These are listed in increasing order by price. The Four Points by Sheraton is the only one that's walking distance (1.4 miles) from the meeting location; the others are downtown, a short drive away. [https://docs.google.com/document/d/1DaSiBXlW6gjH840h9kdC3FVbuVuetqglcsgrDvB7maE/edit| This map] shows the relative locations of the hotels.<br />
<br />
For travel to our building, we will arrange for attendees to have access to the LBNL Potter St. shuttle to our building from downtown Berkeley.<br />
<br />
===[http://downtownberkeleyinn.com/| Downtown Berkeley Inn]===<br />
* '''Address''': 2001 Bancroft Way, Berkeley (2.4 miles from the meeting location)<br />
* '''Phone''': (510) 843-4043<br />
* '''Rate''': LBNL rate is $129/night (normal rate $139/night).<br />
* '''How to book''': Phone (don't book online) and ask for “LBL” or “Gene Ontology” room block.<br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': Very basic, but adequate.<br />
* '''Advantages''': Cheapest option. Fairly close to downtown Berkeley.<br />
<br />
===[https://www.marriott.com/hotels/travel/sfofp-four-points-san-francisco-bay-bridge/| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the meeting location),<br />
* '''Phone''': 1-800-325-3535<br />
* '''Rate''': $175/night (single or double) block rate for “Gene Ontology / GO meeting”.<br />
* '''How to book''': Book using this link: https://www.marriott.com/events/start.mi?id=1563407776453&key=GRP or call 1-800-325-3535 and ask for the “Gene Ontology” room block. <br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': A normal hotel. Has an outdoor pool and a fitness center.<br />
* '''Advantages''': Closest hotel to meeting location.<br />
<br />
===[https://www.graduatehotels.com/berkeley/| The Graduate] (formerly the Hotel Durant)===<br />
* '''Address''': 2600 Durant Ave, Berkeley (2.9 miles from the meeting location)<br />
* '''Phone''': 510-845-8981<br />
* '''Rate''': Average of $210/night for a room with one queen.<br />
* '''How to book''': No special rates; you can book [https://www.graduatehotels.com/berkeley| online]<br />
* '''Description''': No pool or fitness center. More distinctive than the similarly-priced Hotel Shattuck Plaza. A recent article about The Graduate noted, "Berkeley's quirky counterculture is represented by bong-shaped lamps in the guestrooms and a restroom urinal painted with the logo and colors of Stanford, Cal-Berkeley’s arch-rival." Known for having made a brief appearance in the movie of the same name.<br />
* '''Advantages''': Near UC Campus and Telegraph Avenue, a colorful if slightly sketchy part of Berkeley.<br />
<br />
===[http://www.hotelshattuckplaza.com| Hotel Shattuck Plaza]===<br />
* '''Address''': 2086 Allston Way, Berkeley (2.5 miles from the meeting location)<br />
* '''Phone''': 866-466-9199<br />
* '''Rate''': UC Berkeley rate: $215/night. Same price for double or single. <br />
* '''How to book''': You will need to phone and ask for the UC Berkeley rate--not available online.<br />
* '''Description''': A more upscale hotel than the previous three, it was completely remodeled a few years ago. Has a fitness center but no pool.<br />
* '''Advantages''': Right in the heart of downtown Berkeley, near BART, Potter St. shuttle, and many world-class restaurants<br />
<br />
= Getting around / To do / Local activities =<br />
<br />
The organizers have lived in the area for a very long time. If you have *any* questions, do not hesitate to reach out to us and let us make your stay in the Bay Area more more pleasant.<br />
<br />
== Getting around ==<br />
<br />
The LBL Potter Street site is located near a highway in a mixed business park and light industrial area.<br />
<br />
=== Walking ===<br />
<br />
Walking from the Emeryville hotel (Four Points Sheraton) to the meeting site is doable, but not necessarily a "pleasant" walk. It takes about half an hour.<br />
<br />
Walking from downtown is not advised and would take about an hour.<br />
<br />
=== By car (inc. "rideshare") ===<br />
<br />
If you are driving to the GO meeting, parking should not be an issue--while there will be no on-site parking, there is usually plenty of on-street parking in the surrounding area if you can walk a little. If you intend on driving, contact Seth or Nomi for details.<br />
<br />
The are usually plenty of Lyfts and Ubers in the area. The downtown area is about 10-12 minutes away.<br />
<br />
=== By public transportation ===<br />
<br />
==== From downtown ====<br />
<br />
===== LBL shuttle =====<br />
<br />
There is a fairly frequent LBL shuttle that directly connects downtown Berkeley area and the Potter Street site:<br />
<br />
https://commute.lbl.gov/resource/shuttle-buses/maps-routes-schedules/potter-st-jbei-route/<br />
<br />
You will need to show an LBL guest pass to board this shuttle. We can provide these on request--contact Seth or Nomi. The shuttle is often a 15-person van, so large groups may need to split up at peak times.<br />
<br />
===== Bus (AC Transit) =====<br />
<br />
There is also a bus that departs from near downtown and the Durant hotel and has a stop quite near the Potter Street site:<br />
<br />
http://www.actransit.org/maps/schedule_results.php?quick_line=36&Go=Go<br />
<br />
==== From Emeryville ====<br />
<br />
While it does not run directly by the hotel, one would need to walk a little and cross a bridge over the tracks, there is a free public shuttle that runs from near the hotel to near the Potter Street site: The Emery Go-round ():<br />
<br />
https://www.emerygoround.com/standard-service.html<br />
<br />
=== Biking and scootering ===<br />
<br />
The are is fairly well served by various "last mile" solutions.<br />
<br />
Rental bikes (now Lyft, previously Ford GoBikes) are available at various locations (https://member.baywheels.com/map/), including downtown Berkeley and near the meeting site (next to the Berkeley Bowl grocery store).<br />
<br />
==Food and drinks==<br />
<br />
=== Overview ===<br />
<br />
Downtown Berkeley has lots of places to eat. The LBL Potter Street location is much more limited for cafes and restaurants, but there is a large supermarket with a cafe (Berkeley Bowl) a few blocks away. Ubereats and the like are always an option for people wanting more variety and many of the organizers will have vehicles and may be doing various errands about town anyways, if there is something in particular you want or need.<br />
<br />
Seth will be happy to talk nearly endlessly about local restaurant, bar, and tea/cafe opportunities.<br />
<br />
==Exercise==<br />
<br />
For people interested in hitting the gym or swimming, the UC Berkeley recreational facilities are open to the general public with day passes:<br />
<br />
https://recsports.berkeley.edu/day-passes/<br />
<br />
The main rec facility and pool location is a short walk from downtown Berkeley. Several of the satellite pools have reduced day pass rates.<br />
<br />
==Things to do in the Berkeley area==<br />
The popular [http://www.hardlystrictlybluegrass.com/2019/ "Hardly Strictly Bluegrass" festival] (which leans more towards alternative rock than bluegrass) will take place in San Francisco, Fri-Sun October 4-6.<br />
<br />
On Wednesday, Oct 8, we will break early for an optional hike in Tilden Park.<br />
<br />
On Thursday, Oct 9, there will be an optional outing to the Exploratorium in San Francisco. The Exploratorium is open [https://www.exploratorium.edu/visit/calendar/after-dark Thursday evenings until 10pm for adults only (18+)]. To add to the fun, we'll take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] and then get dinner near there.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend! Don't forget to register and pay via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351%7C| Eventbrite].<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
|Judy Blake<br />
|JAX<br />
|Yes<br />
|Yes<br />
|Yes<br />
|Four Points<br />
|Yes<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| TBD<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| yes<br />
| yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Nash Hotel<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not booked yet<br />
| not yet<br />
|-<br />
| Adam Wright<br />
| OICR<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hilton Garden Inn<br />
| Yes<br />
|-<br />
| Justin Reese<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase, Northwestern<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not yet booked<br />
|<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Oakland airbnb<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| not yet<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| <br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| <br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| TBD<br />
| not yet<br />
|-<br />
| Suvarna Nadendla<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| TBD<br />
| not yet<br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=760672019 Berkeley GOC Meeting Logistics2019-08-28T17:08:56Z<p>Mlgwinn: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Berkeley, October 7-10, 2019=<br />
<br />
* Location: [https://goo.gl/maps/cfabKMyCSPZmFkFf7| 717 Potter Street, Berkeley, CA]<br />
<br />
==Registration==<br />
* Via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351| Eventbrite]--pay online with credit or debit card or Paypal<br />
* $130 registration fee covers coffee & snacks for the 2.5-day GOC meeting, as well as 2 lunches and the Consortium dinner on Oct 9 (not including alcoholic beverages)<br />
* Please also fill in the fields in the Attendees list at the bottom of this page. If you don't have edit permission, you can instead fill out [https://bit.ly/2019GOBerkeley this signup form].<br />
<br />
==Overall schedule== <br />
*Monday, October 7: User Meeting (8:30am-5pm)<br />
*Tuesday-Thursday October 8-10: GOC Meeting (8:30am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11 (time TBA): SAB Meeting, UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley). More details soon.<br />
<br />
=SAB Meeting=<br />
* Meeting: Friday, October 11 (time TBA) in Stanley Hall on the UC Berkeley campus. Logistics [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| here].<br />
* SAB dinner: Thursday, October 10, 7pm: place TBD<br />
<br />
=Arriving=<br />
<br />
The closest airports are San Francisco (SFO) and Oakland (OAK). From either of those, you can take BART to Berkeley and get a taxi/Lyft/Uber from the Ashby BART station.<br />
<br />
Scroll down to the "Getting around" section for more info.<br />
<br />
=Hotels=<br />
These are listed in increasing order by price. The Four Points by Sheraton is the only one that's walking distance (1.4 miles) from the meeting location; the others are downtown, a short drive away. [https://docs.google.com/document/d/1DaSiBXlW6gjH840h9kdC3FVbuVuetqglcsgrDvB7maE/edit| This map] shows the relative locations of the hotels.<br />
<br />
For travel to our building, we will arrange for attendees to have access to the LBNL Potter St. shuttle to our building from downtown Berkeley.<br />
<br />
===[http://downtownberkeleyinn.com/| Downtown Berkeley Inn]===<br />
* '''Address''': 2001 Bancroft Way, Berkeley (2.4 miles from the meeting location)<br />
* '''Phone''': (510) 843-4043<br />
* '''Rate''': LBNL rate is $129/night (normal rate $139/night).<br />
* '''How to book''': Phone (don't book online) and ask for “LBL” or “Gene Ontology” room block.<br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': Very basic, but adequate.<br />
* '''Advantages''': Cheapest option. Fairly close to downtown Berkeley.<br />
<br />
===[https://www.marriott.com/hotels/travel/sfofp-four-points-san-francisco-bay-bridge/| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the meeting location),<br />
* '''Phone''': 1-800-325-3535<br />
* '''Rate''': $175/night (single or double) block rate for “Gene Ontology / GO meeting”.<br />
* '''How to book''': Book using this link: https://www.marriott.com/events/start.mi?id=1563407776453&key=GRP or call 1-800-325-3535 and ask for the “Gene Ontology” room block. <br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': A normal hotel. Has an outdoor pool and a fitness center.<br />
* '''Advantages''': Closest hotel to meeting location.<br />
<br />
===[https://www.graduatehotels.com/berkeley/| The Graduate] (formerly the Hotel Durant)===<br />
* '''Address''': 2600 Durant Ave, Berkeley (2.9 miles from the meeting location)<br />
* '''Phone''': 510-845-8981<br />
* '''Rate''': Average of $210/night for a room with one queen.<br />
* '''How to book''': No special rates; you can book [https://www.graduatehotels.com/berkeley| online]<br />
* '''Description''': No pool or fitness center. More distinctive than the similarly-priced Hotel Shattuck Plaza. A recent article about The Graduate noted, "Berkeley's quirky counterculture is represented by bong-shaped lamps in the guestrooms and a restroom urinal painted with the logo and colors of Stanford, Cal-Berkeley’s arch-rival." Known for having made a brief appearance in the movie of the same name.<br />
* '''Advantages''': Near UC Campus and Telegraph Avenue, a colorful if slightly sketchy part of Berkeley.<br />
<br />
===[http://www.hotelshattuckplaza.com| Hotel Shattuck Plaza]===<br />
* '''Address''': 2086 Allston Way, Berkeley (2.5 miles from the meeting location)<br />
* '''Phone''': 866-466-9199<br />
* '''Rate''': UC Berkeley rate: $215/night. Same price for double or single. <br />
* '''How to book''': You will need to phone and ask for the UC Berkeley rate--not available online.<br />
* '''Description''': A more upscale hotel than the previous three, it was completely remodeled a few years ago. Has a fitness center but no pool.<br />
* '''Advantages''': Right in the heart of downtown Berkeley, near BART, Potter St. shuttle, and many world-class restaurants<br />
<br />
= Getting around / To do / Local activities =<br />
<br />
The organizers have lived in the area for a very long time. If you have *any* questions, do not hesitate to reach out to us and let us make your stay in the Bay Area more more pleasant.<br />
<br />
== Getting around ==<br />
<br />
The LBL Potter Street site is located near a highway in a mixed business park and light industrial area.<br />
<br />
=== Walking ===<br />
<br />
Walking from the Emeryville hotel (Four Points Sheraton) to the meeting site is doable, but not necessarily a "pleasant" walk. It takes about half an hour.<br />
<br />
Walking from downtown is not advised and would take about an hour.<br />
<br />
=== By car (inc. "rideshare") ===<br />
<br />
If you are driving to the GO meeting, parking should not be an issue--while there will be no on-site parking, there is usually plenty of on-street parking in the surrounding area if you can walk a little. If you intend on driving, contact Seth or Nomi for details.<br />
<br />
The are usually plenty of Lyfts and Ubers in the area. The downtown area is about 10-12 minutes away.<br />
<br />
=== By public transportation ===<br />
<br />
==== From downtown ====<br />
<br />
===== LBL shuttle =====<br />
<br />
There is a fairly frequent LBL shuttle that directly connects downtown Berkeley area and the Potter Street site:<br />
<br />
https://commute.lbl.gov/resource/shuttle-buses/maps-routes-schedules/potter-st-jbei-route/<br />
<br />
You will need to show an LBL guest pass to board this shuttle. We can provide these on request--contact Seth or Nomi. The shuttle is often a 15-person van, so large groups may need to split up at peak times.<br />
<br />
===== Bus (AC Transit) =====<br />
<br />
There is also a bus that departs from near downtown and the Durant hotel and has a stop quite near the Potter Street site:<br />
<br />
http://www.actransit.org/maps/schedule_results.php?quick_line=36&Go=Go<br />
<br />
==== From Emeryville ====<br />
<br />
While it does not run directly by the hotel, one would need to walk a little and cross a bridge over the tracks, there is a free public shuttle that runs from near the hotel to near the Potter Street site: The Emery Go-round ():<br />
<br />
https://www.emerygoround.com/standard-service.html<br />
<br />
=== Biking and scootering ===<br />
<br />
The are is fairly well served by various "last mile" solutions.<br />
<br />
Rental bikes (now Lyft, previously Ford GoBikes) are available at various locations (https://member.baywheels.com/map/), including downtown Berkeley and near the meeting site (next to the Berkeley Bowl grocery store).<br />
<br />
==Food and drinks==<br />
<br />
=== Overview ===<br />
<br />
Downtown Berkeley has lots of places to eat. The LBL Potter Street location is much more limited for cafes and restaurants, but there is a large supermarket with a cafe (Berkeley Bowl) a few blocks away. Ubereats and the like are always an option for people wanting more variety and many of the organizers will have vehicles and may be doing various errands about town anyways, if there is something in particular you want or need.<br />
<br />
Seth will be happy to talk nearly endlessly about local restaurant, bar, and tea/cafe opportunities.<br />
<br />
==Exercise==<br />
<br />
For people interested in hitting the gym or swimming, the UC Berkeley recreational facilities are open to the general public with day passes:<br />
<br />
https://recsports.berkeley.edu/day-passes/<br />
<br />
The main rec facility and pool location is a short walk from downtown Berkeley. Several of the satellite pools have reduced day pass rates.<br />
<br />
==Things to do in the Berkeley area==<br />
The popular [http://www.hardlystrictlybluegrass.com/2019/ "Hardly Strictly Bluegrass" festival] (which leans more towards alternative rock than bluegrass) will take place in San Francisco, Fri-Sun October 4-6.<br />
<br />
On Wednesday, Oct 8, we will break early for an optional hike in Tilden Park.<br />
<br />
On Thursday, Oct 9, there will be an optional outing to the Exploratorium in San Francisco. The Exploratorium is open [https://www.exploratorium.edu/visit/calendar/after-dark Thursday evenings until 10pm for adults only (18+)]. To add to the fun, we'll take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] and then get dinner near there.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend! Don't forget to register and pay via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351%7C| Eventbrite].<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
|Judy Blake<br />
|JAX<br />
|Yes<br />
|Yes<br />
|Yes<br />
|Four Points<br />
|Yes<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| TBD<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| yes<br />
| yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Nash Hotel<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not booked yet<br />
| not yet<br />
|-<br />
| Adam Wright<br />
| OICR<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hilton Garden Inn<br />
| Yes<br />
|-<br />
| Justin Reese<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase, Northwestern<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not yet booked<br />
|<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Oakland airbnb<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| not yet<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| <br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| <br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| TBD<br />
| not yet<br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Logistics&diff=711392018 Montreal GOC Meeting Logistics2018-08-31T15:53:29Z<p>Mlgwinn: /* Attendees */</p>
<hr />
<div><br />
=Start and end of meeting=<br />
* Main meeting starts on: Wednesday October 17, 8h30 AM<br />
* Meeting ends on Friday October 19th, 4 PM <br />
<br />
=Registration fee=<br />
To be announced <br />
<br />
=Meeting site=<br />
'''Université du Québec à Montreal (UQAM), Pavillon Président-Kennedy'''<br />
* 201 Avenue du Président-Kennedy, Montréal, QC H2X 3Y7<br />
* Location: https://goo.gl/V1ZrsJ<br />
<br />
=Call-in information=<br />
To be announced<br />
<br />
=Travel=<br />
<br />
remember to get a Canadian [https://www.canada.ca/en/immigration-refugees-citizenship/services/visit-canada/eta.html?utm_source=slash-eta_ave&utm_medium=short-url-en&utm_campaign=eta eTA] $7<br />
<br />
=Accommodations=<br />
<br />
Two options: Delta Hotel and Hotel Zero1<br />
<br />
==1) Delta Hotel Montreal==<br />
* https://www.marriott.com/hotels/travel/yuldb-delta-hotels-montreal/<br />
* '''Address:''' 475 President-Kennedy Avenue, Montreal, QC H3A 1J7<br />
* '''Directions to meeting venue:''' https://goo.gl/ha8fay<br />
* '''Phone:''' 1 (514) 286-1986<br />
* '''Reservation:''' Call Marriott Reservations at 1 (844) 860-3753 or use this link: <br />
https://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=UQAM%20GO%20Meeting%202018^yuldb`q78q78z`188.00`CAD`false`4`10/15/18`10/21/18`9/18/18&app=resvlink&stop_mobi=yes<br />
<br />
** Book under: UQAM GO Meeting 2018<br />
** All reservations must be guaranteed with a major credit card.<br />
* '''Rate available until Tuesday, September 18, 2018'''. <br />
* '''Cancellation policy''': Individual reservations may be cancelled up until 48 hours local time prior to arrival with no penalty. Cancellations received after this time will be subject to one night’s room & tax, applied to the credit card used to guarantee the reservation.<br />
* '''Rates for October 16th-19th (rates are valid from Oct 15th to the 20th (checkout on the 21st))'''<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Room Type <br />
! Daily rate (excl tax)<br />
! Daily rate (incl tax; estimate)<br />
|-<br />
| Single/Double<br />
| CAN $188<br />
| CAN $222<br />
|-<br />
| Triple<br />
| CAN $208 <br />
| CAN $246<br />
|-<br />
| Quad<br />
| CAN $228<br />
| CAN $270<br />
|-<br />
|}<br />
<br />
<br />
'''Rate includes: '''<br />
* Free WiFi in room (+ wires) and WiFi in all public areas<br />
* Breakfast not included<br />
* Gym<br />
* Parking available: On-site parking: CAN $ 26.50 daily; Valet parking: CAN $32 daily<br />
<br />
==2) Hotel Zero1 Montreal== <br />
* http://www.zero1-mtl.com/en/default.html<br />
* '''Address:''' 1 RenéLévesque Est Montréal QC H2X 3Z5<br />
* '''Directions to meeting venue:''' https://goo.gl/1BkxYh<br />
* '''Phone:''' 1 (514) 871-9696 / 1 (855) 301-0001<br />
* '''Reservation:''' Call the hotel at 1 (514) 871-9696 / 1 (855) 301-0001<br />
** Book under: GO meeting at UQAM<br />
** All reservations must be guaranteed with a major credit card.<br />
* '''Rate available until September 8st, 2018'''. <br />
* '''Cancellation policy''': Inform the hotel in writing 48 hours prior to arrival date. If no notice is received, a penalty of one night (including all taxes) will be charged on the credit card on file (no show). <br />
* Upon arrival of the participant at the hotel, a deposit corresponding to the total accommodation fees (including taxes) + a security deposit will be due. <br />
* '''Rates for October 16th-19th (rates are valid from Oct 13th to the 24th)'''<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Room Type <br />
! Daily rate (excl tax)<br />
! Daily rate (incl tax; estimate)<br />
|-<br />
| "Pop room" - 1 queen bed <br />
| CAN $169<br />
| CAN $200<br />
|-<br />
|}<br />
<br />
'''Rate includes: '''<br />
* Free WiFi in room and all public areas<br />
* Free local calls<br />
* Shower only<br />
* Gym (seems small)<br />
* American buffet breakfast included at the Z Tapas Lounge<br />
* Valet service available for CAN $28.00/day + applicable taxes.<br />
<br />
=Food=<br />
* World-famous Montreal bagels: [http://www.stviateurbagel.com/ St. Viateur] and [https://fairmountbagel.com/ Fairmount Bagel] (both opened 24 hours, in case you need a 3 am warm snack)<br />
* World-famous Montreal smoked meat: [http://www.schwartzsdeli.com/ Schwartzs Deli]<br />
* Poutine: [http://labanquise.com/ La Banquise] (opened 24h) and [https://www.yelp.ca/biz/chez-claudette-montr%C3%A9al Chez Claudette] (opened 24h Thu-Sat)<br />
* Croissants and Kouign-Amann: [https://www.yelp.ca/biz/au-kouign-amann-montr%C3%A9al-2 Au Kouign-Amann]<br />
* [http://dieuduciel.com/en/ Dieu du Ciel] microbrewery <br />
* [http://saintbock.com/ Saint Bock] microbrewery<br />
* [http://www.brasseriebenelux.com/ Benelux] artisanal brewery<br />
<br />
=Bicycling and walking / running=<br />
* The venue is less than 1 km away from [https://goo.gl/v5fyYq Parc Mont Royal], great for walking and running (and biking if you like small hills)<br />
* [https://goo.gl/maps/6kscfTfshhw Parc La Fontaine]<br />
* [https://www.yelp.ca/search?cflt=bikerentals&find_loc=Montreal%2C+QC Bike rental] places<br />
* If you have an afternoon, rent a bike or roller blades in the Old port and bike the Canal Lachine<br />
<br />
=To do and see=<br />
* [https://www.quartierdesspectacles.com/en/ Quartier des spectacles] (the venue is right in that neighborhood)<br />
* Rue [http://www.ruesaintdenis.ca/en/ Saint-Denis]<br />
* Boulevard [http://boulevardsaintlaurent.com/en/ Saint-Laurent] ("La Main")<br />
* [https://localfoodtours.com/montreal/10-things-to-do-in-the-mile-end-montreal/ Mile End neighbourhood] (a couple of km North/East of the venue; very trendy right now)<br />
* [http://www.oldportofmontreal.com/ Old port]<br />
* [https://www.mtl.org/en/explore/neighbourhoods/old-montreal Old Montreal]<br />
* [https://www.marchespublics-mtl.com/en/marches/jean-talon-market/ Jean Talon Market]<br />
* [https://www.marchespublics-mtl.com/en/marches/atwater-market/ Atwater Market]<br />
* [https://www.saint-joseph.org/en/ Saint Joseph's Oratory] of Mount Royal<br />
* [https://www.basiliquenotredame.ca/en Notre-Dame Basilica]<br />
* [http://espacepourlavie.ca/en/botanical-garden Botanical Garden]<br />
* [https://www.mbam.qc.ca/en/ Montreal Museum of Fine Arts]<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting, and the dinner, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name <br />
! Organization <br />
! Attend the GOC dinner (Thursday 18th)? <br />
! Food restrictions<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GO Central<br />
| Yes<br />
| <br />
|-<br />
| Val Wood<br />
| PomBase<br />
| Yes<br />
| <br />
|-<br />
| Suzanna Lewis<br />
| BBOP/LBNL<br />
| Yes<br />
| <br />
|-<br />
| Seth Carbon<br />
| BBOP/LBNL<br />
| Yes<br />
| <br />
|-<br />
| David Hill (leaving early 10/19)<br />
| GOC/MGI<br />
| Yes? Yes :)<br />
|<br />
|-<br />
| Harold Drabkin<br />
| MGI/GO/PRO<br />
| Yes<br />
|<br />
|-<br />
| Mary Dolan<br />
| MGI/GO<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Yes<br />
| Vegetarian preferred<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
|<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
|<br />
|--<br />
| Tony Sawford<br />
| EBI<br />
| Yes<br />
| <br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
|-<br />
| Alex Ignachenko<br />
| EBI<br />
| Yes<br />
| <br />
|--<br />
| Sandra Orchard<br />
| EBI<br />
| Yes<br />
| <br />
|--<br />
| Maria Martin<br />
| EBI<br />
| Yes<br />
| <br />
|--<br />
| Laurent-Philippe Albou<br />
| USC / LBNL<br />
| Yes<br />
| <br />
|--<br />
| Debby Siegele<br />
| TAMU<br />
| Yes<br />
|<br />
|--<br />
| Sandy LaBonte<br />
| TAMU<br />
| Yes<br />
|<br />
|--<br />
| Jim Hu<br />
| TAMU<br />
| Yes<br />
|<br />
|--<br />
| Tanya Berardini<br />
| TAIR/Phoenix<br />
| Yes<br />
|--<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Fish and Vegetarian<br />
|--<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
|<br />
|--<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Fish and Vegetarian<br />
|--<br />
| Liz Bolton<br />
| RGD<br />
| Yes<br />
| Fish and Vegetarian<br />
|--<br />
| Paul Thomas<br />
| GOC-USC<br />
| Yes<br />
| <br />
|--<br />
| Michelle Giglio<br />
| IGS/UMB<br />
| Yes<br />
|<br />
|--<br />
|}<br />
<br />
=Remote attendees=<br />
If you plan to attend remotely, please sign up here and indicate the sessions you are likely to attend:<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name <br />
! Organization <br />
|-<br />
|}<br />
<br />
[[Category: GO Consortium Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Logistics&diff=682602018 NYU GOC Meeting Logistics2018-03-22T19:35:39Z<p>Mlgwinn: /* Attendees */</p>
<hr />
<div>More details will be available in the next few weeks. Meanwhile, here is some information to help you make travel arrangements. The meeting will start first thing on Saturday May 12 (so plan to arrive on Friday) and will end on Monday May 14 early enough in the afternoon to allow people to get to the airport for overnight flights to Europe.<br><br>See you in May!<br />
<br />
==Registration fee==<br />
Amount and payment details to be determined, but we hope to keep the amount low and find a convenient way to pay.<br />
<br />
==Meeting site==<br />
Translational Research Building, 227 East 30th Street, in the Murray Hill neighborhood of Manhattan. You'll need an official ID (passport, driver's license) to get into the building; the meeting room is immediately on your left at street level.<br />
<br />
=Travel=<br />
Kennedy and Newark Airports both are workable for long-distance flights; Kennedy is somewhat more convenient. LaGuardia Airport is closest to Manhattan but is accessible only by taxi or ride-sharing, or by incredibly inconvenient public transportation.<br />
==[https://www.jfkairport.com/#/ Kennedy Airport] details==<br />
You can get into Manhattan by taxi (up to four people can share a cab for a flat fare plus tolls and tip), or ride-sharing (Uber, Lyft, etc.), or by public transportation, which is fast (about an hour) and cheap ($7.75 per person). Here's how to do it: follow the signs in the terminal to the [https://www.jfkairport.com/#/to-from-airport/air-train AirTrain]. Take an AirTrain to Jamaica. To get off the AirTrain platform, you'll need to buy a MetroCard from a vending machine. If you'll be using the card only to travel to and from the airport, put $15.50 on the card; more if you'll be using the subway to get around New York ($2.75 per ride). Once you're off the AirTrain platform in Jamaica, follow the signs past the Jamaica Long Island Train station (overpass) to an elevator to the subway. Swipe your card again to get into the subway, and take an "E" train in the direction of Manhattan / World Trade Center. At Lexington Avenue / 53rd Street, get off the "E" train and follow the signs to transfer to a "6" train going downtown to Brooklyn Bridge / City Hall. Ride two stops to 33rd Street. Go up to the street (Park Avenue South), walk on Park Avenue South to 37th Street, turn left, walk one block to Lexington Avenue, and the Shelburne Hotel will be on your left on the far side of the street. If you're less adventurous, you can instead take the Long Island Railroad train from Jamaica to Penn Station (buy ticket from vending machine before getting on the train), and walk from Penn Station to the hotel.<br />
==[https://www.newarkairport.com/#/ Newark Airport] details==<br />
You can get into Manhattan by taxi or ride-sharing, or by public transportation, which takes longer and costs more than it does from Kennedy but is still reliable. Follow signs in the terminal to the [https://www.newarkairport.com/#/to-from-airport/air-train air-train]. There's only one choice; it takes you to the Newark Airport Station for Amtrak and New Jersey Transit. From a vending machine, get a combined one-way ticket that will allow you to get off the air-train platform and on to a New Jersey Transit train into New York Penn Station. (Amtrak trains are much more expensive and, for this trip, hardly faster.)<br />
<br />
==[http://laguardiaairport.com/ LaGuardia Airport] details==<br />
There is no good public transportation from LaGuardia Airport into Manhattan. Use a taxi (up to four people can share for the same fare) or ride-sharing service.<br />
<br />
==By train==<br />
Amtrak Northeast Corridor trains (Boston - New York - Washington) all stop at Penn Station as do the Long Island Railroad train from Kennedy / Jamaica or the New Jersey transit train from Newark. To get from Penn Station to the hotel, follow signs inside the station to 7th Avenue. You'll go up a long flight of stairs or escalator to leave the station and come upon a taxi queue. Take a taxi to the hotel or cross 7th Avenue and walk away from the station on 32nd Street until you get to Lexington Avenue, then turn left and walk to 37th Street to get to the hotel (0.8 mile, about 20 minutes per Google).<br />
<br />
==By car==<br />
Try not to. Manhattan is incredibly congested (average speed achieved by cars on weekdays is 4.7 miles per hour) and parking anywhere near the meeting site is incredibly expensive.<br />
<br />
=Accommodations=<br />
New York is a large, busy city with many hotels but mid-May is a popular time (graduation week for many local universities). We have a block of rooms at the [[media:Shelburne Hotel Brochure.pdf | Shelburne NYC]] (a 10 minute half-mile walk from the meeting venue, comfortable, and very convenient to public transportation). They will only hold rooms until April 6, so book early. Rooms have been reserved for arrival on Friday May 11 and departure on Monday May 14 or Tuesday May 15. You can book a room online [https://gc.synxis.com/rez.aspx?Hotel=10146&Chain=5158&Dest=NYC&shell=2014GCF&group=1805NYUMEDI here] or by phone at 866-233-4642 - identify yourself as part of the GO Consortium (NYU Medical) Room Block to guarantee the special rate. The room rate is $289 nightly ($249 + taxes), a very good rate for a room with free WiFi and private bath.<br />
<br />
*'''note: people should book at this hotel rather than at a separate one since we have a block booking'''<br />
<br />
*'''note: if you have any difficulty making your hotel booking, contact Peter D'E (deustp01@med.nyu.edu) immediately for help'''<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting, and the dinner (Sunday), so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name <br />
! Organization <br />
! Attend the GOC meeting? <br />
! Attend the GOC dinner? <br />
<br />
<br />
<br />
|-<br />
| Tony Sawford<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| George Georghiou<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Michele Magrane<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Penelope Garmiri<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Maria Martin<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Alex Ignatchenko<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Suzanna Lewis<br />
| GO@LBNL<br />
| Yes<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI/GOC<br />
| Yes<br />
| No<br />
|-<br />
|Judy Blake<br />
| MGI/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Mary Dolan<br />
| MGI/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Li NI<br />
| MGI/GOC<br />
| Yes (Saturday and Sunday)<br />
| No<br />
|-<br />
|Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
|Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
|Stacia Engel<br />
| SGD Stanford<br />
| Yes<br />
| Yes<br />
|-<br />
|Mike Cherry<br />
| SGD Stanford<br />
| Yes<br />
| Yes<br />
|-<br />
|Suzi Aleksander<br />
| SGD Stanford<br />
| Yes<br />
| Yes<br />
|-<br />
|Helen Attrill<br />
| FlyBase, Cambridge UK<br />
| Yes<br />
| Yes<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase, Caltech<br />
|Yes<br />
|Yes<br />
|-<br />
|Sandra Orchard<br />
|EMBL-EBI<br />
|Yes<br />
|No<br />
|-<br />
|Petra Fey<br />
|dictyBase, Northwestern<br />
|Yes<br />
|Yes<br />
|-<br />
|Ruth Lovering<br />
|University College London<br />
|Yes<br />
|Yes<br />
|-<br />
|Benjamin Good<br />
|LBNL<br />
|Yes<br />
|Yes<br />
|-<br />
|Chris Mungall<br />
|LBNL<br />
|Yes<br />
|Yes<br />
|-<br />
|Tom Hayman<br />
|RGD<br />
|Yes<br />
|Yes<br />
|-<br />
|Jim Balhoff<br />
|RENCI<br />
|Yes<br />
|Yes<br />
|-|-<br />
|Sabrina Toro<br />
|ZFIN<br />
|Yes<br />
|No<br />
|-<br />
|Michelle Giglio<br />
|IGS at U MD School of Medicine<br />
|Yes (Sunday and Monday)<br />
|Yes<br />
|-<br />
|Suvvi Nadendla<br />
|IGS at U MD School of Medicine<br />
|Yes<br />
|No<br />
|-<br />
|Becky Tauber<br />
|IGS at U MD School of Medicine<br />
|Yes<br />
|<br />
|-<br />
|}<br />
<br />
If you plan to attend remotely, please sign up here and indicate the sessions you are likely to attend:<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Saturday AM<br />
! Saturday PM<br />
! Sunday AM<br />
! Sunday PM<br />
! Monday AM<br />
|-<br />
| Birgit Meldal<br />
| EBI<br />
| no<br />
| no<br />
| no<br />
| maybe<br />
| maybe<br />
|-<br />
| Li Ni<br />
| MGI<br />
| no<br />
| no<br />
| no<br />
| no<br />
| yes<br />
|-<br />
|}<br />
<br />
AM sessions will start at approximately 9 AM EDT / 2 PM BST / 6 AM PDT; PM sessions will start at approximately 2 PM EDT / 7 PM BST / 11 AM PDT.<br />
<br />
[[Category: GO Consortium Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Logistics&diff=682592018 NYU GOC Meeting Logistics2018-03-22T19:10:52Z<p>Mlgwinn: /* Attendees */</p>
<hr />
<div>More details will be available in the next few weeks. Meanwhile, here is some information to help you make travel arrangements. The meeting will start first thing on Saturday May 12 (so plan to arrive on Friday) and will end on Monday May 14 early enough in the afternoon to allow people to get to the airport for overnight flights to Europe.<br><br>See you in May!<br />
<br />
==Registration fee==<br />
Amount and payment details to be determined, but we hope to keep the amount low and find a convenient way to pay.<br />
<br />
==Meeting site==<br />
Translational Research Building, 227 East 30th Street, in the Murray Hill neighborhood of Manhattan. You'll need an official ID (passport, driver's license) to get into the building; the meeting room is immediately on your left at street level.<br />
<br />
=Travel=<br />
Kennedy and Newark Airports both are workable for long-distance flights; Kennedy is somewhat more convenient. LaGuardia Airport is closest to Manhattan but is accessible only by taxi or ride-sharing, or by incredibly inconvenient public transportation.<br />
==[https://www.jfkairport.com/#/ Kennedy Airport] details==<br />
You can get into Manhattan by taxi (up to four people can share a cab for a flat fare plus tolls and tip), or ride-sharing (Uber, Lyft, etc.), or by public transportation, which is fast (about an hour) and cheap ($7.75 per person). Here's how to do it: follow the signs in the terminal to the [https://www.jfkairport.com/#/to-from-airport/air-train AirTrain]. Take an AirTrain to Jamaica. To get off the AirTrain platform, you'll need to buy a MetroCard from a vending machine. If you'll be using the card only to travel to and from the airport, put $15.50 on the card; more if you'll be using the subway to get around New York ($2.75 per ride). Once you're off the AirTrain platform in Jamaica, follow the signs past the Jamaica Long Island Train station (overpass) to an elevator to the subway. Swipe your card again to get into the subway, and take an "E" train in the direction of Manhattan / World Trade Center. At Lexington Avenue / 53rd Street, get off the "E" train and follow the signs to transfer to a "6" train going downtown to Brooklyn Bridge / City Hall. Ride two stops to 33rd Street. Go up to the street (Park Avenue South), walk on Park Avenue South to 37th Street, turn left, walk one block to Lexington Avenue, and the Shelburne Hotel will be on your left on the far side of the street. If you're less adventurous, you can instead take the Long Island Railroad train from Jamaica to Penn Station (buy ticket from vending machine before getting on the train), and walk from Penn Station to the hotel.<br />
==[https://www.newarkairport.com/#/ Newark Airport] details==<br />
You can get into Manhattan by taxi or ride-sharing, or by public transportation, which takes longer and costs more than it does from Kennedy but is still reliable. Follow signs in the terminal to the [https://www.newarkairport.com/#/to-from-airport/air-train air-train]. There's only one choice; it takes you to the Newark Airport Station for Amtrak and New Jersey Transit. From a vending machine, get a combined one-way ticket that will allow you to get off the air-train platform and on to a New Jersey Transit train into New York Penn Station. (Amtrak trains are much more expensive and, for this trip, hardly faster.)<br />
<br />
==[http://laguardiaairport.com/ LaGuardia Airport] details==<br />
There is no good public transportation from LaGuardia Airport into Manhattan. Use a taxi (up to four people can share for the same fare) or ride-sharing service.<br />
<br />
==By train==<br />
Amtrak Northeast Corridor trains (Boston - New York - Washington) all stop at Penn Station as do the Long Island Railroad train from Kennedy / Jamaica or the New Jersey transit train from Newark. To get from Penn Station to the hotel, follow signs inside the station to 7th Avenue. You'll go up a long flight of stairs or escalator to leave the station and come upon a taxi queue. Take a taxi to the hotel or cross 7th Avenue and walk away from the station on 32nd Street until you get to Lexington Avenue, then turn left and walk to 37th Street to get to the hotel (0.8 mile, about 20 minutes per Google).<br />
<br />
==By car==<br />
Try not to. Manhattan is incredibly congested (average speed achieved by cars on weekdays is 4.7 miles per hour) and parking anywhere near the meeting site is incredibly expensive.<br />
<br />
=Accommodations=<br />
New York is a large, busy city with many hotels but mid-May is a popular time (graduation week for many local universities). We have a block of rooms at the [[media:Shelburne Hotel Brochure.pdf | Shelburne NYC]] (a 10 minute half-mile walk from the meeting venue, comfortable, and very convenient to public transportation). They will only hold rooms until April 6, so book early. Rooms have been reserved for arrival on Friday May 11 and departure on Monday May 14 or Tuesday May 15. You can book a room online [https://gc.synxis.com/rez.aspx?Hotel=10146&Chain=5158&Dest=NYC&shell=2014GCF&group=1805NYUMEDI here] or by phone at 866-233-4642 - identify yourself as part of the GO Consortium (NYU Medical) Room Block to guarantee the special rate. The room rate is $289 nightly ($249 + taxes), a very good rate for a room with free WiFi and private bath.<br />
<br />
*'''note: people should book at this hotel rather than at a separate one since we have a block booking'''<br />
<br />
*'''note: if you have any difficulty making your hotel booking, contact Peter D'E (deustp01@med.nyu.edu) immediately for help'''<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting, and the dinner (Sunday), so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name <br />
! Organization <br />
! Attend the GOC meeting? <br />
! Attend the GOC dinner? <br />
<br />
<br />
<br />
|-<br />
| Tony Sawford<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| George Georghiou<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Michele Magrane<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Penelope Garmiri<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Maria Martin<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Alex Ignatchenko<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Suzanna Lewis<br />
| GO@LBNL<br />
| Yes<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI/GOC<br />
| Yes<br />
| No<br />
|-<br />
|Judy Blake<br />
| MGI/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Mary Dolan<br />
| MGI/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Li NI<br />
| MGI/GOC<br />
| Yes (Saturday and Sunday)<br />
| No<br />
|-<br />
|Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
|Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
|Stacia Engel<br />
| SGD Stanford<br />
| Yes<br />
| Yes<br />
|-<br />
|Mike Cherry<br />
| SGD Stanford<br />
| Yes<br />
| Yes<br />
|-<br />
|Suzi Aleksander<br />
| SGD Stanford<br />
| Yes<br />
| Yes<br />
|-<br />
|Helen Attrill<br />
| FlyBase, Cambridge UK<br />
| Yes<br />
| Yes<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase, Caltech<br />
|Yes<br />
|Yes<br />
|-<br />
|Sandra Orchard<br />
|EMBL-EBI<br />
|Yes<br />
|No<br />
|-<br />
|Petra Fey<br />
|dictyBase, Northwestern<br />
|Yes<br />
|Yes<br />
|-<br />
|Ruth Lovering<br />
|University College London<br />
|Yes<br />
|Yes<br />
|-<br />
|Benjamin Good<br />
|LBNL<br />
|Yes<br />
|Yes<br />
|-<br />
|Chris Mungall<br />
|LBNL<br />
|Yes<br />
|Yes<br />
|-<br />
|Tom Hayman<br />
|RGD<br />
|Yes<br />
|Yes<br />
|-<br />
|Jim Balhoff<br />
|RENCI<br />
|Yes<br />
|Yes<br />
|-|-<br />
|Sabrina Toro<br />
|ZFIN<br />
|Yes<br />
|No<br />
|-<br />
|Michelle Giglio<br />
|IGS at U MD School of Medicine<br />
|Yes (Sunday and Monday)<br />
|Yes<br />
|-<br />
|}<br />
<br />
If you plan to attend remotely, please sign up here and indicate the sessions you are likely to attend:<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Saturday AM<br />
! Saturday PM<br />
! Sunday AM<br />
! Sunday PM<br />
! Monday AM<br />
|-<br />
| Birgit Meldal<br />
| EBI<br />
| no<br />
| no<br />
| no<br />
| maybe<br />
| maybe<br />
|-<br />
| Li Ni<br />
| MGI<br />
| no<br />
| no<br />
| no<br />
| no<br />
| yes<br />
|-<br />
|}<br />
<br />
AM sessions will start at approximately 9 AM EDT / 2 PM BST / 6 AM PDT; PM sessions will start at approximately 2 PM EDT / 7 PM BST / 11 AM PDT.<br />
<br />
[[Category: GO Consortium Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=652222017 Cambridge GOC Meeting Logistics2017-09-25T16:10:12Z<p>Mlgwinn: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: 8:30-9am Monday 2nd October at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
*The meeting will be £120 in total (£85 for meeting only). Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
==Consortium dinner ==<br />
<br />
*7:30pm, Tuesday 3rd October at [http://www.galleriacambridge.co.uk/ The Galleria Restaurant], 33 Bridge St, Cambridge CB2 1UW<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm.<br />
:** 12:30-1:30pm Lunch at the University Centre (paid for individually).<br />
:** 5:00-8:00pm Mixer:Posters & Pizza.<br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
:** 12:30-2:00pm Lunch (picnic/sandwiches)<br />
:** 7:30pm Consortium dinner (drinks paid for individually).<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 12:30pm.<br />
:** 12:30-1:30pm Lunch at the University Centre (paid for individually).<br />
:** Afternoon: Optional workshop(s)<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 (detailes 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, the dinner (Tuesday), so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you planning to bring a poster? (indicate number)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes, 3 perhaps 4<br />
|-<br />
| Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Chris Mungall<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Seth Carbon<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Eric Douglass<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Nick Brown<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| No<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-UniProt, GOA, IntAct<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| No<br />
|<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mary Dolan<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Paul Thomas<br />
| GOC/USC<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| GOC/neXtProt <br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Shur-Jen Wang<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes, w/Liz, (1) signaling<br />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes, w/Shur-Jen, (1)<br />
|-<br />
| Kimberly Van Auken<br />
| WB/Caltech<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
|Michele Magrane <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Tony Sawford <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Penelope Garmiri <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|George Georghiou <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alex Ignatchenko <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Maria Martin <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
<br />
|- <br />
|Alan Bridge <br />
|SIB<br />
|Yes <br />
|Yes <br />
| Yes (1) <br />
|- <br />
|Marc Feuermann <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Patrick Masson <br />
|SIB<br />
|Yes <br />
|Yes <br />
|<br />
|- <br />
|Sylvain Poux <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|<br />
|- <br />
|Jacky Hayles <br />
|PomBase<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Huaiyu Mi<br />
|USC<br />
|Yes <br />
|Yes<br />
|<br />
|- <br />
|Astrid Laegreid<br />
|NTNU<br />
|Yes<br />
|Yes<br />
|No<br />
|<br />
|-<br />
|Marcio Luis Acencio<br />
|NTNU<br />
|Yes<br />
|Yes<br />
|Yes (1)<br />
|<br />
|-<br />
|Susan Tweedie <br />
| HGNC<br />
|Yes (Mon. only)<br />
|No<br />
|Yes (1)<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| TAMU/EcoliWiki<br />
| Yes<br />
| Yes<br />
| <br />
|-<br />
|}<br />
<br />
NOT attending (please indicate if you will attend remotely):<br />
<br />
Peter D'Eustachio<br /><br />
Doug Howe <br><br />
TAIR representative (Attending remotely)<br><br />
Harold Drabkin (Attending remotely)<br><br />
Moni Munoz-Torres<br> <br />
Alice Shypitsyna<br><br />
Rebecca Tauber (for ECO) (Attending remotely)<br><br />
<br />
=Accommodations=<br />
*Cambridge is a small, busy city and accommodation is limited. Please book early, as the beginning of October is drop-off time for the students and lots of worried-looking parents will be in town.<br />
<br />
<br />
*We have a block allocation of rooms at The Royal Hotel (5-10 min walk from the meeting venue). They will only hold until the 1st August, so book early! The allocation is from the Sunday 1st-Thurs 5th. After this date the rooms will not be held but can still be booked at the discounted rate. There are an extra 10 rooms allocated for 30th September for those attending the signalling workshop.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631, email: reservations.cambridge@sjhotels.co.uk<br />
**The special room rate for the The Royal Cambridge Hotel cannot be accessed via the hotel website. Please contact the hotel directly via email or phone.<br />
** To book phone +44 (0)1223 351631 or e-mail reservations.cambridge@sjhotels.co.uk. To get the discount rate, please quote CAMB63710<br />
** Rates:<br />
*** twin/double room - £160 per room per night included breakfast and VAT<br />
*** single room - £130 per person per night included breakfast and VAT<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. Quote University of Cambridge code LCCUNI to get a discounted rate (~£210-£220/night). Approx. 30 minute walk to meeting venue.<br />
**[http://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree by Hilton.] Granta Place Mill Lane, Cambridge, CB2 1RT, United Kingdom TEL: +44 (0) 1223 259988. Located opposite the meeting venue, but has some building work going on at the moment and is on the more expensive side.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 5-10 min walk from the meeting venue. Approx. £200/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. Please keep in mind that, since the meeting will be in the first week of the University term, you may have some trouble in getting tables in some places.<br />
<br />
*[http://www.themillworks.co.uk/ Millworks]: really close to the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam.<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 more quiet<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>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Sign_Up_GOC2015&diff=56691Sign Up GOC20152015-04-21T15:38:08Z<p>Mlgwinn: /* Attendees */</p>
<hr />
<div>[[Category:GO_Consortium_Meetings]]<br />
<br />
==Attendees==<br />
We would like to have an estimate of the interest to attend the GOC2015 Meeting in Washington DC. In order to better produce this estimate (to most accurately reserve rooms), we would like to kindly ask you to write your name on this table. This IS NOT the registration for the meeting, only a way for the GOC to have an idea of your intention to attend. Thank you very much for signing up!<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
|-<br />
| Moni Munoz-Torres<br />
| Lawrence Berkeley National Lab, BBOP<br />
|-<br />
| David Osumi-Sutherland<br />
| EBI<br />
|-<br />
| Paola Roncaglia<br />
| EBI<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
|-<br />
| possibly another UCL name<br />
| UCL<br />
|-<br />
| Harold Drabkin<br />
| MGI<br />
|-<br />
| Karen Christie<br />
| MGI<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
|-<br />
| Rex Chisholm<br />
| dictyBase<br />
|-<br />
| Michelle Giglio<br />
| Institute for Genome Sciences, U of MD Sch of Med<br />
<br />
|-)</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2010_GO_camp_Meeting_Logistics&diff=256682010 GO camp Meeting Logistics2010-03-17T15:09:52Z<p>Mlgwinn: /* Remote Attendees */</p>
<hr />
<div>=Dates=<br />
The 3rd GO annotation camp (3 days) will be held from June 16-18, 2010 (Wednesday-Friday). <br />
<br />
=Objectives=<br />
This annotation camp will be focused on updating and refining skills of existing GO biocurators including new GO biocurators in existing annotation groups and including the Swiss-Prot curation team. We hope members of each MOD will be represented. <br />
<br />
* '''Deliverables''': (1) final annotation documentation for each of the three annotation topics. <br />
**There will be a special emphasis on the reference genome project. Deliverable: (2) annotation propagation rules for the reference genome project. <br />
<br />
<br />
=Venue=<br />
Swiss Institute for Bioinformatics (SIB)<br/><br />
Centre Médical Universitaire (CMU)<br/><br />
1, rue Michel Servet<br/><br />
CH-1211 Geneva 4<br/><br />
Switzerland<br/><br />
<br />
=Registration=<br />
Register by entering your name in the Attendees section below ([[2010_GO_camp_Meeting_Logistics#Attendees]])<br />
<br />
We anticipate a minimal registration fee to cover lunch and coffee breaks but the amount is still to be announced (depends on funding).<br />
<br />
=Lodging Information=<br />
<br />
Hotel Adriatica [http://www.hotel-adriatica.com/ Hotel Adriatica]<br/><br />
21 rue Sautter<br/><br />
1205 Genève - SUISSE<br/><br />
Tel: +41-22-703 53 83<br/><br />
Fax: +41-22-703 53 88 <br/><br />
<br/><br />
15 single rooms from 15-19 june 2010 (04 nights)<br/><br />
Special prize CMU 2010, single room with breakfast: CHF 190.00 (instead of CHF 256.00).<br/><br />
Special prize CMU 2010, double room, double occupancy with breakfast: CHF 265.00 (instead de CHF 367.00).<br/><br />
this offer is valid until the 31 of March 2010<br/><br />
3 min. walking distance from the SIB<br/><br />
----<br />
Hotel Le Prince [http://www.hotel-le-prince.ch/ Hotel le Prince]<br/><br />
16 rue des Voisins<br/><br />
1205 Genève - SUISSE<br/><br />
Tel: +41-22-807 05 00<br/><br />
Fax: +41-22-320 28 70<br/><br />
<br/><br />
4 rooms left from the 15-19 june 2010 (04 nights)<br/><br />
2 double rooms: CHF 130.00 <br/><br />
2 twin rooms: CHF 115.00<br/><br />
10 min. walking distance from the SIB<br/><br />
---- <br />
Hotel Les Hauts de Rive [http://www.hotel-leshautsderive.ch/fr/ Hotel Les Hauts-de-Rive]<br/><br />
48, Boulevard des Tranchées<br/><br />
1206 Genève - SUISSE<br/><br />
Tel: +41-22-346 29 33<br/><br />
Fax: +41-22-346 22 11<br/><br />
<br/><br />
6 single/double rooms left from the 15-19 june 2010 (04 nights)<br/><br />
double rooms with breakfast: CHF 150.00 <br/><br />
single rooms with breakfast: CHF 120.00<br/><br />
11 min. walking distance from the SIB<br/><br />
----<br />
=Maps and Transportation=<br />
[http://www.isb-sib.ch/about-sib/how-to-find-us/geneva-english.html How to find the CMU]<br />
<br />
If you arrive by plane (Cointrin airport)<br/><br />
BUS:<br/><br />
You will have to take only one bus. The bus stop is in front of the airport on the check-in level. You must have your ticket before getting onto the bus. Beware, the ticket inspectors are heartless! There are machines at every bus stop. Only one ticket is needed: choose the option "tout genève" (cost: CHF 3.- or € 1.90.-, you need the exact change).<br/> <br />
'''Geneva Airport is now offering a free public transport tickets valid for 80 minutes to new arrivals. This free ticket can be taken from a machine in the baggage claim area. This ticket is only valid with your flight ticket to prove that you have arrived on that day.'''<br/><br />
So, take BUS NUMBER 5 (direction: "HÔPITAL"). The bus ride takes about 30 minutes. Get off at the bus terminus ("HÔPITAL").<br />
<br />
All visitors staying at a hotel, can benefit from the [http://www.geneve-tourisme.ch/?rubrique=0000000417 Geneva Transport Card], with no additional cost.<br />
This personal and non-transferable pass is established upon the visitor’s check-in in the hotel, enabling its holder to use of the entire public transportation network without restriction (bus, train and boat), with validity for the entire duration of his (her) stay including the departure day.<br />
<br />
[http://map.search.ch/geneve Geneva map] (Adress: 1, rue Michel Servet)<br />
<br />
<br />
=To do=<br />
<br />
[http://www.geneve-tourisme.ch/ Welcome to Geneva] <br />
<br />
The annual massive, city-wide festival which spans 3 days, with hundreds of musical performances will take place on the 18-20 of June.<br />
You can find a short article on the last year festival here: [http://switzerland-travel.suite101.com/article.cfm/genevas_fete_de_la_musique Geneva's Fête de la Musique 2009].<br />
<br />
[http://www.ville-ge.ch/culture/fm/ Fête de la Musique 2010] The program is not yet available.<br />
<br />
=[[2010_GO_camp_Meeting_Agenda | Agenda]]= <br />
'''Structure''': There will be '''three (3) ‘focused annotation sessions’''' where specific annotation issues will be discussed. Suggestion for discussion topics should be added to the GO camp agenda: [[2010_GO_camp_Meeting_Logistics#Focused annotation issues]]<br />
<br />
The agenda is not yet finalized.<br />
<br />
<br />
== Focused annotation issues==<br />
<br />
'''Please enter your name for participation in the working groups here: <br />
[[2010_GO_camp_working_groups_composition]]<br />
<br />
===1. Binding and complexes===<br />
<br />
====1.a. Binding documentation ====<br />
The binding group presented annotation policy suggestions at the last GO Consortium meeting [http://gocwiki.geneontology.org/index.php/Binding_terms_working_group#2010_discussion]<br />
These annotation guidelines should be finalized, and a full set of annotation guidelines on how annotation data is curated and presented in GAF files should be fully documented. <br />
For instance determine:<br />
* that binding annotations, especially those where the GO term does not specify a particular binding partner, should where possible, indicate the interacting partner in the 'with' column<br />
* fully describe the usage of pipes etc in the 'with' column.<br />
* ask that protein binding annotations should be reciprocal - that if protein A is annotated as binding protein B, the reverse annotation should be provided<br />
<br />
The use of column 16 to identify protein/gene targets of an molecular function GO annotation, could benefit this binding discussion.<br />
<br />
'''Working group'''<br />
(tentative) <br />
Emily, Donghui, Yasmin, Susan, Pascale, Ruth, Fiona, Lakshmi, Li, Serenella<br />
Please confirm here: [[2010_GO_camp_working_groups_composition]]<br />
----<br />
<br />
====1.b. Annotation of complexes====<br />
# Can IPI be used to annotate molecular function? For example ribosomal subunits are annotated to 'structural constituent of ribosome' (a function)<br />
# 'Structural components activity' function terms: some ribosome proteins are annotated to 'structural constituent of ribosome' by IDA (for example SGD:S000005760); but the paper (PMID: 18782943) only shows purification of the complex. <br />
# Chromatin? See NIPBL discussion from Feb 22 jamboree. The general question is when is a protein part of a complex or organelle or when it binds to it? <br />
# (Rama:) Interpretation of author statements: Authors very often use the word complex when two proteins are interacting, but there may not be enough evidence to show the existence of a stable complex. Should curators not add another layer of critiquing and request/annotate to the complex? How far should curators go with interpreting evidence and when should we let go thinking the reviewers are okay with that language, let us go with that.<br />
<br />
<br />
'''Working group'''<br />
(tentative)<br />
Pascale, Stan, Manu, Li, Serenella<br />
<br />
Please confirm here: [[2010_GO_camp_working_groups_composition]]<br />
----<br />
<br />
<br />
<br />
=== 2. Use of regulation ===<br />
<br />
* This would include process beginning/end (maybe in the context of the new signaling terms)<br />
* How to decide whether to annotate to 'regulates process x' or 'process x'? <br />
<br />
Notes: How do groups decide on when to annotate to 'regulates process x' or 'process x'? <br />
For instance does SLIT regulate axon guidance or involved in the process of axon guidance?<br />
Val - this depends on the defined start/end of a process and somethings can be annotated to BOTH the regulates term and also directly to the process term. <br />
Some groups decide that if removing the activity of a gene product produces an all/nothing event - then they define it as being part of the process.<br />
When should annotations be inherited up the regulates relationship?<br />
<br />
Notes: Annotations could be checked more efficiently if GO term definitions could include the beginning and end of a process.<br />
<br />
(Comment from Val: This is largely overlapping with the regulation issue. Where a process begins and ends is central to the decision to annotate directly to a process or to the regulation of a process )<br />
<br />
(Comment from Pascale: 'regulation' and 'process beginning/end' have been merged now)<br />
<br />
(Comment from Ruth: Should we also consider how the 'activity' of a protein is defined when making these regulation/process decisions. The definition for transcription factor activity is: The function of binding to a specific DNA sequence in order to modulate transcription.... This suggests that a transcription factor is involved in the process of regulating transcription rather than involved in the process of transcription itself. However, some of us in the UK feel that many transcription factors are involved in the transcription process itself definition: The synthesis of either RNA on a template of DNA or DNA on a template of RNA. Does the definition for transcription factor activity need modification to enable this annotation, or are only the polymerases involved in the synthesis?)<br />
<br />
'''Working group'''<br />
(tentative) <br />
Emily, Donghui,Val, Stan, Pascale, Yasmin, Jane, Rachael, Susan, Rama, Ruth, Fiona, Lakshmi, Jodi, Serenella<br />
<br />
Please confirm here: [[2010_GO_camp_working_groups_composition]]<br />
<br />
----<br />
<br />
====3.a Response to terms, how will these relate to signaling terms and to final cellular effect====<br />
<br />
* Question (Pascale): Can you have a 'response to' annotation with an IDA evidence? <br />
<br />
'''Working group'''<br />
(tentative)<br />
Varsha, Yasmin, Ruth, Becky, Manu<br />
<br />
Please confirm here: [[2010_GO_camp_working_groups_composition]]<br />
<br />
----<br />
<br />
====3.b. How is a downstream effect defined (i.e when not to capture phenotypes )====<br />
<br />
from 22nd Feb Jamboree call [http://gowiki.tamu.edu/wiki/index.php/Category:RefGenome_Electronic_Jamboree_2010-02_NIPBL#Minutes], Tanya: It's not uncommon for the initial publications to describe a mutant phenotype, with a developmental defect, and then later publications to describe much more explicit functions or processes. You should always annotate based on whatever evidence is available. Once you've done that, the question becomes, "When do we keep or remove the phenotype-based annotations?" At TAIR, their policy is to keep the developmental terms if they think that their users would expect to see them. Some participants suggested that one would expect all orthologs to have the same development-type annotations, across organisms. Others disagreed with this expectation. <br />
<br />
'''Working group'''<br />
(tentative) <br />
Donghui, Val, Rachael, Rama, Ruth, Fiona, Ranjana, Jodi<br />
<br />
Please confirm here: [[2010_GO_camp_working_groups_composition]]<br />
----<br />
<br />
== Other suggestions for agenda items ==<br />
# What is the bottle neck for manual annotations (with experimental evidence)? How can we step up manual curation? (Rama)<br />
# How are the various annotating groups keeping with all the ontology development/changes (new relationships specifically)? (Rama)<br />
# How to define the limits of ISS propagation from phylogenetic studies ? (Manu)<br />
# How to distinguish between large-scale experiments (LSE) and specific experiments derived GO annotation ? PubMed list of LSE, additional tags ?!? (Manu)<br />
<br />
== Posters being presented at the camp ==<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organisation<br />
! Title of Poster<br />
|-<br />
|Varsha Khodiyar<br />
|BHF-UCL<br />
|Process-centric annotation can lead to large-scale ontology development <br />
|-<br />
|}<br />
<br />
=Attendees=<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport <br />
! Departure Date/Time from Airport<br />
|-<br />
| Rachael Huntley<br />
| GOA<br />
| June 15 16.35<br />
| June 18 20.05<br />
|-<br />
| Yasmin Alam-Faruque<br />
| GOA<br />
| June 15 16.35<br />
| June 18 20.05<br />
|-<br />
| Pascale Gaudet<br />
| dictyBase<br />
| <br />
|<br />
|-<br />
| Susan Tweedie<br />
| FlyBase<br />
| June 15 16.35<br />
| June 18 20.05<br />
|-<br />
| Ruth Lovering<br />
| BHF-UCL<br />
| June 15 19:55<br />
| June 18 20.05<br />
|-<br />
| Rama Balakrishnan<br />
| SGD, Stanford University<br />
|<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford University<br />
| <br />
|<br />
|-<br />
| Suzi Lewis<br />
| Berkeley<br />
| <br />
|<br />
|-<br />
| Judy Blake<br />
| Jackson Laboratory<br />
|<br />
|<br />
|-<br />
| Varsha Khodiyar<br />
| BHF-UCL<br />
| <br />
| <br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
|<br />
|-<br />
| Paul Thomas<br />
| Panther<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 />
!Lakshmi Pillai<br />
!AgBase<br />
!pillai@cvm.msstate.edu<br />
!<br />
|-<br />
!Fiona McCarthy<br />
!AgBase<br />
!fmccarthy@cvm.msstate.edu<br />
!<br />
|-<br />
!Michelle Giglio<br />
!Institute for Genome Sciences (IGS)<br />
!mgiglio@som.umaryland.edu<br />
!<br />
|}<br />
<br />
----<br />
Return to [[Consortium_Meetings]] page</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2010_GO_camp_Meeting_Logistics&diff=250342010 GO camp Meeting Logistics2010-02-23T21:41:59Z<p>Mlgwinn: /* 4. use of column 16 */</p>
<hr />
<div>=Dates=<br />
The 3rd GO annotation camp (3 days) will be held from June 16-18, 2010 (Wednesday-Friday). <br />
<br />
=Objectives=<br />
This annotation camp will be focused on updating and refining skills of existing GO biocurators including new GO biocurators in existing annotation groups and including the Swiss-Prot curation team. We hope members of each MOD will be represented. <br />
<br />
* '''Deliverables''': (1) final annotation documentation for each of the three annotation topics. <br />
**There will be a special emphasis on the reference genome project. Deliverable: (2) annotation propagation rules for the reference genome project. <br />
<br />
<br />
=Venue=<br />
Swiss Institute for Bioinformatics (SIB), Geneva, Switzerland. <br />
<br />
=Registration=<br />
Not yet open. <br />
<br />
=Lodging Information=<br />
To be announced. <br />
<br />
=Maps=<br />
To be announced. <br />
<br />
=Agenda= <br />
'''Structure''': There will be '''three (3) ‘focused annotation sessions’''' where specific annotation issues will be discussed. Suggestion for discussion topics should be added to the GO camp agenda: [[2010_GO_camp_Meeting_Logistics#Suggestions_for_annotation_issues_to_be_discussed]]<br />
<br />
The agenda is not yet finalized.<br />
<br />
<br />
== Suggestions for annotation issues to be discussed ==<br />
* Please add any concerns you have regarding specific GO annotation issues here, or add your comments to an existing annotation issue. <br />
* As three topics will be selected for further discussion for the GO camp, please indicate '''which 3 issues''' are of most interest to you.<br />
<br />
<br />
===1. Binding (binding working group would like to finalize the annotation documentation)===<br />
<br />
Notes: The binding group presented annotation policy suggestions at the last GO Consortium meeting [http://gocwiki.geneontology.org/index.php/Binding_terms_working_group#2010_discussion]<br />
These annotation guidelines should be finalized, and a full set of annotation guidelines on how annotation data is curated and presented in GAF files should be fully documented. <br />
For instance determine:<br />
* that binding annotations, especially those where the GO term does not specify a particular binding partner, should where possible, indicate the interacting partner in the 'with' column<br />
* fully describe the usage of pipes etc in the 'with' column.<br />
* ask that protein binding annotations should be reciprocal - that if protein A is annotated as binding protein B, the reverse annotation should be provided<br />
<br />
The use of column 16 to identify protein/gene targets of an molecular function GO annotation, could benefit this binding discussion.<br />
<br />
'''Curators interested in discussing this topic at the GO Camp:'''<br />
<br />
Emily, Donghui, Yasmin<br />
<br />
----<br />
<br />
===2.annotation of complexes===<br />
# Can IPI be used to annotate molecular function? For example ribosomal subunits are annotated to 'structural constituent of ribosome' (a function)<br />
# 'Structural components activity' function terms: some ribosome proteins are annotated to 'structural constituent of ribosome' by IDA (for example SGD:S000005760); but the paper (PMID: 18782943) only shows purification of the complex. <br />
# Chromatin? See NIPBL discussion from Feb 22 jamboree. The general question is when is a protein part of a complex or organelle or when it binds to it? <br />
<br />
'''Curators interested in discussing this topic at the GO Camp:'''<br />
Pascale, Stan<br />
<br />
<br />
----<br />
<br />
===3. use of regulation ===<br />
<br />
This would include process beginning/end (maybe in the context of the new signaling terms)<br />
<br />
<br />
Notes: How do groups decide on when to annotate to 'regulates process x' or 'process x'? <br />
For instance does SLIT regulate axon guidance or involved in the process of axon guidance?<br />
Val - this depends on the defined start/end of a process and somethings can be annotated to BOTH the regulates term and also directly to the process term. <br />
Some groups decide that if removing the activity of a gene product produces an all/nothing event - then they define it as being part of the process.<br />
When should annotations be inherited up the regulates relationship?<br />
<br />
Notes:Annotations could be checked more efficiently if GO term definitions could include the beginning and end of a process.<br />
<br />
(Comment from Val: This is largely overlapping with the regulation issue. Where a process begins and ends is central to the decision to annotate directly to a process or to the regulation of a process )<br />
<br />
(Comment from Pascale: 'regulation' and 'process beginning/end' have been merged now)<br />
<br />
'''Curators interested in discussing this topic at the GO Camp'''<br />
<br />
<br />
Emily, Donghui,Val, Stan, Pascale, Yasmin<br />
<br />
----<br />
<br />
===4. use of column 16===<br />
<br />
Notes: The suggested use of Cell Type in column 16 seems to be progressing [http://wiki.geneontology.org/index.php/Column_16_discussion_12-12-09], and a date for GAF2.0 has been agreed for the 1st June. However this discussion needs to progress to decide how targets of a molecular function/biological process should be best captured in this field, as well as the linking of terms between different annotation lines.<br />
<br />
'''Curators interested in discussing this topic at the GO Camp:'''<br />
Stan, Varsha, Michelle<br />
<br />
----<br />
<br />
===5. response to terms, how will these relate to signaling terms and to final cellular effect===<br />
<br />
<br />
<br />
'''Curators interested in discussing this topic at the GO Camp'''<br />
<br />
Varsha, Yasmin<br />
<br />
----<br />
<br />
===6. How is a downstream effect defined (i.e when not to capture phenotypes )===<br />
<br />
<br />
<br />
'''Curators interested in discussing this topic at the GO Camp'''<br />
Donghui, Val<br />
----<br />
<br />
== Other suggestions for agenda items ==<br />
# What is the bottle neck for manual annotations (with experimental evidence)? How can we step up manual curation? (Rama)<br />
# How are the various annotating groups keeping with all the ontology development/changes (new relationships specifically)? (Rama)<br />
<br />
=Attendees=<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Arrival Date/Time to Airport <br />
! Departure Date/Time from Airport<br />
|-<br />
|}<br />
<br />
<br />
=Remote Attendees=<br />
We will try to provide Webex and Telephone Conferencing. <br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! email (needed to set up your remote access)<br />
|-<br />
|}<br />
<br />
----<br />
Return to [[Consortium_Meetings]] page</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2010_Stanford_Meeting_Logistics&diff=246732010 Stanford Meeting Logistics2010-02-04T15:26:05Z<p>Mlgwinn: /* 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 />
<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 />
| March 29<br />
| April 2<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 />
| 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 />
| TBA<br />
| TBA<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 />
|SFO TBA<br />
|-<br />
|Dianna Fisk<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 />
|on site<br />
|on site<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<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 />
<br />
<br />
----<br />
Return to [[Consortium_Meetings]] page</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Outreach_September_2009_Report&diff=22383Outreach September 2009 Report2009-10-02T14:35:05Z<p>Mlgwinn: </p>
<hr />
<div>Jennifer Deegan attended the '''Cambridge Clinical Neuroscience and Mental Health Symposium''', 29th - 30th September 2009, taking a poster about analysis of high-throughput experiments using GO. The work presented at the meeting was very predominantly imaging rather than genomics. However she did find two people using ontologies for analysis. One was using GO at the Sanger Centre (UK) and said he was completely happy with it, though he did not know the details of all of the biological domains well enough to spot any problems in the graph. The other researcher was using Ingenuity and said she was also very happy with that system.<br />
<br />
September 15-17, IGS Genomics Workshop included a 2-hour lecture on the GO and hands-on manual annotation exercises that included GO annotation. The workshop was attended by 15 people and held on the IGS University of Maryland Campus. One more workshop is planned for 2009 in November. Additional workshops will be held in 2010.</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2009_Cambridge_Meeting_Logistics&diff=218872009 Cambridge Meeting Logistics2009-09-10T17:45:59Z<p>Mlgwinn: /* Remote Attendees */</p>
<hr />
<div>=Dates=<br />
* GO consortium meeting: September 23-24, 2009<br />
* GO SAB meeting: September 25, 2009<br />
<br />
=Venue=<br />
Meetings, lodging and some meals will be in [http://conference.jesus.cam.ac.uk Jesus College], Cambridge, UK.<br />
<br />
Meetings will be held in the Upper Hall room, and meals will be served in the the Prioress's Room.<br />
<br />
==Maps==<br />
[http://www.cam.ac.uk/map/ Official Cambridge University map]<br />
<br />
Portion of Cambridge University map showing Jesus College [http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=1900;yy=560;gf=png view 1] [http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=2017;yy=535;mt=c;ms=150;tl=Jesus%20College view 2]<br />
<br />
Other selections from the Cambridge University map:<br />
*[http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=1900;yy=1040 central Cambridge]<br />
*[http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=region Cambridge and surrounding region]<br />
<br />
Google Maps:<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=jesus+college,+cambridge+cb5+8bl,+uk&sll=52.208198,0.123575&sspn=0.009296,0.012617&ie=UTF8&ll=52.208751,0.122824&spn=0.009296,0.012617&z=16 Jesus College]<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=183+east+road,+cambridge+cb1+1bg,+uk&sll=52.204522,0.133312&sspn=0.009297,0.012617&ie=UTF8&ll=52.204609,0.133209&spn=0.009297,0.012617&z=16&iwloc=A Cotto], 183 East Road (Tuesday dinner venue)<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=quayside,+cambridge,+uk&sll=52.261854,0.083771&sspn=0.297125,0.403748&ie=UTF8&ll=52.209803,0.117202&spn=0.009296,0.012617&z=16 Cambridge Quayside] (location of River Bar & Kitchen, Thursday dinner venue)<br />
<br />
=Registration=<br />
Registration is now open, via [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 web form].<br />
<br />
'''Deadline:''' Please register by '''September 4''' if you want to stay at Jesus College (more info below), or by '''September 14''' if you don't need accommodation. If you miss the deadline, we can try to squeeze you into the meeting room, but you'll be on your own not only for lodging, but also for all meals, including lunch.<br />
<br />
Note that there is a table of attendees below, but this time we are using it only to gather arrival and departure information for airport ride shares. '''You must register using the online form.'''<br />
<br />
Additional note about the registration form: there is a page that asks about pick-up and drop-off, but it's only there because we're using a standardized EMBL web form. For these meetings, please just skip that page (it has a "Skip" button).<br />
<br />
==Registration Fee==<br />
Fees and payment methods are noted on the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form]. Quick summary:<br />
<br />
*GBP 109.20 (about $177 as of July 10) for both meetings Sept. 23-25<br />
*GBP 72.80 for only the GO Consortium meeting Sept. 23-24<br />
*GBP 36.40 for only the SAB meeting Sept. 25<br />
<br />
Payable by credit card or bank transfer (note to US participants: if you're considering paying by bank transfer, check with your bank first to find out how much they charge for an international transfer, as some charge quite a bit); [[#Contact|contact]] us if you have problems or questions about paying.<br />
<br />
A receipt will be provided.<br />
<br />
=Lodging Information (deadline Sept. 4)=<br />
'''Please note that the deadline to reserve accommodation at Jesus College has passed. If you have not already booked a college room, you will have to arrange your own accommodation elsewhere in Cambridge.'''<br />
<br />
We have reserved 40 single ensuite bedrooms in Jesus College from September 22 (check-in) to 26 (check-out), 2009. Room booking is part of the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form]; all you have to do is check the boxes for the dates you'll need a room.<br />
<br />
Rate: GBP 59.50 per night (about $97 as of July 10)<br><br />
This includes breakfast and wireless network, and is payable with your meeting registration fee.<br />
<br />
Deadline: '''September 4, 2009'''<br><br />
After Sept. 4, you will still be able to register for the meeting, but you will have to arrange your own lodging. If you need suggestions, please get in touch with Holly or Midori ([[#Contact|see below]]).<br />
<br />
=Food=<br />
You can indicate dietary restrictions on the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form].<br />
<br />
Lunch will be provided by Jesus College on all three days.<br />
<br />
Dinners are noted on the registration form. Quick summary:<br />
*Tuesday, Sept. 22: Arrival dinner at [http://www.cottocambridge.co.uk/ Cotto], Cambridge<br />
**Time: (to be confirmed)<br />
**Menu: Choose from the small selection on the evening.<br />
*Wednesday, Sept. 23: Dinner at Jesus College<br />
*Thursday, Sept. 24: Dinner at [http://www.riverbarkitchen.com River Bar & Kitchen], Cambridge<br />
**Time: 7:30 PM<br />
**Menu: Pre-order by '''September 22''' (Tuesday) from the [http://www.riverbarkitchen.com/menuParty.asp?pre-order=1 set menu for parties]. Note: don't fill out the restaurant web form; we'll collect your selections by email after you've registered.<br />
*Friday, Sept. 25: Dinner at Jesus College<br />
<br />
When you [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 register], please sign up for all dinners that you plan to attend. For the two restaurant dinners, the cost of the food is payable with your registration fee and will appear on your registration receipt. Drinks are not included, and must be paid separately on the night (we'll collect as we've done at a few recent GO dinners).<br />
<br />
=Managing Remote Participation=<br />
We plan to offer remote access along roughly the same lines as at the last GOC meeting in Oregon: We'll use a combination of the GO Ready Conference and Stanford's WebEx to allow remote attendees to participate. The meeting room will be equipped with a single conference phone, plus the usual projector and screen. Remote attendees will be asked to mute their lines unless they would like to speak. Someone will be monitoring remote attendees either on the WebEx 'raise your hand' feature or on a skype chat to ensure that remote attendees get an opportunity to be heard. All presenters are asked to use their mouse to interact with their slides so the WebEx participants can see what you are pointing to. Where possible we encourage remote participants to share a single connection to the teleconference as this will reduce the number of connections and likely increase the sound quality for everyone.<br />
<br />
=Transportation=<br />
Cambridge University [http://www.cam.ac.uk/visitors/gettingto.html "Getting to Cambridge" page]<br />
<br />
Train and bus transport is available from the major London airports. Or, if there are three or more people arriving or departing together, it can be time- and cost-effective to share a pre-booked taxi. Contact us if you would like a quote or for us to book a taxi. Note: '''do not''' take a taxi from Heathrow or Gatwick without booking in advance -- it's staggeringly expensive.<br />
<br />
Also note the registration form there is a page that asks about pick-up and drop-off, but it's only there because we're using a standardized EMBL web form. For these meetings, you can skip that page (it has a "Skip" button).<br />
<br />
=Things To Do=<br />
[http://www.visitcambridge.org/ Official Cambridge tourism site]<br />
<br />
[http://www.cam.ac.uk/visitors/ Cambridge University Visitors page]<br />
<br />
[http://www.cam.ac.uk/visitors/places.html Cambridge University "places and events to visit" page]<br />
<br />
=Attendees=<br />
Please [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 register online].<br />
<br />
Please fill in the Arrival and Departure table below if you would like to try a carpool to/from the airport.<br />
<br />
Airport codes: LHR = Heathrow; LGW = Gatwick; STN = Stansted; LTN = Luton; LCY = London City<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 />
| Judy Blake<br />
| GO / MGI<br />
|Sept 22 / AA 108 arr 6:50 am to LHR<br />
|Sept 27 / AA 109 dep 10:55 am from LHR<br />
|-<br />
| Brenley McIntosh<br />
| EcoliWiki<br />
| Sept 18 arr 9:35am to LHR<br />
| Sept 28 dep 8:40am from LHR<br />
|-<br />
| Pascale Gaudet<br />
| dictybase<br />
| Sep 22 06:20 UA 958 LHR<br />
| Sep 26 12:20 from LHR<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 />
! Attending GOC (Sept. 23-24)<br />
! Attending SAB (Sept. 25)<br />
! Calling in alone or in a group (with whom and from where, if known)<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Peter.D'Eustachio@nyumc.org<br />
| yes<br />
| ?<br />
| alone<br />
|-<br />
| Marcus Chibucos<br />
| Institute for Genome Sciences<br />
| mchibucos at som dot umaryland dot edu<br />
| yes<br />
| not sure<br />
| Michelle Gwinn-Giglio from IGS (Baltimore, MD, USA)<br />
|-<br />
|Harold Drabkin<br />
|MGI<br />
|hjd@informatics.jax.org<br />
|yes<br />
|yes<br />
|unsure<br />
|-<br />
|Michelle Giglio<br />
|Institute for Genome Sciences<br />
|mgiglio at som dot umaryland dot edu<br />
|yes<br />
|only for PM GO clinic<br />
|depending on how the times work out - may be along with Marcus at IGS (Baltimore) or alone at home<br />
|-<br />
|Alexander Diehl<br />
|MGI<br />
|adiehl@informatics.jax.org<br />
|yes<br />
|yes<br />
|unsure<br />
|-<br />
|Amina Abdulla<br />
|LBL BerkeleyBOP<br />
|aabdulla [at] berkeleybop [dot] org<br />
|yes<br />
|yes<br />
|Alone - work and home<br />
|-<br />
|Mary Dolan<br />
|MGI<br />
|mdolan@informatics.jax.org<br />
|yes<br />
|yes<br />
|unsure<br />
|-<br />
-<br />
|Kara Dolinski<br />
|Princeton<br />
|kara@genomics.princeton.edu<br />
|yes<br />
|unsure<br />
|unsure<br />
|-<br />
|Li Ni<br />
|MGI<br />
|adiehl@informatics.jax.org<br />
|yes<br />
|yes<br />
|alone - home<br />
|-<br />
|Lakshmi Pillai<br />
|AgBase<br />
|pillai@cvm.msstate.edu<br />
|yes<br />
|no<br />
|unsure<br />
|-<br />
|}<br />
<br />
=Contact=<br />
'''Please contact Midori Harris (midori at ebi dot ac dot uk) or Holly Edwards (holly dot edwards at ebi dot ac dot uk) if you have any questions.'''<br />
<br />
[[Category:Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2009_Cambridge_Meeting_Logistics&diff=212412009 Cambridge Meeting Logistics2009-08-17T17:20:24Z<p>Mlgwinn: /* Remote Attendees */</p>
<hr />
<div>=Dates=<br />
* GO consortium meeting: September 23-24, 2009<br />
* GO SAB meeting: September 25, 2009<br />
<br />
=Venue=<br />
Meetings, lodging and some meals will be in [http://conference.jesus.cam.ac.uk Jesus College], Cambridge, UK.<br />
<br />
Meetings will be held in the Upper Hall room, and meals will be served in the the Prioress's Room.<br />
<br />
==Maps==<br />
[http://www.cam.ac.uk/map/ Official Cambridge University map]<br />
<br />
Portion of Cambridge University map showing Jesus College [http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=1900;yy=560;gf=png view 1] [http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=2017;yy=535;mt=c;ms=150;tl=Jesus%20College view 2]<br />
<br />
Other selections from the Cambridge University map:<br />
*[http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=1900;yy=1040 central Cambridge]<br />
*[http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=region Cambridge and surrounding region]<br />
<br />
Google Maps:<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=jesus+college,+cambridge+cb5+8bl,+uk&sll=52.208198,0.123575&sspn=0.009296,0.012617&ie=UTF8&ll=52.208751,0.122824&spn=0.009296,0.012617&z=16 Jesus College]<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=183+east+road,+cambridge+cb1+1bg,+uk&sll=52.204522,0.133312&sspn=0.009297,0.012617&ie=UTF8&ll=52.204609,0.133209&spn=0.009297,0.012617&z=16&iwloc=A Cotto], 183 East Road (Tuesday dinner venue)<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=quayside,+cambridge,+uk&sll=52.261854,0.083771&sspn=0.297125,0.403748&ie=UTF8&ll=52.209803,0.117202&spn=0.009296,0.012617&z=16 Cambridge Quayside] (location of River Bar & Kitchen, Thursday dinner venue)<br />
<br />
=Registration=<br />
Registration is now open, via [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 web form].<br />
<br />
'''Deadline:''' Please register by '''September 4''' if you want to stay at Jesus College (more info below), or by '''September 14''' if you don't need accommodation. If you miss the deadline, we can try to squeeze you into the meeting room, but you'll be on your own not only for lodging, but also for all meals, including lunch.<br />
<br />
Note that there is a table of attendees below, but this time we are using it only to gather arrival and departure information for airport ride shares. '''You must register using the online form.'''<br />
<br />
Additional note about the registration form: there is a page that asks about pick-up and drop-off, but it's only there because we're using a standardized EMBL web form. For these meetings, please just skip that page (it has a "Skip" button).<br />
<br />
==Registration Fee==<br />
Fees and payment methods are noted on the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form]. Quick summary:<br />
<br />
*GBP 109.20 (about $177 as of July 10) for both meetings Sept. 23-25<br />
*GBP 72.80 for only the GO Consortium meeting Sept. 23-24<br />
*GBP 36.40 for only the SAB meeting Sept. 25<br />
<br />
Payable by credit card or bank transfer (note to US participants: if you're considering paying by bank transfer, check with your bank first to find out how much they charge for an international transfer, as some charge quite a bit); [[#Contact|contact]] us if you have problems or questions about paying.<br />
<br />
A receipt will be provided.<br />
<br />
=Lodging Information=<br />
We have reserved 40 single ensuite bedrooms in Jesus College from September 22 (check-in) to 26 (check-out), 2009. Room booking is part of the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form]; all you have to do is check the boxes for the dates you'll need a room.<br />
<br />
Rate: GBP 59.50 per night (about $97 as of July 10)<br><br />
This includes breakfast and wireless network, and is payable with your meeting registration fee.<br />
<br />
Deadline: '''September 4, 2009'''<br><br />
After Sept. 4, you will still be able to register for the meeting, but you will have to arrange your own lodging. If you need suggestions, please get in touch with Holly or Midori ([[#Contact|see below]]).<br />
<br />
=Food=<br />
You can indicate dietary restrictions on the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form].<br />
<br />
Lunch will be provided by Jesus College on all three days.<br />
<br />
Dinners are noted on the registration form. Quick summary:<br />
*Tuesday, Sept. 22: Arrival dinner at [http://www.cottocambridge.co.uk/ Cotto], Cambridge<br />
**Time: (to be confirmed)<br />
**Menu: Choose from the small selection on the evening.<br />
*Wednesday, Sept. 23: Dinner at Jesus College<br />
*Thursday, Sept. 24: Dinner at [http://www.riverbarkitchen.com River Bar & Kitchen], Cambridge<br />
**Time: 7:30 PM<br />
**Menu: Pre-order by '''September 22''' (Tuesday) from the [http://www.riverbarkitchen.com/menuParty.asp?pre-order=1 set menu for parties]. Note: don't fill out the restaurant web form; we'll collect your selections by email after you've registered.<br />
*Friday, Sept. 25: Dinner at Jesus College<br />
<br />
When you [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 register], please sign up for all dinners that you plan to attend. For the two restaurant dinners, the cost of the food is payable with your registration fee and will appear on your registration receipt. Drinks are not included, and must be paid separately on the night (we'll collect as we've done at a few recent GO dinners).<br />
<br />
=Managing Remote Participation=<br />
We plan to offer remote access along roughly the same lines as at the last GOC meeting in Oregon: We'll use a combination of the GO Ready Conference and Stanford's WebEx to allow remote attendees to participate. The meeting room will be equipped with a single conference phone, plus the usual projector and screen. Remote attendees will be asked to mute their lines unless they would like to speak. Someone will be monitoring remote attendees either on the WebEx 'raise your hand' feature or on a skype chat to ensure that remote attendees get an opportunity to be heard. All presenters are asked to use their mouse to interact with their slides so the WebEx participants can see what you are pointing to. Where possible we encourage remote participants to share a single connection to the teleconference as this will reduce the number of connections and likely increase the sound quality for everyone.<br />
<br />
=Transportation=<br />
Cambridge University [http://www.cam.ac.uk/visitors/gettingto.html "Getting to Cambridge" page]<br />
<br />
Train and bus transport is available from the major London airports. Or, if there are three or more people arriving or departing together, it can be time- and cost-effective to share a pre-booked taxi. Contact us if you would like a quote or for us to book a taxi. Note: '''do not''' take a taxi from Heathrow or Gatwick without booking in advance -- it's staggeringly expensive.<br />
<br />
Also note the registration form there is a page that asks about pick-up and drop-off, but it's only there because we're using a standardized EMBL web form. For these meetings, you can skip that page (it has a "Skip" button).<br />
<br />
=Things To Do=<br />
[http://www.visitcambridge.org/ Official Cambridge tourism site]<br />
<br />
[http://www.cam.ac.uk/visitors/ Cambridge University Visitors page]<br />
<br />
[http://www.cam.ac.uk/visitors/places.html Cambridge University "places and events to visit" page]<br />
<br />
=Attendees=<br />
Please [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 register online].<br />
<br />
Please fill in the Arrival and Departure table below if you would like to try a carpool to/from the airport.<br />
<br />
Airport codes: LHR = Heathrow; LGW = Gatwick; STN = Stansted; LTN = Luton; LCY = London City<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 />
| <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 />
! Attending GOC (Sept. 23-24)<br />
! Attending SAB (Sept. 25)<br />
! Calling in alone or in a group (with whom and from where, if known)<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Peter.D'Eustachio@nyumc.org<br />
| yes<br />
| ?<br />
| alone<br />
|-<br />
| Marcus Chibucos<br />
| Institute for Genome Sciences<br />
| mchibucos at som dot umaryland dot edu<br />
| yes<br />
| not sure<br />
| Michelle Gwinn-Giglio from IGS (Baltimore, MD, USA)<br />
|-<br />
|Harold Drabkin<br />
|MGI<br />
|hjd@informatics.jax.org<br />
|yes<br />
|yes<br />
|unsure<br />
|-<br />
|Michelle Giglio<br />
|Institute for Genome Sciences<br />
|mgiglio at som dot umaryland dot edu<br />
|yes<br />
|no<br />
|depending on how the times work out - may be along with Marcus at IGS (Baltimore) or alone at home<br />
|-<br />
|}<br />
<br />
=Contact=<br />
'''Please contact Midori Harris (midori at ebi dot ac dot uk) or Holly Edwards (holly dot edwards at ebi dot ac dot uk) if you have any questions.'''</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2009_Cambridge_Meeting_Logistics&diff=212402009 Cambridge Meeting Logistics2009-08-17T17:19:33Z<p>Mlgwinn: /* Remote Attendees */</p>
<hr />
<div>=Dates=<br />
* GO consortium meeting: September 23-24, 2009<br />
* GO SAB meeting: September 25, 2009<br />
<br />
=Venue=<br />
Meetings, lodging and some meals will be in [http://conference.jesus.cam.ac.uk Jesus College], Cambridge, UK.<br />
<br />
Meetings will be held in the Upper Hall room, and meals will be served in the the Prioress's Room.<br />
<br />
==Maps==<br />
[http://www.cam.ac.uk/map/ Official Cambridge University map]<br />
<br />
Portion of Cambridge University map showing Jesus College [http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=1900;yy=560;gf=png view 1] [http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=2017;yy=535;mt=c;ms=150;tl=Jesus%20College view 2]<br />
<br />
Other selections from the Cambridge University map:<br />
*[http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=main;xx=1900;yy=1040 central Cambridge]<br />
*[http://www.cam.ac.uk/map/v4/drawmap.cgi?mp=region Cambridge and surrounding region]<br />
<br />
Google Maps:<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=jesus+college,+cambridge+cb5+8bl,+uk&sll=52.208198,0.123575&sspn=0.009296,0.012617&ie=UTF8&ll=52.208751,0.122824&spn=0.009296,0.012617&z=16 Jesus College]<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=183+east+road,+cambridge+cb1+1bg,+uk&sll=52.204522,0.133312&sspn=0.009297,0.012617&ie=UTF8&ll=52.204609,0.133209&spn=0.009297,0.012617&z=16&iwloc=A Cotto], 183 East Road (Tuesday dinner venue)<br />
*[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=quayside,+cambridge,+uk&sll=52.261854,0.083771&sspn=0.297125,0.403748&ie=UTF8&ll=52.209803,0.117202&spn=0.009296,0.012617&z=16 Cambridge Quayside] (location of River Bar & Kitchen, Thursday dinner venue)<br />
<br />
=Registration=<br />
Registration is now open, via [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 web form].<br />
<br />
'''Deadline:''' Please register by '''September 4''' if you want to stay at Jesus College (more info below), or by '''September 14''' if you don't need accommodation. If you miss the deadline, we can try to squeeze you into the meeting room, but you'll be on your own not only for lodging, but also for all meals, including lunch.<br />
<br />
Note that there is a table of attendees below, but this time we are using it only to gather arrival and departure information for airport ride shares. '''You must register using the online form.'''<br />
<br />
Additional note about the registration form: there is a page that asks about pick-up and drop-off, but it's only there because we're using a standardized EMBL web form. For these meetings, please just skip that page (it has a "Skip" button).<br />
<br />
==Registration Fee==<br />
Fees and payment methods are noted on the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form]. Quick summary:<br />
<br />
*GBP 109.20 (about $177 as of July 10) for both meetings Sept. 23-25<br />
*GBP 72.80 for only the GO Consortium meeting Sept. 23-24<br />
*GBP 36.40 for only the SAB meeting Sept. 25<br />
<br />
Payable by credit card or bank transfer (note to US participants: if you're considering paying by bank transfer, check with your bank first to find out how much they charge for an international transfer, as some charge quite a bit); [[#Contact|contact]] us if you have problems or questions about paying.<br />
<br />
A receipt will be provided.<br />
<br />
=Lodging Information=<br />
We have reserved 40 single ensuite bedrooms in Jesus College from September 22 (check-in) to 26 (check-out), 2009. Room booking is part of the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form]; all you have to do is check the boxes for the dates you'll need a room.<br />
<br />
Rate: GBP 59.50 per night (about $97 as of July 10)<br><br />
This includes breakfast and wireless network, and is payable with your meeting registration fee.<br />
<br />
Deadline: '''September 4, 2009'''<br><br />
After Sept. 4, you will still be able to register for the meeting, but you will have to arrange your own lodging. If you need suggestions, please get in touch with Holly or Midori ([[#Contact|see below]]).<br />
<br />
=Food=<br />
You can indicate dietary restrictions on the [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 registration form].<br />
<br />
Lunch will be provided by Jesus College on all three days.<br />
<br />
Dinners are noted on the registration form. Quick summary:<br />
*Tuesday, Sept. 22: Arrival dinner at [http://www.cottocambridge.co.uk/ Cotto], Cambridge<br />
**Time: (to be confirmed)<br />
**Menu: Choose from the small selection on the evening.<br />
*Wednesday, Sept. 23: Dinner at Jesus College<br />
*Thursday, Sept. 24: Dinner at [http://www.riverbarkitchen.com River Bar & Kitchen], Cambridge<br />
**Time: 7:30 PM<br />
**Menu: Pre-order by '''September 22''' (Tuesday) from the [http://www.riverbarkitchen.com/menuParty.asp?pre-order=1 set menu for parties]. Note: don't fill out the restaurant web form; we'll collect your selections by email after you've registered.<br />
*Friday, Sept. 25: Dinner at Jesus College<br />
<br />
When you [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 register], please sign up for all dinners that you plan to attend. For the two restaurant dinners, the cost of the food is payable with your registration fee and will appear on your registration receipt. Drinks are not included, and must be paid separately on the night (we'll collect as we've done at a few recent GO dinners).<br />
<br />
=Managing Remote Participation=<br />
We plan to offer remote access along roughly the same lines as at the last GOC meeting in Oregon: We'll use a combination of the GO Ready Conference and Stanford's WebEx to allow remote attendees to participate. The meeting room will be equipped with a single conference phone, plus the usual projector and screen. Remote attendees will be asked to mute their lines unless they would like to speak. Someone will be monitoring remote attendees either on the WebEx 'raise your hand' feature or on a skype chat to ensure that remote attendees get an opportunity to be heard. All presenters are asked to use their mouse to interact with their slides so the WebEx participants can see what you are pointing to. Where possible we encourage remote participants to share a single connection to the teleconference as this will reduce the number of connections and likely increase the sound quality for everyone.<br />
<br />
=Transportation=<br />
Cambridge University [http://www.cam.ac.uk/visitors/gettingto.html "Getting to Cambridge" page]<br />
<br />
Train and bus transport is available from the major London airports. Or, if there are three or more people arriving or departing together, it can be time- and cost-effective to share a pre-booked taxi. Contact us if you would like a quote or for us to book a taxi. Note: '''do not''' take a taxi from Heathrow or Gatwick without booking in advance -- it's staggeringly expensive.<br />
<br />
Also note the registration form there is a page that asks about pick-up and drop-off, but it's only there because we're using a standardized EMBL web form. For these meetings, you can skip that page (it has a "Skip" button).<br />
<br />
=Things To Do=<br />
[http://www.visitcambridge.org/ Official Cambridge tourism site]<br />
<br />
[http://www.cam.ac.uk/visitors/ Cambridge University Visitors page]<br />
<br />
[http://www.cam.ac.uk/visitors/places.html Cambridge University "places and events to visit" page]<br />
<br />
=Attendees=<br />
Please [http://events.embl.org/iEBMS/reg/reg_p1_form.aspx?oc=20&ct=GBPNORMAL&eventid=5025 register online].<br />
<br />
Please fill in the Arrival and Departure table below if you would like to try a carpool to/from the airport.<br />
<br />
Airport codes: LHR = Heathrow; LGW = Gatwick; STN = Stansted; LTN = Luton; LCY = London City<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 />
| <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 />
! Attending GOC (Sept. 23-24)<br />
! Attending SAB (Sept. 25)<br />
! Calling in alone or in a group (with whom and from where, if known)<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Peter.D'Eustachio@nyumc.org<br />
| yes<br />
| ?<br />
| alone<br />
|-<br />
| Marcus Chibucos<br />
| Institute for Genome Sciences<br />
| mchibucos at som dot umaryland dot edu<br />
| yes<br />
| not sure<br />
| Michelle Gwinn-Giglio from IGS (Baltimore, MD, USA)<br />
|-<br />
|Harold Drabkin<br />
|MGI<br />
|hjd@informatics.jax.org<br />
|yes<br />
|yes<br />
|unsure<br />
|-<br />
|Michelle Giglio<br />
|Institute for Genome Sciences<br />
|mgiglio@som.umaryland.edu<br />
|yes<br />
|no<br />
|depending on how the times work out - may be along with Marcus at IGS (Baltimore) or alone at home<br />
|-<br />
|}<br />
<br />
=Contact=<br />
'''Please contact Midori Harris (midori at ebi dot ac dot uk) or Holly Edwards (holly dot edwards at ebi dot ac dot uk) if you have any questions.'''</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Outreach_July_2009_Report&diff=21048Outreach July 2009 Report2009-08-03T18:18:46Z<p>Mlgwinn: </p>
<hr />
<div>July Report<br />
<br />
<br />
July 28-31 IGS Genomics Workshop included a 2-hour lecture on the GO and then was followed by hands-on manual annotation exercises where part of what attendees had to do was attach GO terms to the exercise genes. The workshop was attended by 17 people and held on the IGS University of Maryland Campus. Two more workshops are planned for September and November.</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Outreach_July_2009_Report&diff=21047Outreach July 2009 Report2009-08-03T18:16:27Z<p>Mlgwinn: </p>
<hr />
<div>July Report<br />
<br />
<br />
July 28-31 IGS Genomics Workshop included a 2-hour lecture on the GO and then was followed by hands-on manual annotation exercises where part of what attendees had to do was attach GO terms to the exercise genes. The workshop was attended by 17 people and held on the IGS University of Maryland Campus.</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2009_Oregon_Meeting_Logistics&diff=182052009 Oregon Meeting Logistics2009-03-02T21:57:14Z<p>Mlgwinn: /* Attendees */</p>
<hr />
<div>===Dates===<br />
* GO consortium meeting: March 30, 31 (half day)<br />
* Reference Genomes meeting: April 1<br />
<br />
===Venue===<br />
University of Oregon, Eugene, Oregon<br />
<br />
Erb Memorial Union (EMU), Fir Room. <br />
<br />
Map of campus,<br />
http://map.uoregon.edu/<br />
<br />
Map of the EMU,<br />
http://emu.uoregon.edu/map_popup.php?x=-50&y=-50&level=main&arrow=SE<br />
<br />
===Registration===<br />
Please add yourself to the table of attendees below.<br />
<br />
===Lodging Information===<br />
New Oregon Motel<br/><br />
1655 Franklin Blvd. (roughly 1/2 mile from the meeting venue)<br/><br />
Eugene OR, 97403<br/><br />
(ph)541-683-3669<br/><br />
(fx)541-484-5556<br/><br />
<br />
<br />
Rate (available from March 29 - April 3): $83.99 + tax<br/><br />
Code: "GO Meeting"<br />
<br />
http://www.bestwesternoregon.com/hotels/best-western-new-oregon-motel/<br />
<br />
===Registration Fee===<br />
More info as we have it...<br />
<br />
===Food===<br />
<br />
Catering will be provided by the University of Oregon catering department, and will include morning snacks, lunches, and afternoon snacks, on each of the full days; and a morning snack on the half day.<br />
<br />
A dinner will be held on the evening of the first day, March 30, at 7 PM. Location TBD. Please indicate on the registration section below whether you will be attending the dinner. <br />
<br />
Vegetarian options will be available.<br />
<br />
===Transportation===<br />
[http://www.eugene-or.gov/portal/server.pt?space=CommunityPage&control=SetCommunity&CommunityID=462&PageID=0 Eugene Airport - Mahlon Sweet Field]<br />
<br />
[http://www.portofportland.com/PDX_home.aspx Portland Airport - PDX]<br />
<br />
===Things To Do===<br />
[http://www.eugene-or.gov/portal/server.pt City of Eugene Website]<br />
<br />
[http://www.portlandonline.com/index.cfm?c=25782 Visit Portland]<br />
<br />
[http://www.eugene-or.gov/portal/server.pt?open=18&objID=268760&parentname=CTPortalSyndicator&parentid=0&mode=2&in_hi_userid=2&cached=true Ruth Bascom Riverbank Trails are right behind the New Oregon Motel]<br />
<br />
[http://mountpisgaharboretum.org/ Mt. Pisgah Arboretum]<br />
<br />
[http://www.co.lane.or.us/parks/mtpisgahpage.htm Hike at Howard Buford Recreation Area]<br />
<br />
[http://www.eugenerunningcompany.com/home/erc1/smartlist_5/Running_in_Eugene.html Go for a run in Track Town USA!]<br />
<br />
[http://www.eraptors.org/ Visit the Cascade Raptor Center]<br />
<br />
[http://www.uoregon.edu/~mnh/ Visit the University of Oregon Museum of Natural and Cultural History]<br />
<br />
[http://www.fs.fed.us/gpnf/mshnvm/ See Mt. St. Helens if you have time in the Portland area]<br />
<br />
===Attendees===<br />
(please use the Arrival and Departure info columns if you would like to try a carpool to/from the airport)<br />
{|border="1" cell spacing="0" cellpadding="4" align="center" class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! email (needed to set up your wireless access)<br />
! Attending GOC (March 30-31)<br />
! Attending Ref.Gen. (April 1)<br />
! Food requirement (None, Veggie, Vegan)<br />
! Yes, I plan on attending the dinner, March 30.<br />
! Arrival Date/Time to Airport (EUG=Eugene or PDX=Portland) <br />
! Departure Date/Time from Airport (EUG=Eugene or PDX=Portland)<br />
|-<br />
| Doug Howe<br />
| ZFIN - University of Oregon<br />
| dhowe@cs.uoregon.edu<br />
| Yes<br />
| Yes<br />
| Yummy only please<br />
| Yes<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| MGI&GO - The Jackson Laboratory<br />
|<br />
| Yes<br />
| Yes<br />
| Yummy only please<br />
| Yes<br />
| PDX, 8:14 pm rental car<br />
| PDX friday 6 am<br />
|-<br />
| Suzanna Lewis<br />
| BBOP&GO (LBNL)<br />
| suzi@berkeleybop.org<br />
| Yes<br />
| Yes<br />
| <br />
| Yes<br />
| TBD<br />
| TBD<br />
|-<br />
| Kara Dolinski<br />
| P-POD - Princeton<br />
|<br />
| Yes<br />
| Yes<br />
| Yummy only please<br />
| Yes<br />
| <br />
|<br />
|-<br />
| Donghui Li<br />
| TAIR<br />
|<br />
| Yes<br />
| Yes<br />
| <br />
| Yes<br />
| EUG 03/29, 11.25am<br />
| EUG 04/02, 8am<br />
|-<br />
| Tanya Berardini<br />
| TAIR<br />
|<br />
| Yes<br />
| No<br />
| <br />
| Yes<br />
| EUG 03/29, 400 pm<br />
| EUG 03/31, 1245 pm<br />
|-<br />
| Mike Cherry<br />
| SGD - Whatsamatter U<br />
|<br />
| Yes<br />
| Yes<br />
| <br />
| Yes<br />
| EUG 03/30 - 1000 am<br />
| EUG 04/01 - 600 pm<br />
|-<br />
| Stan Laulederkind<br />
| RGD - Medical College of Wisconsin<br />
|<br />
| Yes<br />
| Yes<br />
| <br />
| Yes<br />
| PDX 03/29 11:07 am<br />
| EUG 04/02 9:50 am<br />
|-<br />
| Rama Balakrishnan<br />
| SGD- Stanford University<br />
| rama@genome.stanford.edu<br />
| Yes<br />
| Yes<br />
| Vegan if possible. Veggie works<br />
| Yes<br />
| EUG 03/29 8:40 PM<br />
| EUG 04/01 4:50 PM<br />
|-<br />
| Karen Christie<br />
| SGD - Stanford University<br />
| kchris@genome.stanford.edu<br />
| Yes<br />
| Yes<br />
| <br />
| Yes<br />
| EUG 03/29 8:40pm <br />
| EUG 04/01 6:10pm<br />
|-<br />
| Seth Carbon<br />
| BBOP - Berkeley<br />
| [sjcarbon] _at_ [berkeleybop] _dot_ [org]<br />
| Yes<br />
| Yes<br />
| None<br />
| Yes<br />
| TBD<br />
| TBD<br />
|-<br />
| Chris Mungall<br />
| BBOP - Berkeley<br />
|<br />
| Yes<br />
| Yes<br />
| Veg<br />
| Yes<br />
| TBD<br />
| TBD<br />
|-<br />
| Karen Eilbeck<br />
| U of Utah<br />
| keilbeck@genetics.utah.edu<br />
| Yes<br />
| No<br />
| Vegan<br />
| Yes<br />
| 12:17 PM, Portland, OR (PDX) Sunday<br />
| 5:30 PM, Portland, OR (PDX) Tuesday<br />
|-<br />
| Eva Huala<br />
| TAIR<br />
|<br />
| Yes<br />
| Yes<br />
| none<br />
| Yes<br />
| EUG 03/29, 8:40 pm<br />
| EUG 04/01, 6:08 pm<br />
|-<br />
| Amina Abdulla<br />
| BBOP - Berkeley<br />
| [aabdulla] _at_ [berkeleybop] _dot_ [org]<br />
| Yes<br />
| No<br />
| None<br />
| Yes<br />
| TBD<br />
| TBD<br />
|-<br />
| Ranjana Kishore<br />
| WormBase - Caltech<br />
|<br />
| Yes<br />
| Yes<br />
| Veggie<br />
| Yes<br />
| TBD<br />
| TBD<br />
|-<br />
| Susan Tweedie<br />
| FlyBase - Cambridge<br />
|<br />
| Yes<br />
| Yes<br />
| None<br />
| Yes<br />
| TBD<br />
| TBD<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Peter.D'Eustachio@nyumc.org<br />
| yes<br />
| no<br />
| None<br />
| Yes<br />
| TBD<br />
| TBD<br />
|-<br />
| Michelle Giglio<br />
| Institute for Genome Sciences<br />
| mgiglio@som.umaryland.edu<br />
| Yes<br />
| No<br />
| None<br />
| Yes<br />
| TBD<br />
| TBD<br />
|}<br />
<br />
===Contact===<br />
'''Please contact Jon Knight if you have any questions: knight at uoneuro dot uoregon dot edu'''</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=20th_GO_Consortium_Meeting&diff=1619920th GO Consortium Meeting2008-10-19T14:05:34Z<p>Mlgwinn: /* PAMGO report on successes and some problem annotations from consortium members */</p>
<hr />
<div>=Logistics=<br />
[[Instructions_for_Registration]]<br />
<br />
<br />
=Agenda=<br />
'''ALERT:''' GO Top needs to sign off on agenda prior to these meetings. If there is no action item, or discussion point proposed in advance, the meeting is not the forum for first initiating a discussion.<br />
<br />
==Action Items==<br />
http://wiki.geneontology.org/index.php/SLC_GO_Consortium_Meeting_Minutes_April_2008#ACTION_ITEMS<br />
<br />
==Ontology Content Development==<br />
<br />
===Work in progress===<br />
*MF-BP links : [[Function-Process_Links]]<br />
** (Note from the managers' meeting: Chris has been updating the wiki pages; we should probably organize that by 'types' of links to be adding; this also involves the new relations to be added) <br />
** Outline of scope of project, progress report (Chris, ~25 slides)<br />
*** relations to be used - [[part_of]], [[has_part]] and [[regulates]]<br />
*** Implementation plan<br />
*** [[Mining_function_process_links_from_pathway_databases|Automatically extracting links from pathway databases]]<br />
** Manually curated links - pilot projects (Jennifer, Harold)<br />
:The electron transport working group have been discussing this issue in depth. We present our conclusions. In brief, our proposal is that links between function and process should only be made when we can use part_of (rather than has_part) or when there is a single step process term. (Jennifer presenting 29 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/FunctionProcessLinksPhotosynthesisJDeegan.ppt Slides])<br />
:*Plans to add regulates relationships within the molecular function (MF) ontology, and between MF and BP (David, Tanya, Chris) -- this is now covered<br />
*[[Ontology_Quality_Control|Ontology content QC]]<br />
**Ongoing regulation-term QC (David, Tanya, Chris) - think this is covered?<br />
**[[:Category:Cross Products]] - use of XP defs and logical reasoning to do QC. See [[XP:Progress 2008]]. (~5 slides, Chris)<br />
*"Trigger" files for annotation QC - first set based on taxon correlation (Jennifer, Chris)(Jennifer presenting 11 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/AnnotationQCJDeegan.ppt Slides])<br />
*[[Signaling|Signal transduction]] - New high level term proposal (Jennifer, David)<br />
:Jennifer and David have been working on a proposal for a new set of high level signaling terms. The new terms are ready to go live and we present them for comment. (~5 min talk) [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/SignalingProposalJDeegan.ppt Slides]<br />
*[[Cellular_component_processes|Processes affecting cellular components]], e.g. CC organization and biogenesis (Midori, Jane, David?)<br />
*PAMGO collaboration - brief report on new term additions and QC (Jane)<br />
*Collaboration with IMG to map to IMG terms to GO terms (Jane)<br />
*[[Proteases|Peptidase activity terms]] - reorganization completed<br />
<br />
===Ontology development discussion topics===<br />
*Setting priorities across different types of content development task<br />
**How to allocate effort among (a) overall logical enhancements (e.g. improving genus-differentia aspects of definitions or adding new relationship types); (b) keeping up with SF submissions; (c) content meeting changes; anything else<br />
**More generally, what's the right balance between retrofitting the existing ontology (definition style, relationship types just two examples) versus new additions?<br />
<br />
===OBO-Edit===<br />
* Update on latest version (Amina)<br />
** Using Reasoner and Cross-product definitions for Ontology QC and automated ontology management (Amina and Chris)<br />
* [[OBO-Edit progress statistics]]<br />
* Michael Schroeder et al. plug-in<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418257 Sourceforge Bug Tracker]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418260 Sourceforge Feature Requests]<br />
* [http://sourceforge.net/project/showfiles.php?group_id=36855&package_id=148487 Download the latest OBO-Edit2 beta]<br />
<br />
===Organization/Management===<br />
*SourceForge clearout done<br />
*Possible forthcoming changes to day-to-day editing practices (David, Midori, Chris?)<br />
**Creating and using cross-products<br />
**Using new relationship types<br />
**Integrating QC into editing pipeline<br />
<br />
==General Annotation==<br />
===Evidence Codes===<br />
* Using the ECO as the primary source (and definition) for evidence codes. The documentation should <em>reflect</em> (not define) the evidence codes found in the ontology. Also, need to make sure that there is a tracker for this.<br />
Plan to get some people together to work on it for 2-3 days and fix it (somewhat)<br />
* Michelle will be ECO editor<br />
* HTP evidence code? (Eurie)<br />
* [[Electronically curated flag]] in GAF proposal<br />
* New subcodes of IGC will be going into ECO: inferred from system reconstruction (ISR) and inferred from genome cluster (ICL). Currently IGC encompasses more than one type of evidence - it includes both pathway reconstruction/protein complex reconstruction and also operon structure/synteny. In order to be able to more precisely describe which was used we want to have the two new codes. These are currently being used by the Bioinformatics Resource Centers (BRCs). This was discussed on the evidence code mail list and there was no objection. (Michelle)<br />
<br />
===Annotation and ontologies===<br />
<br />
*A (re-)introduction to the new column 16, [[Annotation_Cross_Products]]<br />
*Ontological relationships between gene products and functions, processes and components<br />
<br />
===GO Database===<br />
* APIs<br />
** GHOUL GO Hibernate Object Utility Layer. An API to the GO database for Java programmers<br />
** Lucene indexing<br />
* Regular reporting of statistics, sanity checks, and such on the GO database.<br />
* New way of calculating the [[Transitive_closure]]<br />
<br />
===PAMGO report on successes and some problem annotations from consortium members===<br />
* PAMGO terms are in wide use, however they are sometimes being used incorrectly by consortium members. Candace will outline the way the terms should be used, Michelle will outline the problems and suggest some solutions. Also will touch on alternate taxon id resources that we might want to incoroporate. (Candace and Michelle)<br />
<br />
* Update on loading dual taxon into database/AmiGO. Also will touch on alternate taxon id resources that we might want to incoroporate. (Michelle and Chris?)<br />
<br />
==22 OCT AM: Reference Genome 1/2 day==<br />
<br />
<br />
<br />
===8:30 Progress Report===<br />
<br />
==Improvements in annotation depth and breadth ==<br />
(Chris and Mike's data)<br />
<br />
==Improvement in ontology structure==<br />
*Examples of ontology changes stemming from Reference Genome annotation (David?)<br />
<br />
===8:45 progress on homology sets and homology inference===<br />
Paul and Kara<br />
# generating homology sets, including protein set generation<br />
# new paradigm for making homology inferences <br />
# process and implementation for homology set selection, and homology inferences<br />
<br />
===Discussion about protein set generation===<br />
Paul <br />
* Issues: <br />
** incompleteness<br />
** splice forms vs canonical protein <br />
** complete proteome; partial gene predictions<br />
** possible solution: try to work with Swiss Prot?<br />
<br />
* Paul will present problems identified so far<br />
* We will add documentation as to how to generate files and protein sequences<br />
* Regarding gp2protein files: The original aim was to support BLAST server. <br />
** Do we need another file? g2protein? predicted_non_redundant_protein? this file would have just protein??<br />
<br />
===10:45 Annotation Consistency and Quality Issues===<br />
Pascale<br />
<br />
# How to improve documentation<br />
# How to address the QC issue<br />
# Make working groups for recurrent problems: <br />
#* binding<br />
#* regulation<br />
#* most evidence codes<br />
<br />
==Web presence, Outreach and User Advocacy==<br />
<br />
===Outreach===<br />
<br />
*Short update on Outreach going on throughout the Consortium. Highlights presented by Tanya Berardini (Author submission of annotations - 3 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/OutreachTAIR_PlantPhys_TBerardini.ppt Slides]) and Michelle Gwinn-Giglio (PAMGO outreach and University of Maryland Annotation courses - 6 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/OutreachMGwinnGiglio.ppt Slides]).<br />
*Swiss-Prot to do GO annotations (Michael)<br />
<br />
===AmiGO 1.6 for Reference Genome (Seth & Amelia)===<br />
# Present progress on AmiGO graphical views<br />
===Resource Usage statistics (Mike)===<br />
<br />
===User Support===<br />
# Evaluation of helpdesk performance<br />
<br />
===GO Papers, Publications and Presentations===<br />
# Ref Genome paper status report<br />
# AmiGO app. note<br />
# News letter impact<br />
<br />
==Other items==<br />
===Consortium meetings===<br />
*'''Next GOC meeting''' : Coordinate with [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html Third International Biocurator Meeting], Berlin, April 16-19, 2009?<br />
===Breakout sessions to fit in somehow===<br />
* Final preparations for SAB meeting<br />
* Amina, Chris and OBO-Edit users (including cross-products)<br />
* Pascale, Suzi and reference genome curators<br />
<br />
Return to [[Consortium_Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=20th_GO_Consortium_Meeting&diff=1619820th GO Consortium Meeting2008-10-19T14:05:12Z<p>Mlgwinn: /* PAMGO report on successes and some problem annotations from consortium members */</p>
<hr />
<div>=Logistics=<br />
[[Instructions_for_Registration]]<br />
<br />
<br />
=Agenda=<br />
'''ALERT:''' GO Top needs to sign off on agenda prior to these meetings. If there is no action item, or discussion point proposed in advance, the meeting is not the forum for first initiating a discussion.<br />
<br />
==Action Items==<br />
http://wiki.geneontology.org/index.php/SLC_GO_Consortium_Meeting_Minutes_April_2008#ACTION_ITEMS<br />
<br />
==Ontology Content Development==<br />
<br />
===Work in progress===<br />
*MF-BP links : [[Function-Process_Links]]<br />
** (Note from the managers' meeting: Chris has been updating the wiki pages; we should probably organize that by 'types' of links to be adding; this also involves the new relations to be added) <br />
** Outline of scope of project, progress report (Chris, ~25 slides)<br />
*** relations to be used - [[part_of]], [[has_part]] and [[regulates]]<br />
*** Implementation plan<br />
*** [[Mining_function_process_links_from_pathway_databases|Automatically extracting links from pathway databases]]<br />
** Manually curated links - pilot projects (Jennifer, Harold)<br />
:The electron transport working group have been discussing this issue in depth. We present our conclusions. In brief, our proposal is that links between function and process should only be made when we can use part_of (rather than has_part) or when there is a single step process term. (Jennifer presenting 29 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/FunctionProcessLinksPhotosynthesisJDeegan.ppt Slides])<br />
:*Plans to add regulates relationships within the molecular function (MF) ontology, and between MF and BP (David, Tanya, Chris) -- this is now covered<br />
*[[Ontology_Quality_Control|Ontology content QC]]<br />
**Ongoing regulation-term QC (David, Tanya, Chris) - think this is covered?<br />
**[[:Category:Cross Products]] - use of XP defs and logical reasoning to do QC. See [[XP:Progress 2008]]. (~5 slides, Chris)<br />
*"Trigger" files for annotation QC - first set based on taxon correlation (Jennifer, Chris)(Jennifer presenting 11 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/AnnotationQCJDeegan.ppt Slides])<br />
*[[Signaling|Signal transduction]] - New high level term proposal (Jennifer, David)<br />
:Jennifer and David have been working on a proposal for a new set of high level signaling terms. The new terms are ready to go live and we present them for comment. (~5 min talk) [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/SignalingProposalJDeegan.ppt Slides]<br />
*[[Cellular_component_processes|Processes affecting cellular components]], e.g. CC organization and biogenesis (Midori, Jane, David?)<br />
*PAMGO collaboration - brief report on new term additions and QC (Jane)<br />
*Collaboration with IMG to map to IMG terms to GO terms (Jane)<br />
*[[Proteases|Peptidase activity terms]] - reorganization completed<br />
<br />
===Ontology development discussion topics===<br />
*Setting priorities across different types of content development task<br />
**How to allocate effort among (a) overall logical enhancements (e.g. improving genus-differentia aspects of definitions or adding new relationship types); (b) keeping up with SF submissions; (c) content meeting changes; anything else<br />
**More generally, what's the right balance between retrofitting the existing ontology (definition style, relationship types just two examples) versus new additions?<br />
<br />
===OBO-Edit===<br />
* Update on latest version (Amina)<br />
** Using Reasoner and Cross-product definitions for Ontology QC and automated ontology management (Amina and Chris)<br />
* [[OBO-Edit progress statistics]]<br />
* Michael Schroeder et al. plug-in<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418257 Sourceforge Bug Tracker]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418260 Sourceforge Feature Requests]<br />
* [http://sourceforge.net/project/showfiles.php?group_id=36855&package_id=148487 Download the latest OBO-Edit2 beta]<br />
<br />
===Organization/Management===<br />
*SourceForge clearout done<br />
*Possible forthcoming changes to day-to-day editing practices (David, Midori, Chris?)<br />
**Creating and using cross-products<br />
**Using new relationship types<br />
**Integrating QC into editing pipeline<br />
<br />
==General Annotation==<br />
===Evidence Codes===<br />
* Using the ECO as the primary source (and definition) for evidence codes. The documentation should <em>reflect</em> (not define) the evidence codes found in the ontology. Also, need to make sure that there is a tracker for this.<br />
Plan to get some people together to work on it for 2-3 days and fix it (somewhat)<br />
* Michelle will be ECO editor<br />
* HTP evidence code? (Eurie)<br />
* [[Electronically curated flag]] in GAF proposal<br />
* New subcodes of IGC will be going into ECO: inferred from system reconstruction (ISR) and inferred from genome cluster (ICL). Currently IGC encompasses more than one type of evidence - it includes both pathway reconstruction/protein complex reconstruction and also operon structure/synteny. In order to be able to more precisely describe which was used we want to have the two new codes. These are currently being used by the Bioinformatics Resource Centers (BRCs). This was discussed on the evidence code mail list and there was no objection. (Michelle)<br />
<br />
===Annotation and ontologies===<br />
<br />
*A (re-)introduction to the new column 16, [[Annotation_Cross_Products]]<br />
*Ontological relationships between gene products and functions, processes and components<br />
<br />
===GO Database===<br />
* APIs<br />
** GHOUL GO Hibernate Object Utility Layer. An API to the GO database for Java programmers<br />
** Lucene indexing<br />
* Regular reporting of statistics, sanity checks, and such on the GO database.<br />
* New way of calculating the [[Transitive_closure]]<br />
<br />
===PAMGO report on successes and some problem annotations from consortium members===<br />
* PAMGO terms are in wide use, however they are sometimes being used incorrectly by consortium members. Candace will outline the way the terms should be used, Michelle will outline the problems and suggest some solutions. Also will touch on alternate taxon id resources that we might want to incoroporate. (Candace and Michelle)<br />
<br />
* Update on loading dual taxon into database/AmiGO. Also will touch on alternate taxon id resources that we might want to incoroporate. (Michelle and Chris)<br />
<br />
==22 OCT AM: Reference Genome 1/2 day==<br />
<br />
<br />
<br />
===8:30 Progress Report===<br />
<br />
==Improvements in annotation depth and breadth ==<br />
(Chris and Mike's data)<br />
<br />
==Improvement in ontology structure==<br />
*Examples of ontology changes stemming from Reference Genome annotation (David?)<br />
<br />
===8:45 progress on homology sets and homology inference===<br />
Paul and Kara<br />
# generating homology sets, including protein set generation<br />
# new paradigm for making homology inferences <br />
# process and implementation for homology set selection, and homology inferences<br />
<br />
===Discussion about protein set generation===<br />
Paul <br />
* Issues: <br />
** incompleteness<br />
** splice forms vs canonical protein <br />
** complete proteome; partial gene predictions<br />
** possible solution: try to work with Swiss Prot?<br />
<br />
* Paul will present problems identified so far<br />
* We will add documentation as to how to generate files and protein sequences<br />
* Regarding gp2protein files: The original aim was to support BLAST server. <br />
** Do we need another file? g2protein? predicted_non_redundant_protein? this file would have just protein??<br />
<br />
===10:45 Annotation Consistency and Quality Issues===<br />
Pascale<br />
<br />
# How to improve documentation<br />
# How to address the QC issue<br />
# Make working groups for recurrent problems: <br />
#* binding<br />
#* regulation<br />
#* most evidence codes<br />
<br />
==Web presence, Outreach and User Advocacy==<br />
<br />
===Outreach===<br />
<br />
*Short update on Outreach going on throughout the Consortium. Highlights presented by Tanya Berardini (Author submission of annotations - 3 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/OutreachTAIR_PlantPhys_TBerardini.ppt Slides]) and Michelle Gwinn-Giglio (PAMGO outreach and University of Maryland Annotation courses - 6 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/OutreachMGwinnGiglio.ppt Slides]).<br />
*Swiss-Prot to do GO annotations (Michael)<br />
<br />
===AmiGO 1.6 for Reference Genome (Seth & Amelia)===<br />
# Present progress on AmiGO graphical views<br />
===Resource Usage statistics (Mike)===<br />
<br />
===User Support===<br />
# Evaluation of helpdesk performance<br />
<br />
===GO Papers, Publications and Presentations===<br />
# Ref Genome paper status report<br />
# AmiGO app. note<br />
# News letter impact<br />
<br />
==Other items==<br />
===Consortium meetings===<br />
*'''Next GOC meeting''' : Coordinate with [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html Third International Biocurator Meeting], Berlin, April 16-19, 2009?<br />
===Breakout sessions to fit in somehow===<br />
* Final preparations for SAB meeting<br />
* Amina, Chris and OBO-Edit users (including cross-products)<br />
* Pascale, Suzi and reference genome curators<br />
<br />
Return to [[Consortium_Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=20th_GO_Consortium_Meeting&diff=1619720th GO Consortium Meeting2008-10-19T14:04:36Z<p>Mlgwinn: /* PAMGO report on successes and some problem annotations from consortium members */</p>
<hr />
<div>=Logistics=<br />
[[Instructions_for_Registration]]<br />
<br />
<br />
=Agenda=<br />
'''ALERT:''' GO Top needs to sign off on agenda prior to these meetings. If there is no action item, or discussion point proposed in advance, the meeting is not the forum for first initiating a discussion.<br />
<br />
==Action Items==<br />
http://wiki.geneontology.org/index.php/SLC_GO_Consortium_Meeting_Minutes_April_2008#ACTION_ITEMS<br />
<br />
==Ontology Content Development==<br />
<br />
===Work in progress===<br />
*MF-BP links : [[Function-Process_Links]]<br />
** (Note from the managers' meeting: Chris has been updating the wiki pages; we should probably organize that by 'types' of links to be adding; this also involves the new relations to be added) <br />
** Outline of scope of project, progress report (Chris, ~25 slides)<br />
*** relations to be used - [[part_of]], [[has_part]] and [[regulates]]<br />
*** Implementation plan<br />
*** [[Mining_function_process_links_from_pathway_databases|Automatically extracting links from pathway databases]]<br />
** Manually curated links - pilot projects (Jennifer, Harold)<br />
:The electron transport working group have been discussing this issue in depth. We present our conclusions. In brief, our proposal is that links between function and process should only be made when we can use part_of (rather than has_part) or when there is a single step process term. (Jennifer presenting 29 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/FunctionProcessLinksPhotosynthesisJDeegan.ppt Slides])<br />
:*Plans to add regulates relationships within the molecular function (MF) ontology, and between MF and BP (David, Tanya, Chris) -- this is now covered<br />
*[[Ontology_Quality_Control|Ontology content QC]]<br />
**Ongoing regulation-term QC (David, Tanya, Chris) - think this is covered?<br />
**[[:Category:Cross Products]] - use of XP defs and logical reasoning to do QC. See [[XP:Progress 2008]]. (~5 slides, Chris)<br />
*"Trigger" files for annotation QC - first set based on taxon correlation (Jennifer, Chris)(Jennifer presenting 11 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/AnnotationQCJDeegan.ppt Slides])<br />
*[[Signaling|Signal transduction]] - New high level term proposal (Jennifer, David)<br />
:Jennifer and David have been working on a proposal for a new set of high level signaling terms. The new terms are ready to go live and we present them for comment. (~5 min talk) [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/SignalingProposalJDeegan.ppt Slides]<br />
*[[Cellular_component_processes|Processes affecting cellular components]], e.g. CC organization and biogenesis (Midori, Jane, David?)<br />
*PAMGO collaboration - brief report on new term additions and QC (Jane)<br />
*Collaboration with IMG to map to IMG terms to GO terms (Jane)<br />
*[[Proteases|Peptidase activity terms]] - reorganization completed<br />
<br />
===Ontology development discussion topics===<br />
*Setting priorities across different types of content development task<br />
**How to allocate effort among (a) overall logical enhancements (e.g. improving genus-differentia aspects of definitions or adding new relationship types); (b) keeping up with SF submissions; (c) content meeting changes; anything else<br />
**More generally, what's the right balance between retrofitting the existing ontology (definition style, relationship types just two examples) versus new additions?<br />
<br />
===OBO-Edit===<br />
* Update on latest version (Amina)<br />
** Using Reasoner and Cross-product definitions for Ontology QC and automated ontology management (Amina and Chris)<br />
* [[OBO-Edit progress statistics]]<br />
* Michael Schroeder et al. plug-in<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418257 Sourceforge Bug Tracker]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418260 Sourceforge Feature Requests]<br />
* [http://sourceforge.net/project/showfiles.php?group_id=36855&package_id=148487 Download the latest OBO-Edit2 beta]<br />
<br />
===Organization/Management===<br />
*SourceForge clearout done<br />
*Possible forthcoming changes to day-to-day editing practices (David, Midori, Chris?)<br />
**Creating and using cross-products<br />
**Using new relationship types<br />
**Integrating QC into editing pipeline<br />
<br />
==General Annotation==<br />
===Evidence Codes===<br />
* Using the ECO as the primary source (and definition) for evidence codes. The documentation should <em>reflect</em> (not define) the evidence codes found in the ontology. Also, need to make sure that there is a tracker for this.<br />
Plan to get some people together to work on it for 2-3 days and fix it (somewhat)<br />
* Michelle will be ECO editor<br />
* HTP evidence code? (Eurie)<br />
* [[Electronically curated flag]] in GAF proposal<br />
* New subcodes of IGC will be going into ECO: inferred from system reconstruction (ISR) and inferred from genome cluster (ICL). Currently IGC encompasses more than one type of evidence - it includes both pathway reconstruction/protein complex reconstruction and also operon structure/synteny. In order to be able to more precisely describe which was used we want to have the two new codes. These are currently being used by the Bioinformatics Resource Centers (BRCs). This was discussed on the evidence code mail list and there was no objection. (Michelle)<br />
<br />
===Annotation and ontologies===<br />
<br />
*A (re-)introduction to the new column 16, [[Annotation_Cross_Products]]<br />
*Ontological relationships between gene products and functions, processes and components<br />
<br />
===GO Database===<br />
* APIs<br />
** GHOUL GO Hibernate Object Utility Layer. An API to the GO database for Java programmers<br />
** Lucene indexing<br />
* Regular reporting of statistics, sanity checks, and such on the GO database.<br />
* New way of calculating the [[Transitive_closure]]<br />
<br />
===PAMGO report on successes and some problem annotations from consortium members===<br />
* PAMGO terms are in wide use, however they are sometimes being used incorrectly by consortium members. Candace will outline the way the terms should be used, Michelle will outline the problems and suggest some solutions. Also will touch on alternate taxon id resources that we might want to incoroporate.<br />
<br />
* Update on loading dual taxon into database/AmiGO. Also will touch on alternate taxon id resources that we might want to incoroporate.<br />
<br />
==22 OCT AM: Reference Genome 1/2 day==<br />
<br />
<br />
<br />
===8:30 Progress Report===<br />
<br />
==Improvements in annotation depth and breadth ==<br />
(Chris and Mike's data)<br />
<br />
==Improvement in ontology structure==<br />
*Examples of ontology changes stemming from Reference Genome annotation (David?)<br />
<br />
===8:45 progress on homology sets and homology inference===<br />
Paul and Kara<br />
# generating homology sets, including protein set generation<br />
# new paradigm for making homology inferences <br />
# process and implementation for homology set selection, and homology inferences<br />
<br />
===Discussion about protein set generation===<br />
Paul <br />
* Issues: <br />
** incompleteness<br />
** splice forms vs canonical protein <br />
** complete proteome; partial gene predictions<br />
** possible solution: try to work with Swiss Prot?<br />
<br />
* Paul will present problems identified so far<br />
* We will add documentation as to how to generate files and protein sequences<br />
* Regarding gp2protein files: The original aim was to support BLAST server. <br />
** Do we need another file? g2protein? predicted_non_redundant_protein? this file would have just protein??<br />
<br />
===10:45 Annotation Consistency and Quality Issues===<br />
Pascale<br />
<br />
# How to improve documentation<br />
# How to address the QC issue<br />
# Make working groups for recurrent problems: <br />
#* binding<br />
#* regulation<br />
#* most evidence codes<br />
<br />
==Web presence, Outreach and User Advocacy==<br />
<br />
===Outreach===<br />
<br />
*Short update on Outreach going on throughout the Consortium. Highlights presented by Tanya Berardini (Author submission of annotations - 3 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/OutreachTAIR_PlantPhys_TBerardini.ppt Slides]) and Michelle Gwinn-Giglio (PAMGO outreach and University of Maryland Annotation courses - 6 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/OutreachMGwinnGiglio.ppt Slides]).<br />
*Swiss-Prot to do GO annotations (Michael)<br />
<br />
===AmiGO 1.6 for Reference Genome (Seth & Amelia)===<br />
# Present progress on AmiGO graphical views<br />
===Resource Usage statistics (Mike)===<br />
<br />
===User Support===<br />
# Evaluation of helpdesk performance<br />
<br />
===GO Papers, Publications and Presentations===<br />
# Ref Genome paper status report<br />
# AmiGO app. note<br />
# News letter impact<br />
<br />
==Other items==<br />
===Consortium meetings===<br />
*'''Next GOC meeting''' : Coordinate with [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html Third International Biocurator Meeting], Berlin, April 16-19, 2009?<br />
===Breakout sessions to fit in somehow===<br />
* Final preparations for SAB meeting<br />
* Amina, Chris and OBO-Edit users (including cross-products)<br />
* Pascale, Suzi and reference genome curators<br />
<br />
Return to [[Consortium_Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=20th_GO_Consortium_Meeting&diff=1619620th GO Consortium Meeting2008-10-19T14:03:03Z<p>Mlgwinn: /* Evidence Codes */</p>
<hr />
<div>=Logistics=<br />
[[Instructions_for_Registration]]<br />
<br />
<br />
=Agenda=<br />
'''ALERT:''' GO Top needs to sign off on agenda prior to these meetings. If there is no action item, or discussion point proposed in advance, the meeting is not the forum for first initiating a discussion.<br />
<br />
==Action Items==<br />
http://wiki.geneontology.org/index.php/SLC_GO_Consortium_Meeting_Minutes_April_2008#ACTION_ITEMS<br />
<br />
==Ontology Content Development==<br />
<br />
===Work in progress===<br />
*MF-BP links : [[Function-Process_Links]]<br />
** (Note from the managers' meeting: Chris has been updating the wiki pages; we should probably organize that by 'types' of links to be adding; this also involves the new relations to be added) <br />
** Outline of scope of project, progress report (Chris, ~25 slides)<br />
*** relations to be used - [[part_of]], [[has_part]] and [[regulates]]<br />
*** Implementation plan<br />
*** [[Mining_function_process_links_from_pathway_databases|Automatically extracting links from pathway databases]]<br />
** Manually curated links - pilot projects (Jennifer, Harold)<br />
:The electron transport working group have been discussing this issue in depth. We present our conclusions. In brief, our proposal is that links between function and process should only be made when we can use part_of (rather than has_part) or when there is a single step process term. (Jennifer presenting 29 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/FunctionProcessLinksPhotosynthesisJDeegan.ppt Slides])<br />
:*Plans to add regulates relationships within the molecular function (MF) ontology, and between MF and BP (David, Tanya, Chris) -- this is now covered<br />
*[[Ontology_Quality_Control|Ontology content QC]]<br />
**Ongoing regulation-term QC (David, Tanya, Chris) - think this is covered?<br />
**[[:Category:Cross Products]] - use of XP defs and logical reasoning to do QC. See [[XP:Progress 2008]]. (~5 slides, Chris)<br />
*"Trigger" files for annotation QC - first set based on taxon correlation (Jennifer, Chris)(Jennifer presenting 11 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/AnnotationQCJDeegan.ppt Slides])<br />
*[[Signaling|Signal transduction]] - New high level term proposal (Jennifer, David)<br />
:Jennifer and David have been working on a proposal for a new set of high level signaling terms. The new terms are ready to go live and we present them for comment. (~5 min talk) [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/SignalingProposalJDeegan.ppt Slides]<br />
*[[Cellular_component_processes|Processes affecting cellular components]], e.g. CC organization and biogenesis (Midori, Jane, David?)<br />
*PAMGO collaboration - brief report on new term additions and QC (Jane)<br />
*Collaboration with IMG to map to IMG terms to GO terms (Jane)<br />
*[[Proteases|Peptidase activity terms]] - reorganization completed<br />
<br />
===Ontology development discussion topics===<br />
*Setting priorities across different types of content development task<br />
**How to allocate effort among (a) overall logical enhancements (e.g. improving genus-differentia aspects of definitions or adding new relationship types); (b) keeping up with SF submissions; (c) content meeting changes; anything else<br />
**More generally, what's the right balance between retrofitting the existing ontology (definition style, relationship types just two examples) versus new additions?<br />
<br />
===OBO-Edit===<br />
* Update on latest version (Amina)<br />
** Using Reasoner and Cross-product definitions for Ontology QC and automated ontology management (Amina and Chris)<br />
* [[OBO-Edit progress statistics]]<br />
* Michael Schroeder et al. plug-in<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418257 Sourceforge Bug Tracker]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418260 Sourceforge Feature Requests]<br />
* [http://sourceforge.net/project/showfiles.php?group_id=36855&package_id=148487 Download the latest OBO-Edit2 beta]<br />
<br />
===Organization/Management===<br />
*SourceForge clearout done<br />
*Possible forthcoming changes to day-to-day editing practices (David, Midori, Chris?)<br />
**Creating and using cross-products<br />
**Using new relationship types<br />
**Integrating QC into editing pipeline<br />
<br />
==General Annotation==<br />
===Evidence Codes===<br />
* Using the ECO as the primary source (and definition) for evidence codes. The documentation should <em>reflect</em> (not define) the evidence codes found in the ontology. Also, need to make sure that there is a tracker for this.<br />
Plan to get some people together to work on it for 2-3 days and fix it (somewhat)<br />
* Michelle will be ECO editor<br />
* HTP evidence code? (Eurie)<br />
* [[Electronically curated flag]] in GAF proposal<br />
* New subcodes of IGC will be going into ECO: inferred from system reconstruction (ISR) and inferred from genome cluster (ICL). Currently IGC encompasses more than one type of evidence - it includes both pathway reconstruction/protein complex reconstruction and also operon structure/synteny. In order to be able to more precisely describe which was used we want to have the two new codes. These are currently being used by the Bioinformatics Resource Centers (BRCs). This was discussed on the evidence code mail list and there was no objection. (Michelle)<br />
<br />
===Annotation and ontologies===<br />
<br />
*A (re-)introduction to the new column 16, [[Annotation_Cross_Products]]<br />
*Ontological relationships between gene products and functions, processes and components<br />
<br />
===GO Database===<br />
* APIs<br />
** GHOUL GO Hibernate Object Utility Layer. An API to the GO database for Java programmers<br />
** Lucene indexing<br />
* Regular reporting of statistics, sanity checks, and such on the GO database.<br />
* New way of calculating the [[Transitive_closure]]<br />
<br />
===PAMGO report on successes and some problem annotations from consortium members===<br />
* PAMGO terms are in wide use, however they are sometimes being used incorrectly by consortium members. Candace will outline the way the terms should be used, Michelle will outline the problems and suggest some solutions. Also will touch on alternate taxon id resources that we might want to incoroporate.<br />
<br />
* Update on loading dual taxon into database/AmiGO<br />
<br />
==22 OCT AM: Reference Genome 1/2 day==<br />
<br />
<br />
<br />
===8:30 Progress Report===<br />
<br />
==Improvements in annotation depth and breadth ==<br />
(Chris and Mike's data)<br />
<br />
==Improvement in ontology structure==<br />
*Examples of ontology changes stemming from Reference Genome annotation (David?)<br />
<br />
===8:45 progress on homology sets and homology inference===<br />
Paul and Kara<br />
# generating homology sets, including protein set generation<br />
# new paradigm for making homology inferences <br />
# process and implementation for homology set selection, and homology inferences<br />
<br />
===Discussion about protein set generation===<br />
Paul <br />
* Issues: <br />
** incompleteness<br />
** splice forms vs canonical protein <br />
** complete proteome; partial gene predictions<br />
** possible solution: try to work with Swiss Prot?<br />
<br />
* Paul will present problems identified so far<br />
* We will add documentation as to how to generate files and protein sequences<br />
* Regarding gp2protein files: The original aim was to support BLAST server. <br />
** Do we need another file? g2protein? predicted_non_redundant_protein? this file would have just protein??<br />
<br />
===10:45 Annotation Consistency and Quality Issues===<br />
Pascale<br />
<br />
# How to improve documentation<br />
# How to address the QC issue<br />
# Make working groups for recurrent problems: <br />
#* binding<br />
#* regulation<br />
#* most evidence codes<br />
<br />
==Web presence, Outreach and User Advocacy==<br />
<br />
===Outreach===<br />
<br />
*Short update on Outreach going on throughout the Consortium. Highlights presented by Tanya Berardini (Author submission of annotations - 3 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/OutreachTAIR_PlantPhys_TBerardini.ppt Slides]) and Michelle Gwinn-Giglio (PAMGO outreach and University of Maryland Annotation courses - 6 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/OutreachMGwinnGiglio.ppt Slides]).<br />
*Swiss-Prot to do GO annotations (Michael)<br />
<br />
===AmiGO 1.6 for Reference Genome (Seth & Amelia)===<br />
# Present progress on AmiGO graphical views<br />
===Resource Usage statistics (Mike)===<br />
<br />
===User Support===<br />
# Evaluation of helpdesk performance<br />
<br />
===GO Papers, Publications and Presentations===<br />
# Ref Genome paper status report<br />
# AmiGO app. note<br />
# News letter impact<br />
<br />
==Other items==<br />
===Consortium meetings===<br />
*'''Next GOC meeting''' : Coordinate with [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html Third International Biocurator Meeting], Berlin, April 16-19, 2009?<br />
===Breakout sessions to fit in somehow===<br />
* Final preparations for SAB meeting<br />
* Amina, Chris and OBO-Edit users (including cross-products)<br />
* Pascale, Suzi and reference genome curators<br />
<br />
Return to [[Consortium_Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=20th_GO_Consortium_Meeting&diff=1619520th GO Consortium Meeting2008-10-19T13:54:41Z<p>Mlgwinn: /* Taxa */</p>
<hr />
<div>=Logistics=<br />
[[Instructions_for_Registration]]<br />
<br />
<br />
=Agenda=<br />
'''ALERT:''' GO Top needs to sign off on agenda prior to these meetings. If there is no action item, or discussion point proposed in advance, the meeting is not the forum for first initiating a discussion.<br />
<br />
==Action Items==<br />
http://wiki.geneontology.org/index.php/SLC_GO_Consortium_Meeting_Minutes_April_2008#ACTION_ITEMS<br />
<br />
==Ontology Content Development==<br />
<br />
===Work in progress===<br />
*MF-BP links : [[Function-Process_Links]]<br />
** (Note from the managers' meeting: Chris has been updating the wiki pages; we should probably organize that by 'types' of links to be adding; this also involves the new relations to be added) <br />
** Outline of scope of project, progress report (Chris, ~25 slides)<br />
*** relations to be used - [[part_of]], [[has_part]] and [[regulates]]<br />
*** Implementation plan<br />
*** [[Mining_function_process_links_from_pathway_databases|Automatically extracting links from pathway databases]]<br />
** Manually curated links - pilot projects (Jennifer, Harold)<br />
:The electron transport working group have been discussing this issue in depth. We present our conclusions. In brief, our proposal is that links between function and process should only be made when we can use part_of (rather than has_part) or when there is a single step process term. (Jennifer presenting 29 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/FunctionProcessLinksPhotosynthesisJDeegan.ppt Slides])<br />
:*Plans to add regulates relationships within the molecular function (MF) ontology, and between MF and BP (David, Tanya, Chris) -- this is now covered<br />
*[[Ontology_Quality_Control|Ontology content QC]]<br />
**Ongoing regulation-term QC (David, Tanya, Chris) - think this is covered?<br />
**[[:Category:Cross Products]] - use of XP defs and logical reasoning to do QC. See [[XP:Progress 2008]]. (~5 slides, Chris)<br />
*"Trigger" files for annotation QC - first set based on taxon correlation (Jennifer, Chris)(Jennifer presenting 11 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/AnnotationQCJDeegan.ppt Slides])<br />
*[[Signaling|Signal transduction]] - New high level term proposal (Jennifer, David)<br />
:Jennifer and David have been working on a proposal for a new set of high level signaling terms. The new terms are ready to go live and we present them for comment. (~5 min talk) [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/SignalingProposalJDeegan.ppt Slides]<br />
*[[Cellular_component_processes|Processes affecting cellular components]], e.g. CC organization and biogenesis (Midori, Jane, David?)<br />
*PAMGO collaboration - brief report on new term additions and QC (Jane)<br />
*Collaboration with IMG to map to IMG terms to GO terms (Jane)<br />
*[[Proteases|Peptidase activity terms]] - reorganization completed<br />
<br />
===Ontology development discussion topics===<br />
*Setting priorities across different types of content development task<br />
**How to allocate effort among (a) overall logical enhancements (e.g. improving genus-differentia aspects of definitions or adding new relationship types); (b) keeping up with SF submissions; (c) content meeting changes; anything else<br />
**More generally, what's the right balance between retrofitting the existing ontology (definition style, relationship types just two examples) versus new additions?<br />
<br />
===OBO-Edit===<br />
* Update on latest version (Amina)<br />
** Using Reasoner and Cross-product definitions for Ontology QC and automated ontology management (Amina and Chris)<br />
* [[OBO-Edit progress statistics]]<br />
* Michael Schroeder et al. plug-in<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418257 Sourceforge Bug Tracker]<br />
* [http://sourceforge.net/tracker/?group_id=36855&atid=418260 Sourceforge Feature Requests]<br />
* [http://sourceforge.net/project/showfiles.php?group_id=36855&package_id=148487 Download the latest OBO-Edit2 beta]<br />
<br />
===Organization/Management===<br />
*SourceForge clearout done<br />
*Possible forthcoming changes to day-to-day editing practices (David, Midori, Chris?)<br />
**Creating and using cross-products<br />
**Using new relationship types<br />
**Integrating QC into editing pipeline<br />
<br />
==General Annotation==<br />
===Evidence Codes===<br />
* Using the ECO as the primary source (and definition) for evidence codes. The documentation should <em>reflect</em> (not define) the evidence codes found in the ontology. Also, need to make sure that there is a tracker for this.<br />
Plan to get some people together to work on it for 2-3 days and fix it (somewhat)<br />
* Michelle will be ECO editor<br />
* HTP evidence code? (Eurie)<br />
* [[Electronically curated flag]] in GAF proposal<br />
<br />
===Annotation and ontologies===<br />
<br />
*A (re-)introduction to the new column 16, [[Annotation_Cross_Products]]<br />
*Ontological relationships between gene products and functions, processes and components<br />
<br />
===GO Database===<br />
* APIs<br />
** GHOUL GO Hibernate Object Utility Layer. An API to the GO database for Java programmers<br />
** Lucene indexing<br />
* Regular reporting of statistics, sanity checks, and such on the GO database.<br />
* New way of calculating the [[Transitive_closure]]<br />
<br />
===PAMGO report on successes and some problem annotations from consortium members===<br />
* PAMGO terms are in wide use, however they are sometimes being used incorrectly by consortium members. Candace will outline the way the terms should be used, Michelle will outline the problems and suggest some solutions. Also will touch on alternate taxon id resources that we might want to incoroporate.<br />
<br />
* Update on loading dual taxon into database/AmiGO<br />
<br />
==22 OCT AM: Reference Genome 1/2 day==<br />
<br />
<br />
<br />
===8:30 Progress Report===<br />
<br />
==Improvements in annotation depth and breadth ==<br />
(Chris and Mike's data)<br />
<br />
==Improvement in ontology structure==<br />
*Examples of ontology changes stemming from Reference Genome annotation (David?)<br />
<br />
===8:45 progress on homology sets and homology inference===<br />
Paul and Kara<br />
# generating homology sets, including protein set generation<br />
# new paradigm for making homology inferences <br />
# process and implementation for homology set selection, and homology inferences<br />
<br />
===Discussion about protein set generation===<br />
Paul <br />
* Issues: <br />
** incompleteness<br />
** splice forms vs canonical protein <br />
** complete proteome; partial gene predictions<br />
** possible solution: try to work with Swiss Prot?<br />
<br />
* Paul will present problems identified so far<br />
* We will add documentation as to how to generate files and protein sequences<br />
* Regarding gp2protein files: The original aim was to support BLAST server. <br />
** Do we need another file? g2protein? predicted_non_redundant_protein? this file would have just protein??<br />
<br />
===10:45 Annotation Consistency and Quality Issues===<br />
Pascale<br />
<br />
# How to improve documentation<br />
# How to address the QC issue<br />
# Make working groups for recurrent problems: <br />
#* binding<br />
#* regulation<br />
#* most evidence codes<br />
<br />
==Web presence, Outreach and User Advocacy==<br />
<br />
===Outreach===<br />
<br />
*Short update on Outreach going on throughout the Consortium. Highlights presented by Tanya Berardini (Author submission of annotations - 3 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/OutreachTAIR_PlantPhys_TBerardini.ppt Slides]) and Michelle Gwinn-Giglio (PAMGO outreach and University of Maryland Annotation courses - 6 [http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/meeting/consortium/Montreal2008/OutreachMGwinnGiglio.ppt Slides]).<br />
*Swiss-Prot to do GO annotations (Michael)<br />
<br />
===AmiGO 1.6 for Reference Genome (Seth & Amelia)===<br />
# Present progress on AmiGO graphical views<br />
===Resource Usage statistics (Mike)===<br />
<br />
===User Support===<br />
# Evaluation of helpdesk performance<br />
<br />
===GO Papers, Publications and Presentations===<br />
# Ref Genome paper status report<br />
# AmiGO app. note<br />
# News letter impact<br />
<br />
==Other items==<br />
===Consortium meetings===<br />
*'''Next GOC meeting''' : Coordinate with [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html Third International Biocurator Meeting], Berlin, April 16-19, 2009?<br />
===Breakout sessions to fit in somehow===<br />
* Final preparations for SAB meeting<br />
* Amina, Chris and OBO-Edit users (including cross-products)<br />
* Pascale, Suzi and reference genome curators<br />
<br />
Return to [[Consortium_Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=October_2008_Meeting_Logistics&diff=15378October 2008 Meeting Logistics2008-09-12T18:06:58Z<p>Mlgwinn: /* Attendees */</p>
<hr />
<div>===Dates===<br />
* GO consortium meeting will be held on October 21-22, 2008 (Tues-Wed)<br />
* SAB meeting will be held on October 23, 2008 (Thurs)<br />
<br />
===Venue===<br />
[http://www.montgabriel.com/en_home.php Mont Gabriel], 45 miles north of Montreal. <br />
<br />
===Registration===<br />
<br />
* '''Reserve your room by calling the hotel at 1-800-668-5253; ask for "reservations" and identify yourself as part of the Northwestern University group.''' <br><br />
Sorry, no online registration. <br />
* If you participate in both the GO meeting and the SAB, you should check in on the 20th (Monday) and leave on the 24th, as we are planning full days meetings. <br />
* You will need to pay a 50$ deposit by credit card at the time of reservation. <br />
* PLEASE REGISTER BEFORE SEPTEMBER 12, 2008<br />
<br />
====Room====<br />
* There is a choice between three kinds of rooms (depending on availability) [http://www.montgabriel.com/en_accommodations_tyrol.php Tyrol] ("Superior" room with balcony), [http://www.montgabriel.com/en_accommodations_rustique.php Rustique] (log cabin-style) (there are only about 8 rooms available of this type), and [http://www.montgabriel.com/en_accommodations_marquise.php Marquise] (smaller rooms). '''All rooms are the same price.'''<br />
<br />
===Cost===<br />
* The cost per day is CAN $208.00 (~208$ USD), including dinner, accommodation, breakfast and lunch (which includes taxes and service). If you plan to miss a meal, the price will be adjusted accordingly ($17 for breakfast, $22 for lunch, $43 dinner). <br />
* If you want to share a room (two double or queen beds); in that case the price for the room is the same, $126, so that's $63 per person. <br />
* We will need to charge a small fee (10-15$ per day) for coffee breaks but this needs to be done separately.<br />
<br />
===Internet===<br />
Wireless internet will be available in the conference room and in the rooms. <br />
<br />
===Food===<br />
* Bien sur, the menu is French-inspired, which means quite a bit of meat. However, there will always be fish and vegetarian options. Fill in the table below or contact me if you have special requirements.<br />
<br />
===Transportation===<br />
* Fly to Montreal-Trudeau Airport (YUL). This airport used to be called Dorval, you may still see that sometimes (for example, on Google maps...). <br />
* The hotel offers a shuttle from the Montreal Trudeau Airport for up to 6 people for a flat rate of $140. <br />
* A taxi would be about 100$ (Taxis des Pays-d'en-Haut, 450-227-3000; I suggest you call in advance). <br />
* You can also rent a car from the airport. [[YUL-Gabriel Driving instructions]].<br />
<br />
===To do===<br />
<br />
====On site====<br />
<br />
* http://www.montgabriel.com/en_activities.php<br />
Tennis and golf should be open; I am not sure about the pool. It's possible to go jogging on the golf course just outside the hotel.<br />
<br />
====If you want to explore Montreal====<br />
<br />
* Montreal links : http://www.montreal.com/tourism/general.html, http://www.discovermontreal.ca/, http://www.go-montreal.com/<br />
* Cycling in and around the city: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails.jsp <br />
** I quite enjoy this one: http://english.montrealplus.ca/feature/crazy_for_cycling/8536/trails_lachine_canal.jsp<br />
* In October the Montreal Botanical Garden will have their annual 'THE MAGIC OF LANTERNS' event at Chinese gardens http://www2.ville.montreal.qc.ca/jardin/en/chine/programme.htm<br />
* You can combine the visit to the Botanical Garden with the Biodome [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=visite&page=musee&menu=musee] and the Insectarium [http://www2.ville.montreal.qc.ca/insectarium/en/index.php]. The three museums part of the same complex and you can get combined tickets [http://www2.ville.montreal.qc.ca/biodome/site/gabarit.php?dossier=info&page=tarif&menu=tarif]<br />
* On a warm evening the Old Port [http://www.vieux.montreal.qc.ca/] [http://www.go-montreal.com/areas_oldmontreal.htm] is really nice.<br />
<br />
====In the Laurentians====<br />
<br />
* The Laurentians: http://www.laurentians.com/<br />
<br />
* Cycling/walking Le P'tit Train du Nord: http://www.out-there.com/pt-train.htm or http://www.laurentians.com/parclineaire/<br />
<br />
* Golfing http://www.teeingitup.com/canada/laurentians.htm<br />
<br />
* Yoga (they have camps - $80/day- or you can take a ~1.5 h lesson for $10) http://sivananda.hdthost.com/website/Main.aspx?lang=en-CA<br />
<br />
===Contact===<br />
'''Please contact Pascale Gaudet if you have any questions: pgaudet -at- northwestern.edu'''<br />
<br />
<br />
<br />
<br />
===Attendees===<br />
(please use the Arrival and Departure info columns if you would like to try a carpool to/from the airport)<br />
{|border="1" cell spacing="0" cellpadding="4" align="center"<br />
|-<br />
! Name<br />
! Attending GOC (Oct 21-22, 2008)<br />
! Attending SAB (Oct 23, 2008)<br />
! Food requirement (None, Veggie, Vegan)<br />
! Arrival Date/Time to Airport (YUL) <br />
! Departure Date/Time from Airport (YUL)<br />
|-<br />
| Pascale Gaudet<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Amelia Ireland<br />
| yes<br />
|<br />
|<br />
| 20 Oct 18:00<br />
| 26 Oct 08:25<br />
|-<br />
| Chris Mungall<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Michael Ashburner<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| yes<br />
| yes<br />
| yummy<br />
| Oct 20, 5:09PM, UA8185, LGA-Montreal<br />
| Oct 23, 7:55PM, UA8400, Montreal-LGA<br />
|-<br />
| Jennifer Deegan<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Midori Harris<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Jane Lomax<br />
| yes<br />
| yes (am only)<br />
| none<br />
|Oct 20, 425PM, NW8671, Montreal<br />
|Oct 23, 625PM, NW8672, Montreal<br />
|-<br />
| Harold Drabkin<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Rex Chisholm<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Alexander Diehl<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Mike Cherry<br />
| yes<br />
| yes<br />
|<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Doug Howe<br />
| yes<br />
| no<br />
| none<br />
|Oct 20, 440PM United, Montreal<br />
|Oct 23, 240PM United, Montreal<br />
|-<br />
| Mary Dolan<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| yes<br />
| yes<br />
| none<br />
|<br />
|<br />
|-<br />
| Victoria Petri<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Eurie Hong<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Julie Park<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Debby Siegele<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Brenley McIntosh<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Tanya Berardini<br />
| yes<br />
| <br />
| none<br />
|<br />
|<br />
|-<br />
| Kara Dolinski<br />
| yes<br />
| no<br />
| none<br />
|Mon, Oct 20, 4:50PM, Continental<br />
|Wed, Oct 22, 5:30PM departure<br />
|-<br />
| Donghui Li<br />
| yes<br />
| <br />
| none<br />
|Oct 20, 8:10pm United<br />
|Oct 25, 8:40am, leaving from Montreal<br />
|-<br />
| Stan Laulederkind<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Edith Wong<br />
| yes<br />
| yes<br />
| none<br />
| Oct 20, 8:10pm United<br />
| Oct 24, 8:40am United<br />
|-<br />
| Amina Abdulla<br />
| yes<br />
| no<br />
| none<br />
|<br />
|<br />
|-<br />
| Seth Carbon<br />
| yes<br />
| no<br />
| none<br />
| 20 Oct, from SFO<br />
| 24 Oct, from Montreal<br />
|-<br />
| Candace Collmer<br />
| yes<br />
| no<br />
| none<br />
|20 Oct 17:15 US Airways<br />
|23 Oct 13:30 US Airways<br />
|-<br />
| Dmitry Sitnikov<br />
| yes<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|Michelle Gwinn Giglio<br />
|yes<br />
|no<br />
|none<br />
|Oct. 20 6:28 PM United<br />
|Oct. 23 2:23 PM United<br />
|<br />
|}<br />
<br />
<br />
[[Consortium_Meetings|Consortium meetings main page]]<br />
<br />
[[Category:Meetings]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=SLC_GO_Consortium_Meeting&diff=12506SLC GO Consortium Meeting2008-04-16T21:27:37Z<p>Mlgwinn: /* Agenda Items */</p>
<hr />
<div>== Venue ==<br />
<br />
==='''Meeting Room'''===<br />
*The Meeting will be held in the Salt Lake City Library, Conference Room 4<br />
*210 East 400 South, SLC UT 84111<br />
*http://www.slcpl.lib.ut.us/locations.jsp?parent_id=8&page_id=20<br />
<br />
*Conference Room 4 is the large conference room on the 4th floor, located behind the front desk to the right.<br />
*We are not allowed to put posters up to direct you, but if you get lost, the library staff will point you in the right direction.<br />
<br />
==='''Dates:'''=== <br />
*April 22-23, 2008 <br />
*We will be providing lunch on the 22nd<br />
*The meeting ends at lunchtime on the 23rd.<br />
*Dinner will be held on Tuesday 22nd April at [http://www.cannellas.com/ Cannellas]. The reservation is for 6.30, and it is located one block South from the library.<br />
<br />
==='''Cost'''===<br />
* $50.00; Receipt will be provided at registration. We will be taking cash and checks. Checks should be made payable to the Department of Human Genetics. The address if needed for the check is: Eccles Institute of Human Genetics, Building 533, University of Utah, 15 North 2030 East, Salt Lake City, Utah. 84112.<br />
* Dinner: cost TBD; we are looking for a sponsor<br />
* You are responsible for your lodging costs<br />
<br />
==='''Lodging:'''===<br />
*The [http://www.guesthouse.utah.edu/ugh/information.htm University GuestHouse]is a good place to stay as it is a short walk to HSEB. If you are also attending the Reference Genome Meeting, it is a small walk from the that venue, and a TRAX ride from the library - door to door. The one way fare is $1.75 or a day pass can be purchased for $4.50. Tickets can be purchased at the platform. A map is available here: http://www.rideuta.com/images/TRAX082607.jpg<br />
TRAX schedule from the guest house to the library. (The library opens at 9 am.) <br />
{| border="1" cellspacing="0" cellpadding="5" align="center"<br />
| MEDICAL CENTER <br />
| FT DOUGLAS<br />
|SOUTH CAMPUS<br />
|STADIUM TRAX STATION<br />
|900 EAST & 400 SOUTH (TRAX) <br />
|TROLLEY TRAX STATION<br />
|LIBRARY TRAX STATION<br />
|-<br />
|08:23 AM <br />
|08:25 AM <br />
|08:27 AM <br />
|08:29 AM <br />
|08:32 AM <br />
|08:34 AM<br />
|08:36 AM<br />
|-<br />
|08:38 AM <br />
|08:40 AM <br />
|08:42 AM <br />
|08:44 AM <br />
|08:47 AM <br />
|08:49 AM<br />
|08:51 AM<br />
|-<br />
|}<br />
<br />
<br />
<br />
*Please make reservations early as it is a popular place and there will be extra people in town for the marathon.<br />
<br />
*If you need to make other arrangements let me know (Karen E) and I will find a different hotel. <br />
*The [http://marriott79-px.trvlclick.com/hotels/travel/slcup-salt-lake-city-marriott-university-park/ | University_Marriott] at the university is a cab ride from both venues.<br />
<br />
*There are many hotels downtown with reasonable rates such as the Little America and the Red Lion.<br />
*The [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/| Downtown_Marriott] within walking distance of the library, but it is $259 per night!<br />
*To book a taxi from the library to the airport: 801 521 2100<br />
<br />
== Registration ==<br />
Please [[http://gocwiki.geneontology.org/index.php/Register#Registration_for_April_2008_GO_Meetings_at_University_of_Utah.2C_SLC Register]] for one or both meetings.<br />
<br />
== Draft Agenda ==<br />
<b>Tue am - </b> <br />
#9:00- Intro, review agenda<br />
*Annotations<br />
#9:15 - 10:00 - Ref Genome report (Pascale)<br />
##Annotation Metrics<br />
##Annotation Pipeline<br />
##Annotation to Isoforms (new columns ?? )<br />
<br />
*10:00-10:45 Ontology Development<br />
#Report on accomplishments (15 min. for 1st several items; 30 min. for 'regulates')<br />
##[[Sensu Main Page|Sensu]]<br />
##Disjoint violations corrected<br />
##[[Cardiovascular physiology/development|Cardio]] & [[Muscle Development|muscle]] content meeting work<br />
##[[Electron transport]]<br />
##SourceForge statistics<br />
##[[Regulation Main Page|Regulates]] (including activators and inhibitors)<br />
<br />
*break 10:45-11:00<br />
<br />
*11:00-noon Ontology Development continued<br />
#Work in progress<br />
##[[Function-Process Links]] (Harold, Chris, Jen)<br />
### Considerations on Glycolysis [[http://wiki.geneontology.org/index.php/Glycolysis_Cross_Products]] and TCA cycle [[http://wiki.geneontology.org/index.php/TCA_Cycle_Cross_Products]]<br />
###Also see "term granularity" below<br />
##[[Taxon Main Page|Taxon]]<br />
##[[Lung Development]]<br />
#Future work<br />
##[[Signaling|Signal transduction]]<br />
##[[Morphogenesis]]<br />
##[[Transporters| Transport]]<br />
##Metabolism cleanup<br />
#Outstanding issues<br />
##Response to X ([[Response to drug|drug]], toxin) Response to Chemical<br />
##Establishment and Maintenance Terms<br />
##Chemical derivatives and metabolism terms<br />
##Term granularity (and Reactome)<br />
##[[Proteases]]<br />
<br />
*noon - lunch <br />
<br />
<b>Tues Afternoon Session - </b><br />
<br />
# 1:00 - 1:30 Advocacy/Outreach/Collaborations (Jen/Jane)<br />
##Help Desk (stats report) and newsletter<br />
##User Oversight of AmiGO functionality (look and feel)<br />
##Active outreach collaborations<br />
##New outreach contacts. <br />
#1:30 - 2:00 - SO (Karen E)<br />
#2:00 - 2:30 - OBO-Edit<br />
## Might include demo of Michael Schoeder's plug-in<br />
<br />
*break<br />
<br />
#3:00 - 5:00 AmiGO<br />
## ReferenceGenes - DB management extensions<br />
<br />
<b>Wed AM</b><br />
<br />
# Overall Project Management<br />
# Metrics for Success<br />
<br />
==Agenda Items==<br />
<br />
At the moment this is a free-form list of items suggested for discussion.<br />
<br />
# Have Tanya give a presentation on implementation of 'regulates' and the work that she and David and Chris (and others) have done in this area. 'Regulates' will go live at the end of March, so there may be discussion points on this. We will also discuss 'regulation of biological quality' and how their negative and positive children relate.<br />
# Discuss how we are going to handle function terms such as activators and inhibitors. When do we create them and how do they relate to processes and other functions. (David and Tanya)<br />
# Discuss how we are going to handle 'response to drug' SF 1242405 and 1494526 and 'response to toxin' SF1658374. Are they normal biological processes? (David and Tanya)<br />
# Discuss function-process links. What relationships should we use? Who will make the assertions?(Harold, Jen & Chris)<br />
## See current work and discussions [[Function-Process_Links]]<br />
# (from ref genomes group): Would it be useful to add the 'comprehensively annotated' tag to all genes (not just the ref genome genes)? Either in the gene association file or in the database somehow<br />
# At one of our meetings Chris suggested we might keep an archive of gene sets used in publications that were analyzed using GO. Should we do this? (David)<br />
# Collaboration with other projects<br />
## PRO: Protein Ontology (Harold)<br />
## Reactome<br />
## Panther<br />
## NCBO<br />
## MP-PATO<br />
## KARO<br />
# Annotation Objects: how to handle GO annotation to specific isoforms, modified proteins, etc. (Harold)<br />
# Report results of experiment on finding annotation errors using GO-taxon links. (Jen)<br />
# How should we handle derivative compounds in the metabolism parts of GO--should we continue to include metabolism of X derivatives as is_a descendants of X metabolism? It can be confusing. For example, SFs [https://sourceforge.net/tracker/index.php?func=detail&aid=1885151&group_id=36855&atid=440764 1885151] and [https://sourceforge.net/tracker/index.php?func=detail&aid=1847808&group_id=36855&atid=440764 1847808] note that 'gamma-aminobutyric acid metabolic process' is a descendant of 'fatty acid metabolic process' because GABA is a derivative of butyric acid. (Midori and Val)<br />
# Should we approach authors of papers describing computationally assisted annotation of genes from non-MOD species with GO terms to integrate their results into the GO database? If not, can we take any advantage of these studies? For example, click on B2G in Papers on this site [[http://blast2go.de/]] (Tanya)<br />
# Proteases: any objections to making a lot of protease activity MF terms obsolete, on the grounds that they're gene products? See [[Proteases]] for a detailed proposal. (Midori et al.)<br />
# Granularity in GO - Peter (Reactome) has raised this question again, because we've discussed it but not fully reached consensus. An example from Reactome's perspective: "GO, for instance, has a single term GO:0031261 'DNA replication preinitiation complex', with no child terms, while Reactome enumerates all the intermediate stages of its assembly during G1 of the cell cycle and activation at G1/S." Should GO simply add the very specific terms from Reactome? (I think the same question applies to GO process terms -- many Reactome events are much more fine-grained than most GO processes.) (Midori and Peter)<br />
<br />
<br />
##Mixing evidence and annotation method<br><br />
<br />
Email from SGD about the need to annotate new computational datasets.<br><br />
<pre><br />
SGD has come across couple of computationally predicted GO<br />
annotation data sets for S. cerevisiae that we would like to add to<br />
our database. The GO annotations from these data sets are<br />
predictions based on multiple high-throughput data sets. RCA<br />
evidence code came to our minds but according to the documentation,<br />
the annotations all have to be manually reviewed by a curator to<br />
use this evidence. There are several 100 annotations of this kind<br />
and it is not feasible for us to manually review these annotations.<br />
<br />
Hence, we thought these annotations can be bulk loaded with IEA<br />
evidence code. However, in the Jan 2007 (Cambridge) GO meeting, it<br />
was decided that the 'with' column information has to be filled in<br />
for all IEAs (else Mike's filtering script strips them out). But<br />
these GO annotations being predictions based on multiple high-<br />
throughput data sets, don't have any information for the with<br />
column. So, we are left with no choice.<br />
<br />
Which evidence code do people think should be used for these kinds<br />
of computational datasets when there is not an obvious "with"?<br />
<br />
Thanks for your input.<br />
Rama</pre><br />
<br />
Response from Kara (Princeton)<br><br />
<pre><br />
Hi,<br />
<br />
The root of the problem, as I see it, is that we are mixing apples<br />
and oranges with evidence codes. All but one of the evidence codes<br />
indicate the type of experimental evidence for a GO annotation, but<br />
we have one oddball, IEA, that indicates not what the experiment is,<br />
but rather how the annotation was done. We keep running into<br />
variations of the same problem: we have some evidence (whether<br />
experimental or computational) for a GO annotation, but also want to<br />
indicate whether a curator looked at it or not.<br />
<br />
My proposed (albeit radical) solution:<br />
<br />
Remove IEA as an evidence code.<br />
<br />
Create a new property for GO annotations (or add a new type of<br />
qualifier) that captures how the annotation was done: manual or<br />
automated.<br />
<br />
Everything that is currently IEA would be given the 'automated'<br />
property/qualifier, and then would be given a new evidence code as<br />
appropriate (mostly a flavor of ISS I would assume).<br />
There can be a rule that all 'automated' annotations that are a<br />
flavor of ISS must have a 'with' value.<br />
<br />
This would allow us to use 'RCA' as appropriate, in some cases<br />
they'd be 'manual', in others, they'd be 'automated'. In Rama's<br />
case, the annotations would be 'RCA' with an 'automated' qualifier.<br />
<br />
I realize the issues involved in making such a drastic change, so I<br />
understand if we don't go there, but I do think that some approach<br />
such as the one above is the best representation of the information<br />
that we are trying to capture.<br />
</pre></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=External_Database_Contact_Info_(Archived)&diff=12104External Database Contact Info (Archived)2008-03-26T16:21:45Z<p>Mlgwinn: /* */</p>
<hr />
<div>Many groups associated with and outside the GOC consume the resources produced by GO, such as the gene_ontology_edit.obo file and the association files. Any major changes to these files are signaled in advanced on the gofriends list. We also would like to track the persons in charge of the technical aspects of the various different MOD databases in order to make sure they are prepared for forthcoming changes.<br />
<br />
== dictyBase ==<br />
<br />
* siddhartha-basu AT northwestern DOT edu<br />
* pgaudet AT northwestern DOT edu<br />
<br />
Schema: Chado<br />
<br />
== SGD ==<br />
<br />
* Ben Hitz ( hitz AT genome DOT stanford AT edu)<br />
* Mike Cherry (cherry AT stanford DOT edu)<br />
<br />
== RGD ==<br />
<br />
Curation<br />
* Victoria Petri vpetri at mcw dot edu<br />
* Mary Shimoyama shimoyama at mcw dot edu<br />
<br />
Technical<br />
* Alex Stoddard (astoddard at mcw dot edu)<br />
<br />
Admin<br />
* Simon Twigger simont at mcw dot edu<br />
<br />
== MGI ==<br />
<br />
* David Miers <dbm AT informatics DOT jax DOT org><br />
* Jim Kadin <jak AT informatics DOT jax DOT org><br />
<br />
==UniProtKB ==<br />
<br />
* Dan Barrel<br />
* David Binns?<br />
<br />
== WormBase ==<br />
<br />
== FlyBase ==<br />
<br />
Curation/Admin<br />
* s.tweedie AT gen.cam.ac.uk<br />
<br />
Developers<br />
* emmert AT morgan.harvard.edu<br />
* p.leyland AT gen.cam.ac.uk<br />
<br />
Schema: Chado<br />
<br />
== GR (Gramene) ==<br />
<br />
* <br />
* Pankaj?<br />
<br />
== SPombe/GeneDB_* ==<br />
<br />
* Martin Aslett maa AT sanger DOT ac DOT uk<br />
<br />
== NCBI ==<br />
<br />
* ?<br />
<br />
== E Coli ==<br />
<br />
* Jim Hu?<br />
<br />
== ZFIN ==<br />
<br />
* Sierra Moxon?<br />
* Doug?<br />
<br />
== TAIR ==<br />
<br />
== Reactome ==<br />
<br />
* gopinath AT cshl.edu<br />
* eustachi AT cshl.edu<br />
<br />
==Institute for Genome Sciences ==<br />
<br />
*Michelle Gwinn Giglio (mgiglio AT som DOT umaryland DOT edu)</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Register&diff=11654Register2008-02-23T15:01:03Z<p>Mlgwinn: /* Registration for April 2008 GO Meetings at University of Utah, SLC */</p>
<hr />
<div>===Registration for April 2008 GO Meetings at University of Utah, SLC===<br />
<br />
Please register here giving information about which meetings you will be attending. <br />
We are asking for 'years on the project' because this is the 10th year of the GOC and we want to celebrate.<br />
<br />
{|border="1" cell spacing="0" cellpadding="5" align="left"<br />
!Name <br />
!Institution <br />
!Model Organism(s) and/or Speciality <br />
!Years on GOC project <br />
!Role on GOC project <br />
!Coming to Ref Genome? <br />
!Coming to GOC? <br />
!Where are you staying? <br />
!food requirement<br />
|-<br />
|Sue Rhee<br />
|The Arabidopsis Information Resource (TAIR)<br />
|Arabidopsis<br />
|8 years<br />
|Co-PI<br />
|No<br />
|Yes<br />
|not arranged yet<br />
|<br />
|-<br />
|Karen Eilbeck<br />
|University of Utah<br />
|Sequences<br />
|5 years<br />
|SO manager<br />
|yes<br />
|yes<br />
|Home<br />
|veggie<br />
|-<br />
|Judy Blake<br />
|The Jackson Laboratory<br />
|mouse /genomics<br />
|10 years<br />
|PI <br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Suzanna Lewis<br />
|Lawrence Berkeley National Laboratory<br />
|Bioinformatics / fly<br />
|10 years<br />
|PI<br />
|yes<br />
|yes<br />
|?<br />
|<br />
|-<br />
|Harold Drabkin<br />
|The Jackson Laboratory<br />
|mouse / biochemistry<br />
|7 years<br />
|BioCurator<br />
|yes<br />
|yes<br />
|not arranged yet<br />
|<br />
|-<br />
|Amelia Ireland<br />
|GO Editorial Office, EBI<br />
|Jack of all trades<br />
|6<br />
|Senior GO Curator<br />
|yes<br />
|yes<br />
|hopefully not on the streets<br />
|<br />
|-<br />
|Jennifer Deegan<br />
|GO Editorial Office, EBI<br />
|Large scale content efforts. <br />
|5 years<br />
|Ontology Editor, Outreach/Advocacy Manager<br />
|No<br />
|Yes<br />
|Little America<br />
|No restrictions<br />
|-<br />
|Daniel Barrell<br />
|EMBL - The EBI<br />
|UniProt/Human/Chicken/Cow<br />
|7 years<br />
|GOA database programmer<br />
|No<br />
|Yes<br />
|Little America<br />
|none<br />
|-|<br />
|David Hill<br />
|The Jackson Laboratory<br />
|mouse/developmental biology/ontology content<br />
|9 years<br />
|MGI curator/ Ontology Development Co-manager<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Midori Harris<br />
|GO Editorial Office, EBI<br />
|GO content, especially trying to keep up with ordinary SourceForge submissions<br />
|9.5 years<br />
|GO Editor; ontology development co-manager<br />
|yes<br />
|yes<br />
|University Guest House<br />
|no restrictions<br />
|-<br />
|Pascale Gaudet<br />
|Northwestern University<br />
|dictyBase curator<br />
|5 years<br />
|annotation/reference genomes/ontology content/AmiGO-WPWG<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Tanya Berardini<br />
|The Arabidopsis Information Resource<br />
|Arabidopsis/developmental biology/ontology content<br />
|6 years<br />
|annotation/reference genomes/ontology development/OBO-Edit working group/annotation outreach<br />
|yes<br />
|yes<br />
|Not arranged yet<br />
|<br />
|-<br />
|Mary Dolan<br />
|MGI, The Jackson Laboratory<br />
|Mouse<br />
|5 years<br />
|computational methods/tool development/software<br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|none<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase, Caltech<br />
|C. elegans<br />
|5 years<br />
|curator/user advocacy (gohelp)/software development for semi-automated curation<br />
|yes<br />
|yes<br />
|University Guest House<br />
|none<br />
|-<br />
|Mike Cherry<br />
|SGD, Stanford<br />
|S. cerevisiae<br />
|10 years<br />
|PI<br />
|yes<br />
|yes<br />
|University Guesthouse (to be arranged)<br />
|none<br />
|-<br />
|Doug Howe<br />
|ZFIN, U. Oregon<br />
|D. rerio<br />
|4.5 years<br />
|Ontology development/Ref. Genome/GO annotation<br />
|Yes<br />
|Yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Stacia Engel<br />
|SGD, Stanford<br />
|S. cerevisiae<br />
|6 years<br />
|Curator/refGenome<br />
|yes<br />
|yes<br />
|University Guesthouse (to be arranged)<br />
|<br />
|-<br />
|Susan Tweedie<br />
|FlyBase, University of Cambridge<br />
|Drosophila<br />
|2 years<br />
|GO annotation/ref. genome/newsletter team<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|veggie<br />
|-<br />
|Seth Carbon<br />
|Berkeley BOP<br />
|AmiGO/Software<br />
|~1 1/2<br />
|AmiGO/Software and related WGs<br />
|yes<br />
|yes<br />
|TBD<br />
|none<br />
|-<br />
| Valerie Wood<br />
| WT Sanger Institute<br />
| S. pombe MOD DB project manager<br />
| 8<br />
| S. pombe / GO curator/ ref genomes group/ AWG (retired!)<br />
| yes<br />
| yes<br />
| TBD <br />
|<br />
|-<br />
|Fiona McCarthy <br />
|Mississipi State University (AgBase)<br />
|chicken & cow <br />
|3 sort of<br />
|associate GOC member, chick Ref genome, Outreach<br />
|yes <br />
|yes<br />
|TBD<br />
|<br />
|-<br />
|Ranjana Kishore<br />
|WormBase, Caltech<br />
|C. elegans<br />
|5<br />
|Curator/Annotation, Ref genomes, Outreach<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|veggie<br />
<br />
|-<br />
|Chris Mungall<br />
|LBNL<br />
|<br />
|8<br />
|Software Manager<br />
|yes<br />
|yes<br />
|?<br />
|veggie<br />
|-<br />
|Donghui Li<br />
|TAIR<br />
|Arabidopsis/ontology content<br />
|2 years<br />
|annotation/reference genomes/ontology development<br />
|yes<br />
|yes<br />
|not arranged yet<br />
|veggie<br />
|-<br />
|Emily Dimmer<br />
|GOA<br />
|Human<br />
|4.5 years<br />
|curator/GOA co-ordinator<br />
|yes<br />
|yes<br />
|University GuestHouse<br />
|<br />
|-<br />
|Jim Hu<br />
|EcoliWiki/EcoliHub and GONUTS<br />
|''E. coli''<br />
|1.5 years<br />
|E. coli for RefGenome<br />
|yes<br />
|no (have to teach)<br />
|not arranged yet<br />
|<br />
|-<br />
|Debby Siegele<br />
|EcoliWiki/EcoliHub<br />
|''E. coli''<br />
|<br />
|E. coli for RefGenome<br />
|maybe<br />
|no<br />
|<br />
|<br />
|-<br />
|Rex Chisholm<br />
|dictyBase<br />
|D. discoideum<br />
|9 years<br />
|co-PI/reference genomes<br />
|yes<br />
|yes<br />
|University Guesthouse<br />
|<br />
|-<br />
|Michelle Gwinn Giglio<br />
|Institute for Genome Sciences<br />
|prokaryotes<br />
|7 years<br />
|annotator/term developer/PAMGO/outreach group/evidence group<br />
|no<br />
|yes<br />
|University Guest House<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|-<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|<br />
|}<br />
<br />
<br />
[[SLC_GO_Consortium_Meeting|SLC Consortium meeting]] |<br />
[[SLC_GO_Reference_Genome_Project_Meeting|SLC Ref Genomes meeting]] | [[GO_Field_Trip|SLC field trip]] |<br />
[[Consortium_Meetings|Consortium meetings main page]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=2007_GOC_Action_Items&diff=98302007 GOC Action Items2007-09-21T19:08:35Z<p>Mlgwinn: /* Action Items for review at Sept 2007 GOC meeting held at Princeton */</p>
<hr />
<div>==Action Items for review at Sept 2007 GOC meeting held at Princeton==<br />
From Jan. 2007 GOC meeting held in Cambridge U.K. <br />
http://www.geneontology.org/GO.meetings.shtml?all#consort<br />
<br />
<br />
Details for Princeton meeting on [[GO 18th Consortium Meeting ]] pages<br />
<br />
<br />
1. DONE_Action item for Judy – post templates for yearly reports on Wiki<br />
[[http://gocwiki.geneontology.org/index.php/Consortium_Meetings]]<br />
<br />
2. DONE Action Item (Hub): Make proposals for various displays of reference genome data<br />
<BR>See: http://gocwiki.geneontology.org/index.php/AmiGO:_Prototypes#Reference_Genome<br />
<br />
3. DONE (in a sense). Action item for John – make it impossible to add non-is_a complete terms in OBO-Edit.<br />
<br>Addressed by having all GO curators apply a verification check. [mah]<br />
<br />
4. IN PROGRESS Action item for Michelle – get this info [i.e., on TIGR course attendance and whether any participants use GO afterwards -mah]<br />
We just got our Annotation Engine grant funded and as part of that we will be surveying people who attended the classes.<br />
<br />
5. DONE! Action item (David & Chris): create a minimum list of information needed to report methods when doing GO analysis for a publication. This isn't my action item, but this is related. I can tidy this up before the meeting....Val<br />
http://gocwiki.geneontology.org/index.php/Reviewing_papers<br />
I think this item had to do with tool standards, not reviewing papers. [[Tools_standards]]<br />
<br>I seem to recall that both tool standards and paper-reviewing standards were deemed desirable (tho the latter may have transpired after the meeting). [mah]<br />
<br />
6. Action Item for Suzi and Managers: Proposal for each working group to write down their protocols and currently active projects. Timelines and priorities/roadmap would be useful. Metrics too. Ontology development_DONE<br />
<br />
7. DONE! Action Item for Amelia: Post all presentations from the meeting onto the Wiki site.<br />
<br />
8. Action Item: GO-top: Talk with each manager and bring summary reports to the next meeting.<br />
<br />
9. DONE Action Item: Jen and Suzi: Evaluate and make recommendations for project tracking software that might help with this.<br />
<br />
10. NOT DONE. Action Item for John: Add a term creation date to the .obo file. It didn't get added to the feature request tracker so it was overlooked. Now added: <br />
<br />
11. DONE Action Item for Jen: All “sensu XXX” terms will be changed to “sensu the XXX community”. And undone as well, since it was superceded by the decision to remove sensu altogether (see #72 & &73 below)<br />
<br />
12.In progress. Action item for Midori and David (from 2): Find a way to communicate responsibilities and availability viz ontology working groups. Devise a systematic way to bring closure to outstanding term request items. We've made some plans, but not yet acted upon.<br />
<br>We have begun implementing our plans (and refining them, as needed); a respectable number of SF items have been assigned, though for others we still need to find expertise. I think of this as an ongoing ontology development effort rather than a discrete one-off action item. [mah]<br />
<br />
13. NOT DONE: Action item for AmiGO Working Group (from 4): The AmiGO Working Group will implement a strategy to incorporate and display the contents of the GO references. Request is on the AmiGO tracker (thanks Jane) http://sourceforge.net/tracker/index.php?func=detail&aid=1667315&group_id=36855&atid=494390<br />
<br />
14. DONE! Action Item for Content Group (from 5, low priority): Make actin polymerization a function term. [Content group] In progress, may be done by meeting time; see SF 1621572. -- SF:1621572 closed<br />
<br />
15. Action Item for GOA (from 1): Talk to Reactome about getting non-TAS evidence. TAS is no longer considered a useful evidence code and will not be used in any consistency measures of reference genome annotation. Since part of the idea of the reference genomes is to provide a source of IEA annotations for other groups, we strongly encourage reference genome annotators to not use TAS, and instead use experimental evidence codes whenever possible. The GO documentation should also state this in a clear fashion. [annotation camp participants]<br />
<br />
16. Action Item for Judy, Harold, Amelia, Eurie, John Day-Richter (from 3,4,5): Resolve communication issues around obsoletes.<br />
<br />
17. NOT DONE (more discussion required) Action Item for Chris and Jane (Revisit 7): Remove the word 'activity' from the molecular function terms, and consider renaming the molecular function ontology. [note that later on in the meeting after action item 73 notes state that more discussion on this proposal is needed]<br />
<br />
18. [In Progress] Action Item for Jen & Chris (from 8): Assign priorities for contents changes needed to implement sensu plan. Discuss the different aspects of changes to our use of sensu, write documentation on this, and implement the new strategy. This change will then be announced to the community.<br><br />
Comment: There is more discussion to be had on this and a slot has been assigned for this in the meeting. <br />
<br />
19. Action Item for Amelia (Revisit 10): The monthly archive of the GO will also include Release Notes. These notes would include the output of the monthly report script, including the relevant SourceForge IDs, as well as human-readable text that summarizes significant additions or changes to the GO file.<br />
<br />
20. Action Item for Karen C. (from 11): Add to the documentation that it is okay to use experimental evidence codes for perfectly identical gene products from different strains of the same species.<br />
<br />
21. Action Item for Eurie (Revisit 12): No conclusion about how to distinguish large- vs small-scale experiments was reached. People are encouraged to keep thinking about this issue, which clearly needs more discussion.<br />
<br />
22. DONE: Action Item for John: Link OBO-Edit docs to geneontology.org from oboedit.org.<br />
<br />
23. DONE: Action item for Mike: Change documentation to make clear that annotation file column 1 gives the database from which the identifier in column 2 is drawn, NOT (as it currently says) the id of the submitting authority. [changed DB column definition in http://www.geneontology.org/GO.format.annotation.shtml<br />
<br />
24. DONE! Action item for Daniel: Form working group to help groups that are having problems resolving redundancy issues.<br />
<br />
25. DONE! Action Item for User Advocacy Group: Make all multi-species files (UniProt & PDB) readily and obviously available on the GO website. Include obvious and prominent documentation explaining that these multi-species files will contain redundancies with the other files, but don't necessarily contain all annotations from other groups.<br />
<br />
26. Action Item for Karen E.(?) & Rex: –Work out kinks in getting this data [i.e., GFF3 files] and make it readily available from the GO site.<br />
<br />
27. DONE should be checked by Karen E and Suzanna: Action item (Mike): Add SO ids for allowed objects to documentation. (changed doc to say one of gene (SO:0000704), transcript (SO:0000673), protein (SO:0000358), protein_structure, complex. There does not appear to be a SO term for these two concepts protein_structure or complex)<br />
<br />
28. Action item (Suzi, Tanya): Continue developing [protein family-based annotation] tool.<br />
<br />
29. Action item (Midori and Rex): Do it [i.e., new column in annotation files], add the column and document the formalism.<br />
<br>It's not at all clear why this has my name (and I don't remember); it seems more for the software group and annotators. [mah]<br />
<br />
30. REJECTED Action Item (Content Working Group): Pick a new name for cellular component. [note, this was superseded later with decision not to change this name – see action items 81 & 82].<br />
<br />
31. Action Item (Jane): Keep researching CARO integration.<br />
<br />
32. Action Item (AWG): Explore whether this [Mary's graphs] would be a useful addition to AmiGO 2.0.<br />
<br />
33. Action Item (AWG): There should be more tracking of what users are doing in the next AmiGO; explore the options.<br />
<br />
34. Action Item (Seth & AWG): Discussed that these changes should be reflected in AmiGO.<br />
<br />
35. Action Item (John & Jane): Come up with a proposal for a history tracking tool, including timeframe and priority, and send out email.<br />
<br />
36. Action item (David, Jane): Organize first training meeting.(postponed due to the amount happening at this meeting)<br />
<br />
37. Action Item (Nicole, Jane, John, Mark): Create proposal to group for term submission software, including the “minimum standards for each term”.<br />
<br />
38. Action Item (AmiGO Working Group): Change AmiGO to hide (by default) structured comments of certain types. Obsolete comments will not be shown. Structured comments that don’t belong will not be shown. Have option to hide comments.<br />
<br />
39. Action Item (Karen E.): Send the information [microarray tool evaluation] to the group<br />
<br />
40. Action Item (User Advocacy): Create a Wiki page for each tool on GO tools. GO's official tool recommendations (if we have them) can be posted on the Wiki. Link to a Google user group for tool discussions<br />
<br />
41. Action Item (User Advocacy): Publish minimum standards for tools on GO tools. This can just extend the existing questionnaire.<br />
<br />
42. Action Item (Everyone): Email suggestions for meetings at which we'll do outreach to Eurie & Jane & Jen.<br>[Ongoing - working well]<br />
<br />
43. DONE, continuing: Action Item (Everyone): Put meetings on the Google calendar.<br />
<br />
44. Action Item (Eurie & Jane): Create Wiki of meetings gathered from emails.<br />
<br />
45. Action Items (Managers): Revisit metrics & priorities.<br />
<br />
46. Action Item (Managers): Create structure within working group Wikis to allow people to announce what they are working on.<br />
<br>Ontology development started, and ongoing; as "done" as it can be. [mah]<br />
<br />
47. Action Item (Everyone): Create list of projects they are working on, post on Wiki.<br />
<br>Ontology development done. [mah]<br />
<br />
48. DONE! Action Item (John): Tell everyone I'm worried that we don't have enough of a plan.<br />
<br />
49. Action Item (Chris, Karen C.): Publish a succinct paragraph explaining why unknowns were removed. Karen C. will write documentation targeting biologists; Chris writes an explanation targeting software engineers. Publish on website, possibly in newsletter, wherever necessary.<br />
<br />
Items 50-52 are about the WITH field for the IPI code.<br><br />
50. Action Item (MGI, SGD): Change all pipes to commas.<br />
<br />
51. Action Item (Chris, Ben): Work through any database implications.<br />
<br />
52. Action Item (User Advocacy): Announce in newsletter, “what's new” section of GO site.<br />
<br />
53. Action Item (Everyone) – Tell code extension advocates to piss off. Attendees voiced strong opinions against extending evidence codes.<br />
<br />
54. DONE? Action Item (John): Email Simon Twigger OBO-Edit Piccolo/GraphViz source code.<br />
<br />
55. Action item (Karen C): makes these statements very explicit in the documentation.<br />
<br />
56. Action Item (Rex, Eurie): Create a gene page for each reference gene on Wiki. Use Alex's pages as a template. Link Wiki pages to existing annotations.<br />
<br />
57. DONE! Action Item (Everyone): Feel good about WebEx, continue to exploit Tanya's account. Continue to use Ready Conference and Skype. Avoid long-term lock-ins.<br />
<br />
58. DONE! Action Item (MGD): Get a WebEx account.<br />
<br />
59. DONE Action Item (Jen & John & Tanya): Research commercial version of Skype to possibly replace Ready Conference.<br />
<br />
60. Action Item (Evidence Code Working Group): Develop a decision tree for choosing an evidence code. Present results at next consortium meeting. (large scale/small scale, reviewed/un-reviewed. Similarity/not-similarity etc).<br />
<br />
61. Action Item (Rex): Assign programmer to check integrity of WITH field for annotations.<br />
<br />
62. Action Item (Everyone): Add SwissProt keyword ids to WITH column when appropriate.(MGI-DONE, GOA-DONE, ZFIN-DONE)<br />
<br />
63. Action Item (Evidence Code Working Group): Send RCA code back to committee.<br />
<br />
64. Action Item (Evidence Code Working Group): Except where contradicted by other action items above, accept recommendations in Evidence Code Proposals Draft.<br />
<br />
65. Action Item (everyone): Change unknown manual annotations to ND, use GO ref or internal reference, don't reference the paper. IEAs to the root term are acceptable.(MGI-DONE)<br />
<br />
66. Action Item (everyone): When annotating NOT, if no positive annotation can be made, the gene product should ALSO be annotated to the root.<br />
<br />
67. Action Item (Committee): Update documentation to reflect previous action item.<br />
<br />
68. Action Item (Evidence Code Working Group): Send ND back to committee.<br />
<br />
69. Action Item (Reference Genome): Discuss scheduling for a reference genome meeting/annotation camp. DONE<br />
<br />
70. [Done] Action Item (Jen, Michelle): Outreach annotation course organization, publicity.<br />
<br />
71. Action Item (Everyone): Don't use community-specific (limited to being understood only by that community) terms as the primary term name. Create a community-neutral primary term (structured synonym), and use the community-specific term as an exact synonym. Tag these exact synonyms by community as appropriate.<br />
<br />
72. DONE Action Item (Jen): Change all “sensu the XXX community” terms back to "sensu XXX". See #11 and #73<br />
<br />
73. [In Progress] Action Item (Ontology Editors, high priority): Accept Chris & Jen's proposal to get rid of sensu terms. The few remaining terms should be called “sensu the XXX community”. <br><br />
Comment: The few remaining sensu terms are awaiting expert input. They are listed here along with questions for specific people: http://gocwiki.geneontology.org/index.php/Meeting_Notes_3<br />
<br />
74. Action Item (Chris, Jane, Harold): Create concrete proposal for linking between all GO ontologies, get relationship ontology up to speed, do pilot project in metabolism.<br />
<br />
75. Action Item (Amelia): Talk to Stanford about monthly archive release notes.<br />
<br />
76. Action Item (Suzi): Come up with a structure for reporting our time commitments.<br />
<br />
77. DONE: Action Item (GO Top): Get back to Karen C. on proposal to extend evidence code committee.<br />
<br />
78. Action Item (User Advocacy): Draft an official GO brochure.<br />
<br />
79. NOT DONE, can do this when needed. Action Item (Mike): Create GO banners.<br />
<br />
80. [Not Done Yet] Action Item (Jen): Create Wiki page with a checklist of what to bring/do when advocating GO at a meeting.<br><br />
Comment: This is very straightforward to do and has just got lost in the huge number of other things going on. We can do it soon if it is considered high-priority. <br />
<br />
81. Action Item (Everyone): Use the word cellular to refer to things related to a cell but aren't necessarily cells or things contained within a cell. Use the word cell to refer to cells themselves or things contained within a cell. (Change cell signaling to cellular signaling, for example).<br />
<br />
82. Action Item (Jane): Tweak cellular component definition to clearly distinguish cellular component from cell part.</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Meeting_Notes_3&diff=9600Meeting Notes 32007-08-31T18:31:05Z<p>Mlgwinn: /* spores */</p>
<hr />
<div>==Nematode development==<br />
<br />
negative regulation of vulval development (sensu Nematoda) <br><br />
positive regulation of vulval development (sensu Nematoda) <br><br />
regulation of vulval development (sensu Nematoda) <br><br />
vulval development (sensu Nematoda) <br><br />
tail tip morphogenesis (sensu Nematoda) <br><br />
<br />
'''People:'''<br><br />
Kimberly<br><br />
Doug?<br><br />
David<br><br />
<br />
'''Questions:'''<br />
<br />
What is the distinguishing feature of the anatomical structure vulva between species? <br><br />
Do we want a term just called vulval development?<br><br />
Can we handle this by making cross references to anatomical dictionaries?<br><br />
For tail tip morph, do we even need the sensu Nematode?<br />
<br />
'''Plan'''<br><br />
<br />
<br />
==spores==<br />
<br />
spore wall assembly (sensu Bacteria) <br><br />
spore wall assembly (sensu Fungi) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Jim Hu<br><br />
Michelle<br><br />
Midori<br><br />
<br />
'''Questions:'''<br><br />
<br />
Same question as cell walls.<br><br />
What are the distinguishing features of the walls?<br><br />
or<br />
What are the distinguishing features of the assembly of the walls?<br><br />
<br />
<br />
'''Plan:'''<br><br />
<br />
Michelle speaking - I see from below the "sporulation" terms still have sensu designations - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.<br />
<br />
==Chromosome==<br />
<br />
chromosome organization and biogenesis (sensu Bacteria) <br><br />
chromosome organization and biogenesis (sensu Eukaryota) <br><br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
Eurie<br><br />
<br />
'''Questions:'''<br><br />
<br />
What are the distinguishing features?<br><br />
Do we lump mitochondrial and plastid with bacterial?<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
Michelle speaking - It seems to me that these processes are really the same - yes different genes and proteins are involved in the different types of organism, but I don't see why there needs to be separate terms. Can these just be merged into their parent? I think you would want to keep mitochondrial and plastid terms separate as they are "auxillary" chromosomes, not the primary genome of the organism (not that they aren't important).<br />
<br />
==cell polarity==<br />
<br />
establishment and/or maintenance of cell polarity (sensu Fungi) <br><br />
establishment of cell polarity (sensu Fungi) <br><br />
maintenance of cell polarity (sensu Fungi) <br><br />
<br />
'''People:'''<br><br />
<br />
David<br><br />
Midori<br><br />
Rex<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Merge these terms with their non-sensu parents. Fungal cell polarity is the model system for everything on polarity.<br><br />
<br />
==neural rod==<br />
<br />
neural rod cavitation (sensu Teleost) <br><br />
neural rod formation (sensu Teleost) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
Doug<br><br />
David<br><br />
<br />
'''Questions:'''<br><br />
<br />
How do we distinguish neural rods in Teleosts and other things. Does anything else have neural rods?<br />
<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
==gastrulation==<br />
<br />
gastrulation (sensu Vertebrata) <br><br />
gastrulation (sensu Mammalia) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
David<br><br />
Doug<br><br />
Victoria<br><br />
<br />
'''Questions:'''<br><br />
<br />
What distinguishes mammalian gastrulation from other organisms?<br><br />
<br />
'''Plan:'''<br><br />
<br />
Find distinguishing feature or merge terms. <br><br />
<br />
<br />
==pigment==<br />
<br />
pigment cell differentiation (sensu Nematoda and Protostomia) <br><br />
pigment cell differentiation (sensu Vertebrata) <br><br />
<br />
'''People:'''<br><br />
<br />
Kimberly<br><br />
David<br><br />
Doug<br><br />
Victora<br><br />
Susan Tweedie<br><br />
Becky Foulger<br><br />
<br />
'''Questions:'''<br><br />
<br />
Should we have a sensu designation or should we just enumerate the types of pigment cells underneath the parent pigment term. <br><br />
Look to the cell ontology for guidance.<br> <br />
<br />
'''Plan:'''<br><br />
<br />
<br />
==larval development==<br />
<br />
larval development (sensu Amphibia) <br><br />
larval development (sensu Nematoda) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
Becky Foulger<br><br />
Kimberly<br><br />
<br />
'''Questions:'''<br><br />
<br />
What are the distinguishing features?<br><br />
Is it worth having separate terms for each?<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==genderization==<br />
<br />
hermaphrodite germ-line sex determination (sensu Nematoda) <br><br />
feminization of hermaphroditic germ-line (sensu Nematoda) <br><br />
masculinization of hermaphroditic germ-line (sensu Nematoda) <br><br />
hermaphrodite somatic sex determination (sensu Nematoda) <br><br />
feminization of hermaphrodite soma (sensu Nematoda) <br><br />
masculinization of hermaphrodite soma (sensu Nematoda) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
Kimberly<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
Is there any other type or can we just merge into the generic parent?<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==spores==<br />
<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore wall (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Pascale<br><br />
Jen<br><br />
Michelle <br><br />
Jim Hu<br><br />
Tanya<br><br />
Midori<br><br />
Val<br><br />
<br />
<br />
'''Questions:'''<br><br />
Ask Chris Brett if he knows difference between plant, bacterial, and fungal cell walls. <br />
Also relevant to cell walls. [Jen]<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==proteasome==<br />
<br />
proteasome core complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle (sensu Eukaryota) <br><br />
proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
proteasome complex (sensu Eukaryota) <br><br />
cytosolic proteasome complex (sensu Eukaryota) <br><br />
proteasome core complex (sensu Bacteria) <br><br />
proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Bacteria) <br><br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Rama<br><br />
Jim Hu<br><br />
Michelle<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
<br />
==cytosolic ribosome==<br />
<br />
cytosolic large ribosomal subunit (sensu Eukaryota) <br><br />
cytosolic large ribosomal subunit (sensu Archaea) <br><br />
cytosolic large ribosomal subunit (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Archaea) <br><br />
cytosolic ribosome (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Eukaryota) <br><br><br />
cytosolic small ribosomal subunit (sensu Archaea) <br><br />
cytosolic small ribosomal subunit (sensu Bacteria) <br><br />
cytosolic small ribosomal subunit (sensu Eukaryota) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Harold<br><br />
Michelle<br><br />
Jim Hu<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
From Harold's e-mail:<br />
<br />
<br />
The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.<br> <br />
Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. These are generated from post-transcriptional processing of a single rRNA precursor. <br />
Prokaroytic ribosomes contain about 50 proteins. The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt) <br><br />
Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are post-transcriptionally processed from a single rRNA <br />
precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA polymerase III, whereas the large transcript containing <br />
the other three is synthesized by RNA polymerase I. The large rRNA, typically called &ldquo;28s&rdquo;, is in fact much larger than it's bacterial counterpart <br />
(~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt. Eukaryotic ribosomes contain 70-80 proteins.<br><br />
I would think that the most single feature is the 3 vs 4 chain.<br><br />
Although basically, mitochondrial ribosomes are thought to be &ldquo;prokaryote-like&rdquo;, some fungal and animal mitochondrial ribosomes lack 5 sRNA, and are <br />
thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then you would b safe).<br><br />
The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have an intermediate number of proteins, etc. The <br />
expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together. <br><br />
I propose <br><br />
1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)<br><br />
2. Four-RNA chain containing ribosomes. ( 5.8s-, eukarytotic-type)<br><br />
Note, I have tried to get away from using exact S-values in the term name. Using them in the def would be fine, I hope. Although I wouldn't be adverse to using <br />
&ldquo;5.8s-containing ribosome vs ??).<br><br />
Now, the large subunit of each class is where you will have the 3 vs 4 chain difference.<br />
The small subunit is the hard one: more prokaryotic like than eukaryotic, but a work around would be<br><br />
small subunit of a three-chain containing ribosome<br><br />
smll subunit of a four-chain containg ribosome.<br><br><br />
References:<br><br />
Personal communication Dr. Caroline Kohler, Dept. of Biology, MIT, and<br><br />
Lewin, Genes VII ISBN:019879276-X<br><br><br />
The Ribosome, ISBN:0879696206<br />
<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Find previous notes from e-mail. <br><br />
<br />
<br />
<br />
==NADH and reaction centre==<br />
<br />
NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)<br><br />
NADH dehydrogenase complex (quinone) (sensu Bacteria) <br><br />
NADH dehydrogenase complex (ubiquinone) (sensu Bacteria) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
==plasmid partitioning (sensu Bacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
Eurie<br><br />
Michelle<br><br />
Midori<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==somitomeric trunk muscle development (sensu Mammalia) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
David <br><br />
Victoria<br><br />
Emily<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Probably merge with parent.<br><br />
<br />
==otolith==<br />
<br />
otolith mineralization (sensu Actinopterygii) <br><br />
otolith mineralization (sensu Tetrapoda) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
David Fashena<br><br />
https://sourceforge.net/tracker/index.php?func=detail&aid=1109256&group_id=36855&atid=440764 <br><br />
Midori<br><br />
David<br><br />
Emily<br><br />
Victoria<br><br />
Doug (I can consult with Dave F. as he is in the next office over)<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
==outer membrane biogenesis (sensu ProteoBacteria) ==<br />
<br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Jim Hu<br><br />
Michelle<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
Check how we distinguish the outer membrane in the component ontology.<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
==invasive growth (sensu Saccharomyces) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
Maria Costanzo<br><br />
Val<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1583546&group_id=36855 <br><br />
Also consider pseudohyphal growth and filamentous growth.<br><br />
<br />
'''Plan:'''<br><br />
<br />
==reaction center (sensu ProteoBacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
<br />
Jim Hu <br><br />
Michelle<br><br />
Jen<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Meeting_Notes_3&diff=9599Meeting Notes 32007-08-31T18:28:59Z<p>Mlgwinn: /* spores */</p>
<hr />
<div>==Nematode development==<br />
<br />
negative regulation of vulval development (sensu Nematoda) <br><br />
positive regulation of vulval development (sensu Nematoda) <br><br />
regulation of vulval development (sensu Nematoda) <br><br />
vulval development (sensu Nematoda) <br><br />
tail tip morphogenesis (sensu Nematoda) <br><br />
<br />
'''People:'''<br><br />
Kimberly<br><br />
Doug?<br><br />
David<br><br />
<br />
'''Questions:'''<br />
<br />
What is the distinguishing feature of the anatomical structure vulva between species? <br><br />
Do we want a term just called vulval development?<br><br />
Can we handle this by making cross references to anatomical dictionaries?<br><br />
For tail tip morph, do we even need the sensu Nematode?<br />
<br />
'''Plan'''<br><br />
<br />
<br />
==spores==<br />
<br />
spore wall assembly (sensu Bacteria) <br><br />
spore wall assembly (sensu Fungi) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Jim Hu<br><br />
Michelle<br><br />
Midori<br><br />
<br />
'''Questions:'''<br><br />
<br />
Same question as cell walls.<br><br />
What are the distinguishing features of the walls?<br><br />
or<br />
What are the distinguishing features of the assembly of the walls?<br><br />
<br />
<br />
'''Plan:'''<br><br />
<br />
Michelle speaking - I see in AmiGO that the "sporulation" terms still have sensu designations (I think) - didn't we talk once about making terms that were "reproductive sporulation" and "stress-induced sporulation" or something along those lines? If so, could we carry that into these terms? I fear that there might be so much heterogeneity in spore wall structures (even within bacteria) that getting good defs based on that may be hard. But I need to do more checking.... that was just a first thought.<br />
<br />
==Chromosome==<br />
<br />
chromosome organization and biogenesis (sensu Bacteria) <br><br />
chromosome organization and biogenesis (sensu Eukaryota) <br><br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
Eurie<br><br />
<br />
'''Questions:'''<br><br />
<br />
What are the distinguishing features?<br><br />
Do we lump mitochondrial and plastid with bacterial?<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
Michelle speaking - It seems to me that these processes are really the same - yes different genes and proteins are involved in the different types of organism, but I don't see why there needs to be separate terms. Can these just be merged into their parent? I think you would want to keep mitochondrial and plastid terms separate as they are "auxillary" chromosomes, not the primary genome of the organism (not that they aren't important).<br />
<br />
==cell polarity==<br />
<br />
establishment and/or maintenance of cell polarity (sensu Fungi) <br><br />
establishment of cell polarity (sensu Fungi) <br><br />
maintenance of cell polarity (sensu Fungi) <br><br />
<br />
'''People:'''<br><br />
<br />
David<br><br />
Midori<br><br />
Rex<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Merge these terms with their non-sensu parents. Fungal cell polarity is the model system for everything on polarity.<br><br />
<br />
==neural rod==<br />
<br />
neural rod cavitation (sensu Teleost) <br><br />
neural rod formation (sensu Teleost) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
Doug<br><br />
David<br><br />
<br />
'''Questions:'''<br><br />
<br />
How do we distinguish neural rods in Teleosts and other things. Does anything else have neural rods?<br />
<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
==gastrulation==<br />
<br />
gastrulation (sensu Vertebrata) <br><br />
gastrulation (sensu Mammalia) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
David<br><br />
Doug<br><br />
Victoria<br><br />
<br />
'''Questions:'''<br><br />
<br />
What distinguishes mammalian gastrulation from other organisms?<br><br />
<br />
'''Plan:'''<br><br />
<br />
Find distinguishing feature or merge terms. <br><br />
<br />
<br />
==pigment==<br />
<br />
pigment cell differentiation (sensu Nematoda and Protostomia) <br><br />
pigment cell differentiation (sensu Vertebrata) <br><br />
<br />
'''People:'''<br><br />
<br />
Kimberly<br><br />
David<br><br />
Doug<br><br />
Victora<br><br />
Susan Tweedie<br><br />
Becky Foulger<br><br />
<br />
'''Questions:'''<br><br />
<br />
Should we have a sensu designation or should we just enumerate the types of pigment cells underneath the parent pigment term. <br><br />
Look to the cell ontology for guidance.<br> <br />
<br />
'''Plan:'''<br><br />
<br />
<br />
==larval development==<br />
<br />
larval development (sensu Amphibia) <br><br />
larval development (sensu Nematoda) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
Becky Foulger<br><br />
Kimberly<br><br />
<br />
'''Questions:'''<br><br />
<br />
What are the distinguishing features?<br><br />
Is it worth having separate terms for each?<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==genderization==<br />
<br />
hermaphrodite germ-line sex determination (sensu Nematoda) <br><br />
feminization of hermaphroditic germ-line (sensu Nematoda) <br><br />
masculinization of hermaphroditic germ-line (sensu Nematoda) <br><br />
hermaphrodite somatic sex determination (sensu Nematoda) <br><br />
feminization of hermaphrodite soma (sensu Nematoda) <br><br />
masculinization of hermaphrodite soma (sensu Nematoda) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
Kimberly<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
Is there any other type or can we just merge into the generic parent?<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==spores==<br />
<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore wall (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Pascale<br><br />
Jen<br><br />
Michelle <br><br />
Jim Hu<br><br />
Tanya<br><br />
Midori<br><br />
Val<br><br />
<br />
<br />
'''Questions:'''<br><br />
Ask Chris Brett if he knows difference between plant, bacterial, and fungal cell walls. <br />
Also relevant to cell walls. [Jen]<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==proteasome==<br />
<br />
proteasome core complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle (sensu Eukaryota) <br><br />
proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
proteasome complex (sensu Eukaryota) <br><br />
cytosolic proteasome complex (sensu Eukaryota) <br><br />
proteasome core complex (sensu Bacteria) <br><br />
proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Bacteria) <br><br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Rama<br><br />
Jim Hu<br><br />
Michelle<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
<br />
==cytosolic ribosome==<br />
<br />
cytosolic large ribosomal subunit (sensu Eukaryota) <br><br />
cytosolic large ribosomal subunit (sensu Archaea) <br><br />
cytosolic large ribosomal subunit (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Archaea) <br><br />
cytosolic ribosome (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Eukaryota) <br><br><br />
cytosolic small ribosomal subunit (sensu Archaea) <br><br />
cytosolic small ribosomal subunit (sensu Bacteria) <br><br />
cytosolic small ribosomal subunit (sensu Eukaryota) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Harold<br><br />
Michelle<br><br />
Jim Hu<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
From Harold's e-mail:<br />
<br />
<br />
The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.<br> <br />
Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. These are generated from post-transcriptional processing of a single rRNA precursor. <br />
Prokaroytic ribosomes contain about 50 proteins. The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt) <br><br />
Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are post-transcriptionally processed from a single rRNA <br />
precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA polymerase III, whereas the large transcript containing <br />
the other three is synthesized by RNA polymerase I. The large rRNA, typically called &ldquo;28s&rdquo;, is in fact much larger than it's bacterial counterpart <br />
(~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt. Eukaryotic ribosomes contain 70-80 proteins.<br><br />
I would think that the most single feature is the 3 vs 4 chain.<br><br />
Although basically, mitochondrial ribosomes are thought to be &ldquo;prokaryote-like&rdquo;, some fungal and animal mitochondrial ribosomes lack 5 sRNA, and are <br />
thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then you would b safe).<br><br />
The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have an intermediate number of proteins, etc. The <br />
expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together. <br><br />
I propose <br><br />
1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)<br><br />
2. Four-RNA chain containing ribosomes. ( 5.8s-, eukarytotic-type)<br><br />
Note, I have tried to get away from using exact S-values in the term name. Using them in the def would be fine, I hope. Although I wouldn't be adverse to using <br />
&ldquo;5.8s-containing ribosome vs ??).<br><br />
Now, the large subunit of each class is where you will have the 3 vs 4 chain difference.<br />
The small subunit is the hard one: more prokaryotic like than eukaryotic, but a work around would be<br><br />
small subunit of a three-chain containing ribosome<br><br />
smll subunit of a four-chain containg ribosome.<br><br><br />
References:<br><br />
Personal communication Dr. Caroline Kohler, Dept. of Biology, MIT, and<br><br />
Lewin, Genes VII ISBN:019879276-X<br><br><br />
The Ribosome, ISBN:0879696206<br />
<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Find previous notes from e-mail. <br><br />
<br />
<br />
<br />
==NADH and reaction centre==<br />
<br />
NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)<br><br />
NADH dehydrogenase complex (quinone) (sensu Bacteria) <br><br />
NADH dehydrogenase complex (ubiquinone) (sensu Bacteria) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
==plasmid partitioning (sensu Bacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
Eurie<br><br />
Michelle<br><br />
Midori<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==somitomeric trunk muscle development (sensu Mammalia) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
David <br><br />
Victoria<br><br />
Emily<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Probably merge with parent.<br><br />
<br />
==otolith==<br />
<br />
otolith mineralization (sensu Actinopterygii) <br><br />
otolith mineralization (sensu Tetrapoda) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
David Fashena<br><br />
https://sourceforge.net/tracker/index.php?func=detail&aid=1109256&group_id=36855&atid=440764 <br><br />
Midori<br><br />
David<br><br />
Emily<br><br />
Victoria<br><br />
Doug (I can consult with Dave F. as he is in the next office over)<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
==outer membrane biogenesis (sensu ProteoBacteria) ==<br />
<br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Jim Hu<br><br />
Michelle<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
Check how we distinguish the outer membrane in the component ontology.<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
==invasive growth (sensu Saccharomyces) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
Maria Costanzo<br><br />
Val<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1583546&group_id=36855 <br><br />
Also consider pseudohyphal growth and filamentous growth.<br><br />
<br />
'''Plan:'''<br><br />
<br />
==reaction center (sensu ProteoBacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
<br />
Jim Hu <br><br />
Michelle<br><br />
Jen<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Meeting_Notes_3&diff=9598Meeting Notes 32007-08-31T18:24:23Z<p>Mlgwinn: /* Chromosome */</p>
<hr />
<div>==Nematode development==<br />
<br />
negative regulation of vulval development (sensu Nematoda) <br><br />
positive regulation of vulval development (sensu Nematoda) <br><br />
regulation of vulval development (sensu Nematoda) <br><br />
vulval development (sensu Nematoda) <br><br />
tail tip morphogenesis (sensu Nematoda) <br><br />
<br />
'''People:'''<br><br />
Kimberly<br><br />
Doug?<br><br />
David<br><br />
<br />
'''Questions:'''<br />
<br />
What is the distinguishing feature of the anatomical structure vulva between species? <br><br />
Do we want a term just called vulval development?<br><br />
Can we handle this by making cross references to anatomical dictionaries?<br><br />
For tail tip morph, do we even need the sensu Nematode?<br />
<br />
'''Plan'''<br><br />
<br />
<br />
==spores==<br />
<br />
spore wall assembly (sensu Bacteria) <br><br />
spore wall assembly (sensu Fungi) <br><br />
<br />
'''People:'''<br><br />
<br />
Val<br><br />
Maria Costanzo<br><br />
Jim Hu<br><br />
Michelle<br><br />
Midori<br><br />
<br />
'''Questions:'''<br><br />
<br />
Same question as cell walls.<br><br />
What are the distinguishing features of the walls?<br><br />
or<br />
What are the distinguishing features of the assembly of the walls?<br><br />
<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==Chromosome==<br />
<br />
chromosome organization and biogenesis (sensu Bacteria) <br><br />
chromosome organization and biogenesis (sensu Eukaryota) <br><br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
Eurie<br><br />
<br />
'''Questions:'''<br><br />
<br />
What are the distinguishing features?<br><br />
Do we lump mitochondrial and plastid with bacterial?<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
Michelle speaking - It seems to me that these processes are really the same - yes different genes and proteins are involved in the different types of organism, but I don't see why there needs to be separate terms. Can these just be merged into their parent? I think you would want to keep mitochondrial and plastid terms separate as they are "auxillary" chromosomes, not the primary genome of the organism (not that they aren't important).<br />
<br />
==cell polarity==<br />
<br />
establishment and/or maintenance of cell polarity (sensu Fungi) <br><br />
establishment of cell polarity (sensu Fungi) <br><br />
maintenance of cell polarity (sensu Fungi) <br><br />
<br />
'''People:'''<br><br />
<br />
David<br><br />
Midori<br><br />
Rex<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Merge these terms with their non-sensu parents. Fungal cell polarity is the model system for everything on polarity.<br><br />
<br />
==neural rod==<br />
<br />
neural rod cavitation (sensu Teleost) <br><br />
neural rod formation (sensu Teleost) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
Doug<br><br />
David<br><br />
<br />
'''Questions:'''<br><br />
<br />
How do we distinguish neural rods in Teleosts and other things. Does anything else have neural rods?<br />
<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
==gastrulation==<br />
<br />
gastrulation (sensu Vertebrata) <br><br />
gastrulation (sensu Mammalia) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
David<br><br />
Doug<br><br />
Victoria<br><br />
<br />
'''Questions:'''<br><br />
<br />
What distinguishes mammalian gastrulation from other organisms?<br><br />
<br />
'''Plan:'''<br><br />
<br />
Find distinguishing feature or merge terms. <br><br />
<br />
<br />
==pigment==<br />
<br />
pigment cell differentiation (sensu Nematoda and Protostomia) <br><br />
pigment cell differentiation (sensu Vertebrata) <br><br />
<br />
'''People:'''<br><br />
<br />
Kimberly<br><br />
David<br><br />
Doug<br><br />
Victora<br><br />
Susan Tweedie<br><br />
Becky Foulger<br><br />
<br />
'''Questions:'''<br><br />
<br />
Should we have a sensu designation or should we just enumerate the types of pigment cells underneath the parent pigment term. <br><br />
Look to the cell ontology for guidance.<br> <br />
<br />
'''Plan:'''<br><br />
<br />
<br />
==larval development==<br />
<br />
larval development (sensu Amphibia) <br><br />
larval development (sensu Nematoda) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
Becky Foulger<br><br />
Kimberly<br><br />
<br />
'''Questions:'''<br><br />
<br />
What are the distinguishing features?<br><br />
Is it worth having separate terms for each?<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==genderization==<br />
<br />
hermaphrodite germ-line sex determination (sensu Nematoda) <br><br />
feminization of hermaphroditic germ-line (sensu Nematoda) <br><br />
masculinization of hermaphroditic germ-line (sensu Nematoda) <br><br />
hermaphrodite somatic sex determination (sensu Nematoda) <br><br />
feminization of hermaphrodite soma (sensu Nematoda) <br><br />
masculinization of hermaphrodite soma (sensu Nematoda) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
Kimberly<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
Is there any other type or can we just merge into the generic parent?<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==spores==<br />
<br />
sporulation (sensu Bacteria) <br><br />
sporulation (sensu Fungi) <br><br />
spore wall (sensu Fungi) <br><br />
spore development (sensu Magnoliophyta) <br><br />
<br />
'''People:'''<br><br />
<br />
Pascale<br><br />
Jen<br><br />
Michelle <br><br />
Jim Hu<br><br />
Tanya<br><br />
Midori<br><br />
Val<br><br />
<br />
<br />
'''Questions:'''<br><br />
Ask Chris Brett if he knows difference between plant, bacterial, and fungal cell walls. <br />
Also relevant to cell walls. [Jen]<br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==proteasome==<br />
<br />
proteasome core complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle (sensu Eukaryota) <br><br />
proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, base subcomplex (sensu Eukaryota) <br><br />
proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
cytosolic proteasome regulatory particle, lid subcomplex (sensu Eukaryota) <br><br />
proteasome complex (sensu Eukaryota) <br><br />
cytosolic proteasome complex (sensu Eukaryota) <br><br />
proteasome core complex (sensu Bacteria) <br><br />
proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, alpha-subunit complex (sensu Eukaryota) <br><br />
proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
cytosolic proteasome core complex, beta-subunit complex (sensu Eukaryota) <br><br />
proteasome regulatory particle (sensu Bacteria) <br><br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Rama<br><br />
Jim Hu<br><br />
Michelle<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
<br />
==cytosolic ribosome==<br />
<br />
cytosolic large ribosomal subunit (sensu Eukaryota) <br><br />
cytosolic large ribosomal subunit (sensu Archaea) <br><br />
cytosolic large ribosomal subunit (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Archaea) <br><br />
cytosolic ribosome (sensu Bacteria) <br><br />
cytosolic ribosome (sensu Eukaryota) <br><br><br />
cytosolic small ribosomal subunit (sensu Archaea) <br><br />
cytosolic small ribosomal subunit (sensu Bacteria) <br><br />
cytosolic small ribosomal subunit (sensu Eukaryota) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Harold<br><br />
Michelle<br><br />
Jim Hu<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
From Harold's e-mail:<br />
<br />
<br />
The cytosolic ribosomes of prokaryotic and eukaryotic cells differ basically by size, number of proteins, and number or RNA strands.<br> <br />
Prokaryotic ribosomes have three strands, typically called 5s, 16s, and 23s. These are generated from post-transcriptional processing of a single rRNA precursor. <br />
Prokaroytic ribosomes contain about 50 proteins. The 5s is 120 nt, 16s about 1500nt, and 23s about 2900nt) <br><br />
Eukaryotic ribosomes have four strands, typically called 5s, 5.8s, 18s, and 28s. The 5.8, 18, and 28s chains are post-transcriptionally processed from a single rRNA <br />
precursor. The 5s RNA is generated separately from a differerent promoter. The 5s RNA is synthesized by RNA polymerase III, whereas the large transcript containing <br />
the other three is synthesized by RNA polymerase I. The large rRNA, typically called &ldquo;28s&rdquo;, is in fact much larger than it's bacterial counterpart <br />
(~4700 nt vs ~2900nt,). The 18 sRNA is about 1900nt, 5s 120nt, and 5.8s about 160nt. Eukaryotic ribosomes contain 70-80 proteins.<br><br />
I would think that the most single feature is the 3 vs 4 chain.<br><br />
Although basically, mitochondrial ribosomes are thought to be &ldquo;prokaryote-like&rdquo;, some fungal and animal mitochondrial ribosomes lack 5 sRNA, and are <br />
thus only 2 chain). However, if you base the definition on the fact that these are found within the organelle, then you would b safe).<br><br />
The archebacteria vs prokaroytic is harder; it's mostly a size and number difference, in that the archebacteria have an intermediate number of proteins, etc. The <br />
expert I spoke to would not be adverse to a system that lumped the archebacteria and prokaroytic together. <br><br />
I propose <br><br />
1. Three-RNA chain containg ribosome (prokaryotic-type to include prokaroytic and archebacteria ribosomes)<br><br />
2. Four-RNA chain containing ribosomes. ( 5.8s-, eukarytotic-type)<br><br />
Note, I have tried to get away from using exact S-values in the term name. Using them in the def would be fine, I hope. Although I wouldn't be adverse to using <br />
&ldquo;5.8s-containing ribosome vs ??).<br><br />
Now, the large subunit of each class is where you will have the 3 vs 4 chain difference.<br />
The small subunit is the hard one: more prokaryotic like than eukaryotic, but a work around would be<br><br />
small subunit of a three-chain containing ribosome<br><br />
smll subunit of a four-chain containg ribosome.<br><br><br />
References:<br><br />
Personal communication Dr. Caroline Kohler, Dept. of Biology, MIT, and<br><br />
Lewin, Genes VII ISBN:019879276-X<br><br><br />
The Ribosome, ISBN:0879696206<br />
<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Find previous notes from e-mail. <br><br />
<br />
<br />
<br />
==NADH and reaction centre==<br />
<br />
NADH dehydrogenase complex (plastoquinone) (sensu Cyanobacteria)<br><br />
NADH dehydrogenase complex (quinone) (sensu Bacteria) <br><br />
NADH dehydrogenase complex (ubiquinone) (sensu Bacteria) <br><br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Michelle<br><br />
Jim Hu<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
<br />
<br />
<br />
==plasmid partitioning (sensu Bacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
Eurie<br><br />
Michelle<br><br />
Midori<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
<br />
==somitomeric trunk muscle development (sensu Mammalia) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
David <br><br />
Victoria<br><br />
Emily<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
Probably merge with parent.<br><br />
<br />
==otolith==<br />
<br />
otolith mineralization (sensu Actinopterygii) <br><br />
otolith mineralization (sensu Tetrapoda) <br><br />
<br />
<br />
'''People:'''<br><br />
<br />
David Fashena<br><br />
https://sourceforge.net/tracker/index.php?func=detail&aid=1109256&group_id=36855&atid=440764 <br><br />
Midori<br><br />
David<br><br />
Emily<br><br />
Victoria<br><br />
Doug (I can consult with Dave F. as he is in the next office over)<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br><br />
<br />
==outer membrane biogenesis (sensu ProteoBacteria) ==<br />
<br />
<br />
<br />
<br />
'''People:'''<br><br />
<br />
Jim Hu<br><br />
Michelle<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
Check how we distinguish the outer membrane in the component ontology.<br><br />
<br />
'''Plan:'''<br><br />
<br />
<br />
==invasive growth (sensu Saccharomyces) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
Maria Costanzo<br><br />
Val<br><br />
<br />
<br />
'''Questions:'''<br><br />
<br />
https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1583546&group_id=36855 <br><br />
Also consider pseudohyphal growth and filamentous growth.<br><br />
<br />
'''Plan:'''<br><br />
<br />
==reaction center (sensu ProteoBacteria) ==<br />
<br />
<br />
'''People:'''<br><br />
<br />
<br />
Jim Hu <br><br />
Michelle<br><br />
Jen<br><br />
<br />
'''Questions:'''<br><br />
<br />
'''Plan:'''<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Transporters&diff=1819Transporters2007-02-07T21:37:01Z<p>Mlgwinn: </p>
<hr />
<div>First implementation meeting: ?<br><br />
Technology: webex and skype.<br />
<br />
'''Personnel''':<br />
<br />
* Jennifer Clark (Organizing implementation and doing all live editing)<br />
* Michelle Gwinn-Gigio (TIGR transport curator and GO ontology structure expert.)<br />
* Val Wood (Sanger fission yeast curator and GO ontology structure expert.)<br />
<br />
'''Experts''':<br />
<br />
* Ian Paulsen (TIGR transport expert) <br />
<br />
'''Implementation plan:'''<br />
<br />
[[Background]]<br />
<br />
[[Meeting Notes]]</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=GO_Consortium_Meeting_2007&diff=7028GO Consortium Meeting 20072006-10-26T15:10:18Z<p>Mlgwinn: /* Issues to be addressed */</p>
<hr />
<div>== Topics ==<br />
Please add items below that you think need to be presented. We are not -yet- putting these in any particular order or time, we're just collecting the topics we need to address while we are together.<br />
=== GO Team and other Status Reports ===<br />
Listed with potential people to provide the summaries<br />
# Reference Genomes - Rex&Karen<br />
# Ontology Content - David&Midori<br />
#* IS_A complete<br />
#* regulates<br />
#* Cell Ontology links<br />
# Ontology & Software - Chris&Ben/Mike<br />
#* Includes OBO-Edit working group report<br />
# Annotation outreach - Jen&Michelle/Simon<br />
# User Advocacy - Eurie&Jane<br />
#* Includes AmiGO working group report<br />
# Operations - Suzi<br />
# Publications<br />
<br />
=== Issues to be addressed ===<br />
# The issue of using the GO_REF vs extension of the evidence codes to amplify upon the method that is used. <br />
# gp2protein file: <br />
#* The lagtime between when the protein sequences of a newly sequenced and annotated organism are published, and when they make it into UniProt. For example, even now only ~10% of 27,855 arabidopsis protein sequences are contained in Swiss-Prot. For the final release (version 5) of arabidopsis, 306 proteins (~1%) are available in Swiss-Prot and 374 in TrEMBL. Older arabidopsis sequences are found in TrEMBL, but fully 1/3 of the sequences found in the first release have changed over the life of the project. <br />
(Ans From Evelyn):This problem stems from the fact that corrections to the original <br />
genome sequence have not been submitted to EMBL but only to TAIR. Paul Kersey at EBI is responsible for importing sequences from TAIR to UniProtKB (evelyn querying this). Why is this data or annotation not submitted to the EMBL/DDBJ/GenBank international nucleotide sequence databank? or is it??<br />
<br />
#* GOST needs to use the precise sequences, as supplied by the submitting group<br />
#Handling multiple identifiers for gene products and sequences<br />
#Evaluation of project tracking methods<br />
#GO policy on incorporating GOA annotations into MOD annotations (Evelyn and Mike/Judy?)<br />
GO annotations have been stripped out of GOA-UniProt (all species file) on GO site for taxon Id's represented by other GOC members. The idea was that the other GOC members would integrate annotations from GOA. Experimentally verified data from GOA was being lost 6000-ish for Mouse alone. The GOA group have been receiving alot of questions about how to get complete annotation datasets from GOC. GOA-UniProt file unstripped available on EBI ftp site. GOA now integrating all experimental data from all other GOC members on monthly basis. Can we have a GO policy on this? If a GOC member can't integrate GOA manual annotation should that taxon Id continue to be stripped from GOA-UniProt file?<br />
#More?? Claim some? Explain some?<br />
<br />
#Piped data for IPI, need consistency in usage (Evelyn)<br />
IGI data allows piped accessions in the 'with' columns to capture the fact that two or more genes may be interacting simultaneously. IPI data also allows piped accessions in with column but some GOC members here use the pipe to specifically say that in a given paper that protein A, B and C precipitated together or form part of a complex others I think use it also for circumstances where 2 separate experiments in the same paper showed protein A interacted with protein B and to protein C. GOA prefers using it like IGI for a specific circumstance otherwise information is lost? Others??<br />
Related Issue: GOA has decided for the moment not to pipe several protein binding interactions simply because it comes from same paper. We unwrap piped data from MODS because of inconsistency in usage and because this data not normalised (causes problems of database and web services)<br />
#GO Consortium Tools (Evelyn, Emily)<br />
GOA feels that GOC should not have tools on GO tool page unless they are maintained or at least highlight that fact, we also feel that we should consider perhaps a top 10 GOC reviewed set of tools that we can recommend and liase with on a regular basis. GOA can do that independently of GOC if GOC does not want to take such a position. Most users want advice on GO tools and presenting them with over 100 is not overly helpful. We also need to consider how to modify next GO users/tool meeting (already discussed on GO management I think?)<br />
<br />
<br />
#What evidence code to use for profile HMM based annotations.(Michelle)<br />
At the annotation camp a proposal was raised to use RCA for profile HMMs while Michelle has argued that these should remain ISS. There is agreement that the models used for things like TMHMM and SignalP might better belong as RCA. However, there is disagreement about the the HMMs in the TIGRFAM and Pfam sets. The proposal says RCA, others argue it should be ISS.<br />
<br />
=== New proposals ===<br />
#Protein Family based annotation tool - Suzi<br />
#Term history tracking capability - John/Chris/and OBO-Edit group<br />
#Incorporation of all gene product sequences and IDs into GO database and fasta files. How are we to accomplish this.<br />
<br />
== Venue ==<br />
<br />
[http://www.ebi.ac.uk/Information/events/registration/go2007/go_reg.php?meeting_id=66 Click here to register for this meeting. Please do this by October 31st]<br />
Jesus College<br />
Jesus Lane, Cambridge, CB5 8BL, UK<br />
Cambridge, UK</div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Beginning_Annotation_SOP&diff=6927Beginning Annotation SOP2006-10-16T17:56:45Z<p>Mlgwinn: /* SOP for starting annotation */</p>
<hr />
<div>This page is a place to build the SOP on beginning annotation. <br />
<br />
<br />
== These are the guidelines that the PIs gave me: ==<br />
<br />
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful. <br />
<br />
As far as the documentation; you might start with this outline... <br />
<br />
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit. <br />
<br />
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be <br />
used to frame the inquiries of annotation groups and to support these groups in many contexts. <br />
<br />
<br />
<br />
== SOP for starting annotation ==<br />
<br />
'''Automatic Annotation'''<br />
<br />
A. Automatic GO annotation tools<br />
<br />
There are several GO-related annotation tools that have been developed by many groups. Look at the annotation tools on the GO website:<br />
<br />
http://www.geneontology.org/GO.tools.annotation.shtml<br />
<br />
Please write to the GO-Friends mailing list if you have a specific annotation tool needs. All the tool developers are there and will help you to choose a good to tool, or may modify a tool to include the functionality that you need. Mail go-friends at geneontology.org.<br />
<br />
<br />
<br />
B. Automatic annotation based on GO mapping files and GO-annotated protein datasets for those users with database infrastructure in place.<br />
<br />
1) sequence-based methods<br />
<br />
blast2go<br />
You may also like to try BLAST2GO to find GO annotations to sequences similar to yours.<br />
<br><br />
http://www.geneontology.org/GO.tools.other.shtml#blast2go<br />
<br><br />
Use GOst<br><br />
http://www.godatabase.org/cgi-bin/gost/gost.cgi<br />
<br><br />
<br />
2) Domain-based comparison methods<br />
<br />
Interproscan<br />
Run your sequences through [[InterProScan]] either online or by downloading and running the application on your own computer. <br><br />
http://www.ebi.ac.uk/InterProScan/<br />
<br />
3) other<br />
<br />
keyword2go - a mapping of Swiss-Prot keywords to GO<br />
ec2go - a mapping of EC numbers to GO<br />
see additional mappings page on go website (link here)<br />
<br />
<br />
<br />
C. Annotation Services for those without a pre-existing database infrastructure:<br />
<br />
1) TIGR's Annotation Engine Service for prokaryotic genomes. This free service provides automatic annotation and database infrastructure to anyone with a prokaryotic DNA sequence they wish to annotate. More information can be found at: http://www.tigr.org/AnnotationEngine/<br />
In addition, TIGR offers a 3-day Prokaryotic Annotation and Analysis course. This course complements the Annotation Engine service in that it provides detailed information on TIGR's annotation pipeline and use of the free manual annotation tool Manatee. More info can be found at: http://www.tigr.org/AnnotationClass/<br />
<br />
2) GenDB http://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/<br />
<br />
3) The public repositories<br />
<a href="http://www.ebi.ac.uk/Submissions/"> EBI Submissions, including EMBL-bank </a><br><br />
<a href="http://www.ncbi.nlm.nih.gov/Genbank/submit.html">Genbank Submissions</a><br><br />
<a href="http://www.ddbj.nig.ac.jp/sub-e.html">DDBJ Submission</a><br><br />
(EMBL-Bank, GenBank and DDBJ exchange data amongst themselves so you can use any of these submission interfaces and<br />
have your data appear in all three resources.)<br />
Once your sequences have been processed and passed along the pipeline to all the related databases you will be able to retrieve:<br><br />
a) Unique stable identifiers such as UniProt or RefSeq for your sequences.<br />
b) Some level of automatic GO annotation to your sequences. (Publically available.) <br />
<br><br />
'''(I am hoping that I can insert a picture here that shows where sequences go in and where annotated sequences come out so that people can choose their favourite provider and be sure that they know what they are getting and what they are missing out on by choosing to download at that point.)'''<br />
<br />
<br />
<br />
D. GOblet<br />
<br><br />
http://goblet.molgen.mpg.de/<br />
<br><br />
<br />
<br />
'''Manual Annotation'''<br />
<br />
A. Literature based manual annotation - Check and improve your annotations against the literature. <br />
<br />
1) Read the manual annotation guidelines on the GO Consortium website.<br><br />
http://www.geneontology.org/GO.annotation.shtml<br />
<br />
2) Contact the GO Consortium to ask about annotation camps and mentoring.<br><br />
[insert description of camps and mentoring]<br />
<br />
B. Sequence based manual annotation.<br />
<br />
The process of manual annotation based on sequence similarity involves the manual review of a host of sequence based search data including: BLAST-type searches, domain based searches (InterPro,Pfam, TIGRFAMs, PROSITE, etc.), SignalP, TMHMM, paralagous families, COGs, etc. The annotator evalutates this information by looking at alignments, scores, etc. while taking into consideration the genomic context of the gene product being annotated including neighboring genes, possible operons, syntenic regions, pathway and system resconstruction, etc.<br />
<br />
== PAMGO example ==<br />
<br />
Here is an example of how a new group has started working with the GO Consortium. <br />
<br />
'''<br />
The Plant-Associated Microbe Gene Ontology (PAMGO) Group'''<br />
<br />
In 2003 the genome sequence of the tomato pathogen Pseudomonas syringae pv. tomato DC3000 was published. This project was a collaboration between Robin Buell at the The Institute for Genomic Research (TIGR) and Alan Collmer of Cornell University. As part of the annotation of P. syringae TIGR provided some GO assignments to the P. syringae proteins. Dissussion between Alan Collmer and Brett Tyler at the NSF Plant Genome Research Program Awardees Meeting that fall revealed a shared awareness of the potential power of the GO and led to the formation of the Plant-Associated Microbe Gene Ontology (PAMGO) working group. Brett Tyler coordinated the effort to bring together PIs from genome projects representing the major groups of microbial pathogens: Bacteria, Fungi, Oomycetes, and Nematodes. The PAMGO group recognized the potential power of the GO to greatly facilitate research in areas common to all these pathogens by providing a robust framework for comparing functions across species. Since TIGR is a member of the GO consortium, the new PAMGO group entered into collaboration with TIGR staff Michelle Gwinn-Giglio and Linda Hannick to develop terms specific for interactions between pathogens and their hosts.<br />
<br><br><br />
<br />
During 2004 the PAMGO Interest Group worked to develop high level terms to describe processes relevant to plant-microbe associations, which would provide a framework for the later development of more detailed terms. Candace Collmer (Wells College) while on sabbatical leave, and Michelle Gwinn-Giglio (TIGR) led the effort. This activity began with a full-day workshop on April 23, 2004 at TIGR of all the PAMGO participants. The workshop participants defined a set of high level terms and relationships that would be as general as possible, not only for pathogens of all kingdoms, but for the whole range of host-microbe interactions from mutualism to parasitism, and for all hosts, not only plants. Further refinement of the terms and their definitions occurred by email, and on June 2, 2004 the proposed terms were submitted to the GO community for discussion. On Aug 22-23, 2004 Candace and Alan Collmer and Michelle Gwinn-Giglio presented the proposal at a GO content meeting focused on pathogenesis, metabolism, and the cell cycle at the Carnegie Institution, Stanford, CA and on Oct. 15-16, 2004 Michelle Gwinn-Giglio presented three modified options to a GO Consortium Meeting in Chicago. These high level terms generated much debate, both at the original workshop, and within the wider GO community, because of the varied ways in which different communities use words such as "Symbiosis" and "Pathogenesis", and the difficulty of defining the term "Pathogenesis" consistently, given that some organisms may or may not cause disease depending on the physical environment and the physiological or genetic status of the host. This discussion highlighted the varied usage of these terms and stimulated user communities to think about how these terms should be used. A final version was agreed upon and resubmitted to GO on Dec 14, 2004 and made part of the active ontologies on Jan 31, 2005.<br />
<br><br><br />
In addition to the term development activites in 2004, the PAMGO group was also busy writing a grant to the NSF/USDA Microbial Genome Sequencing Program to fund their GO development work. Fortunately, the grant was awarded and provides 3 years of funding (Fall 2005-Fall 2008) for PAMGO to continue the development of more granular terms under the initial PAMGO term set. The PAMGO group is now actively working on terms that will describe the myriad ways that pathogens affect the metabolism of their hosts. A PAMGO jamboree was held in July 2006 where more than 100 new terms were developed.<br><br><br />
<br />
Using the PAMGO terms, as well as the rest of the GO ontologies, PAMGO annotators are assigning GO terms to the proteins from the PAMGO organisms that have a role in interacting with their hosts. It is anticipated that PAMGO will begin sending in association files of these annotations at the end of this year.<br><br><br />
<br />
<br />
'''PAMGO people and pathogens:'''<br />
<br />
'''Virginia Bioinformatics Institute'''<br />
<br />
Phytophthora sojae (Oomycete)<br><br />
Phytophthora ramorum (Oomycete)<br><br />
Brett Tyler<br><br />
Trudy Torto-Alalibo<br><br />
Marcus Chibucos<br><br />
Rays Jiang<br><br />
<br />
Agrobacterium tumefaciens (Bacterium)<br><br />
Joao Setubal<br><br />
Joshua Shallom<br><br />
Tsai-Tien Tseng<br><br />
<br />
<br />
'''Cornell University'''<br />
<br />
Pseudomonas syringae pv. tomato DC3000 (Bacterium)<br><br />
Pseudomonas syringae pv. phaseolicola 1448A (Bacterium)<br><br />
Pseudomonas syringae pv. syringae B728A (Bacterium)<br><br />
Alan Collmer<br><br />
Magdalen Lindeberg<br><br />
Candace Collmer (Wells College, September-May)<br><br />
<br />
<br />
'''University of Wisconsin'''<br />
<br />
Erwinia chrysanthemi 3937 (Bacterium)<br><br />
Nicole Perna<br><br />
Jeremy Glasner<br><br />
Bryan Biehl<br><br />
<br />
<br />
'''North Carolina State University'''<br />
<br />
Magnaporthe grisea (Fungus)<br><br />
Meloidogyne hapla (Nematode)<br><br />
Ralph Dean<br><br />
David Bird<br><br />
Thomas Mitchell<br><br />
Shaowu Meng<br><br />
<br />
<br />
'''The Institute for Genomic Research'''<br />
<br />
Michelle Gwinn-Giglio<br><br />
Linda Hannick<br><br />
Robin Buell<br><br />
Owen White<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Beginning_Annotation_SOP&diff=6926Beginning Annotation SOP2006-10-16T17:52:26Z<p>Mlgwinn: /* SOP for starting annotation */</p>
<hr />
<div>This page is a place to build the SOP on beginning annotation. <br />
<br />
<br />
== These are the guidelines that the PIs gave me: ==<br />
<br />
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful. <br />
<br />
As far as the documentation; you might start with this outline... <br />
<br />
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit. <br />
<br />
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be <br />
used to frame the inquiries of annotation groups and to support these groups in many contexts. <br />
<br />
<br />
<br />
== SOP for starting annotation ==<br />
<br />
'''Automatic Annotation'''<br />
<br />
A. Automatic GO annotation tools<br />
<br />
There are several GO-related annotation tools that have been developed by many groups. Look at the annotation tools on the GO website:<br />
<br />
http://www.geneontology.org/GO.tools.annotation.shtml<br />
<br />
Please write to the GO-Friends mailing list if you have a specific annotation tool needs. All the tool developers are there and will help you to choose a good to tool, or may modify a tool to include the functionality that you need. Mail go-friends at geneontology.org.<br />
<br />
<br />
<br />
B. Automatic annotation based on GO mapping files and GO-annotated protein datasets for those users with database infrastructure in place.<br />
<br />
1) sequence-based methods<br />
<br />
blast2go<br />
You may also like to try BLAST2GO to find GO annotations to sequences similar to yours.<br />
<br><br />
http://www.geneontology.org/GO.tools.other.shtml#blast2go<br />
<br><br />
Use GOst<br><br />
http://www.godatabase.org/cgi-bin/gost/gost.cgi<br />
<br><br />
<br />
2) Domain-based comparison methods<br />
<br />
Interproscan<br />
Run your sequences through [[InterProScan]] either online or by downloading and running the application on your own computer. <br><br />
http://www.ebi.ac.uk/InterProScan/<br />
<br />
3) other<br />
<br />
keyword2go - a mapping of Swiss-Prot keywords to GO<br />
ec2go - a mapping of EC numbers to GO<br />
see additional mappings page on go website (link here)<br />
<br />
<br />
<br />
C. Annotation Services for those without a pre-existing database infrastructure:<br />
<br />
1) TIGR's Annotation Engine Service for prokaryotic genomes. This free service provides automatic annotation and database infrastructure to anyone with a prokaryotic DNA sequence they wish to annotate. More information can be found at: http://www.tigr.org/AnnotationEngine/<br />
In addition, TIGR offers a 3-day Prokaryotic Annotation and Analysis course. This course complements the Annotation Engine service in that it provides detailed information on TIGR's annotation pipeline and use of the free manual annotation tool Manatee. More info can be found at: http://www.tigr.org/AnnotationClass/<br />
<br />
2) GenDB http://www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/<br />
<br />
3) The public repositories<br />
<a href="http://www.ebi.ac.uk/Submissions/"> EBI Submissions, including EMBL-bank </a><br><br />
<a href="http://www.ncbi.nlm.nih.gov/Genbank/submit.html">Genbank Submissions</a><br><br />
<a href="http://www.ddbj.nig.ac.jp/sub-e.html">DDBJ Submission</a><br><br />
(EMBL-Bank, GenBank and DDBJ exchange data amongst themselves so you can use any of these submission interfaces and<br />
have your data appear in all three resources.)<br />
Once your sequences have been processed and passed along the pipeline to all the related databases you will be able to retrieve:<br><br />
a) Unique stable identifiers such as UniProt or RefSeq for your sequences.<br />
b) Some level of automatic GO annotation to your sequences. (Publically available.) <br />
<br><br />
'''(I am hoping that I can insert a picture here that shows where sequences go in and where annotated sequences come out so that people can choose their favourite provider and be sure that they know what they are getting and what they are missing out on by choosing to download at that point.)'''<br />
<br />
<br />
<br />
D. GOblet<br />
<br><br />
http://goblet.molgen.mpg.de/<br />
<br><br />
<br />
<br />
'''Manual Annotation'''<br />
<br />
1. Literature based manual annotation - Check and improve your annotations against the literature. <br />
<br />
a) Read the manual annotation guidelines on the GO Consortium website.<br><br />
http://www.geneontology.org/GO.annotation.shtml<br />
<br />
b) Contact the GO Consortium to ask about annotation camps and mentoring.<br><br />
[insert description of camps and mentoring]<br />
<br />
2. Sequence based manual annotation.<br />
<br />
The process of manual annotation based on sequence similarity involves the manual review of a host of sequence based search data including: BLAST-type searches, domain based searches (InterPro,Pfam, TIGRFAMs, PROSITE, etc.), SignalP, TMHMM, paralagous families, COGs, etc. The annotator evalutates this information by looking at alignments, scores, etc. while taking into consideration the genomic context of the gene product being annotated including neighboring genes, possible operons, syntenic regions, pathway and system resconstruction, etc.<br />
<br />
== PAMGO example ==<br />
<br />
Here is an example of how a new group has started working with the GO Consortium. <br />
<br />
'''<br />
The Plant-Associated Microbe Gene Ontology (PAMGO) Group'''<br />
<br />
In 2003 the genome sequence of the tomato pathogen Pseudomonas syringae pv. tomato DC3000 was published. This project was a collaboration between Robin Buell at the The Institute for Genomic Research (TIGR) and Alan Collmer of Cornell University. As part of the annotation of P. syringae TIGR provided some GO assignments to the P. syringae proteins. Dissussion between Alan Collmer and Brett Tyler at the NSF Plant Genome Research Program Awardees Meeting that fall revealed a shared awareness of the potential power of the GO and led to the formation of the Plant-Associated Microbe Gene Ontology (PAMGO) working group. Brett Tyler coordinated the effort to bring together PIs from genome projects representing the major groups of microbial pathogens: Bacteria, Fungi, Oomycetes, and Nematodes. The PAMGO group recognized the potential power of the GO to greatly facilitate research in areas common to all these pathogens by providing a robust framework for comparing functions across species. Since TIGR is a member of the GO consortium, the new PAMGO group entered into collaboration with TIGR staff Michelle Gwinn-Giglio and Linda Hannick to develop terms specific for interactions between pathogens and their hosts.<br />
<br><br><br />
<br />
During 2004 the PAMGO Interest Group worked to develop high level terms to describe processes relevant to plant-microbe associations, which would provide a framework for the later development of more detailed terms. Candace Collmer (Wells College) while on sabbatical leave, and Michelle Gwinn-Giglio (TIGR) led the effort. This activity began with a full-day workshop on April 23, 2004 at TIGR of all the PAMGO participants. The workshop participants defined a set of high level terms and relationships that would be as general as possible, not only for pathogens of all kingdoms, but for the whole range of host-microbe interactions from mutualism to parasitism, and for all hosts, not only plants. Further refinement of the terms and their definitions occurred by email, and on June 2, 2004 the proposed terms were submitted to the GO community for discussion. On Aug 22-23, 2004 Candace and Alan Collmer and Michelle Gwinn-Giglio presented the proposal at a GO content meeting focused on pathogenesis, metabolism, and the cell cycle at the Carnegie Institution, Stanford, CA and on Oct. 15-16, 2004 Michelle Gwinn-Giglio presented three modified options to a GO Consortium Meeting in Chicago. These high level terms generated much debate, both at the original workshop, and within the wider GO community, because of the varied ways in which different communities use words such as "Symbiosis" and "Pathogenesis", and the difficulty of defining the term "Pathogenesis" consistently, given that some organisms may or may not cause disease depending on the physical environment and the physiological or genetic status of the host. This discussion highlighted the varied usage of these terms and stimulated user communities to think about how these terms should be used. A final version was agreed upon and resubmitted to GO on Dec 14, 2004 and made part of the active ontologies on Jan 31, 2005.<br />
<br><br><br />
In addition to the term development activites in 2004, the PAMGO group was also busy writing a grant to the NSF/USDA Microbial Genome Sequencing Program to fund their GO development work. Fortunately, the grant was awarded and provides 3 years of funding (Fall 2005-Fall 2008) for PAMGO to continue the development of more granular terms under the initial PAMGO term set. The PAMGO group is now actively working on terms that will describe the myriad ways that pathogens affect the metabolism of their hosts. A PAMGO jamboree was held in July 2006 where more than 100 new terms were developed.<br><br><br />
<br />
Using the PAMGO terms, as well as the rest of the GO ontologies, PAMGO annotators are assigning GO terms to the proteins from the PAMGO organisms that have a role in interacting with their hosts. It is anticipated that PAMGO will begin sending in association files of these annotations at the end of this year.<br><br><br />
<br />
<br />
'''PAMGO people and pathogens:'''<br />
<br />
'''Virginia Bioinformatics Institute'''<br />
<br />
Phytophthora sojae (Oomycete)<br><br />
Phytophthora ramorum (Oomycete)<br><br />
Brett Tyler<br><br />
Trudy Torto-Alalibo<br><br />
Marcus Chibucos<br><br />
Rays Jiang<br><br />
<br />
Agrobacterium tumefaciens (Bacterium)<br><br />
Joao Setubal<br><br />
Joshua Shallom<br><br />
Tsai-Tien Tseng<br><br />
<br />
<br />
'''Cornell University'''<br />
<br />
Pseudomonas syringae pv. tomato DC3000 (Bacterium)<br><br />
Pseudomonas syringae pv. phaseolicola 1448A (Bacterium)<br><br />
Pseudomonas syringae pv. syringae B728A (Bacterium)<br><br />
Alan Collmer<br><br />
Magdalen Lindeberg<br><br />
Candace Collmer (Wells College, September-May)<br><br />
<br />
<br />
'''University of Wisconsin'''<br />
<br />
Erwinia chrysanthemi 3937 (Bacterium)<br><br />
Nicole Perna<br><br />
Jeremy Glasner<br><br />
Bryan Biehl<br><br />
<br />
<br />
'''North Carolina State University'''<br />
<br />
Magnaporthe grisea (Fungus)<br><br />
Meloidogyne hapla (Nematode)<br><br />
Ralph Dean<br><br />
David Bird<br><br />
Thomas Mitchell<br><br />
Shaowu Meng<br><br />
<br />
<br />
'''The Institute for Genomic Research'''<br />
<br />
Michelle Gwinn-Giglio<br><br />
Linda Hannick<br><br />
Robin Buell<br><br />
Owen White<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Beginning_Annotation_SOP&diff=6925Beginning Annotation SOP2006-10-16T17:51:20Z<p>Mlgwinn: /* SOP for starting annotation */</p>
<hr />
<div>This page is a place to build the SOP on beginning annotation. <br />
<br />
<br />
== These are the guidelines that the PIs gave me: ==<br />
<br />
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful. <br />
<br />
As far as the documentation; you might start with this outline... <br />
<br />
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit. <br />
<br />
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be <br />
used to frame the inquiries of annotation groups and to support these groups in many contexts. <br />
<br />
<br />
<br />
== SOP for starting annotation ==<br />
<br />
'''Automatic Annotation'''<br />
<br />
A. Automatic GO annotation tools<br />
<br />
There are several GO-related annotation tools that have been developed by many groups. Look at the annotation tools on the GO website:<br />
<br />
http://www.geneontology.org/GO.tools.annotation.shtml<br />
<br />
Please write to the GO-Friends mailing list if you have a specific annotation tool needs. All the tool developers are there and will help you to choose a good to tool, or may modify a tool to include the functionality that you need. Mail go-friends at geneontology.org.<br />
<br />
<br />
<br />
B. Automatic annotation based on GO mapping files and GO-annotated protein datasets for those users with database infrastructure in place.<br />
<br />
1) sequence-based methods<br />
<br />
blast2go<br />
You may also like to try BLAST2GO to find GO annotations to sequences similar to yours.<br />
<br><br />
http://www.geneontology.org/GO.tools.other.shtml#blast2go<br />
<br><br />
Use GOst<br><br />
http://www.godatabase.org/cgi-bin/gost/gost.cgi<br />
<br><br />
<br />
2) Domain-based comparison methods<br />
<br />
Interproscan<br />
Run your sequences through [[InterProScan]] either online or by downloading and running the application on your own computer. <br><br />
http://www.ebi.ac.uk/InterProScan/<br />
<br />
3) other<br />
<br />
keyword2go - a mapping of Swiss-Prot keywords to GO<br />
ec2go - a mapping of EC numbers to GO<br />
see additional mappings page on go website (link here)<br />
<br />
<br />
<br />
C. Annotation Services for those without a pre-existing database infrastructure:<br />
<br />
1) TIGR's Annotation Engine Service for prokaryotic genomes. This free service provides automatic annotation and database infrastructure to anyone with a prokaryotic DNA sequence they wish to annotate. More information can be found at: www.tigr.org/AnnotationEngine/<br />
In addition, TIGR offers a 3-day Prokaryotic Annotation and Analysis course. This course complements the Annotation Engine service in that it provides detailed information on TIGR's annotation pipeline and use of the free manual annotation tool Manatee. More info can be found at: www.tigr.org/AnnotationClass/<br />
<br />
2) GenDB www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/<br />
<br />
3) The public repositories<br />
<a href="http://www.ebi.ac.uk/Submissions/"> EBI Submissions, including EMBL-bank </a><br><br />
<a href="http://www.ncbi.nlm.nih.gov/Genbank/submit.html">Genbank Submissions</a><br><br />
<a href="http://www.ddbj.nig.ac.jp/sub-e.html">DDBJ Submission</a><br><br />
(EMBL-Bank, GenBank and DDBJ exchange data amongst themselves so you can use any of these submission interfaces and<br />
have your data appear in all three resources.)<br />
Once your sequences have been processed and passed along the pipeline to all the related databases you will be able to retrieve:<br><br />
a) Unique stable identifiers such as UniProt or RefSeq for your sequences.<br />
b) Some level of automatic GO annotation to your sequences. (Publically available.) <br />
<br><br />
'''(I am hoping that I can insert a picture here that shows where sequences go in and where annotated sequences come out so that people can choose their favourite provider and be sure that they know what they are getting and what they are missing out on by choosing to download at that point.)'''<br />
<br />
<br />
<br />
D. GOblet<br />
<br><br />
http://goblet.molgen.mpg.de/<br />
<br><br />
<br />
<br />
'''Manual Annotation'''<br />
<br />
1. Literature based manual annotation - Check and improve your annotations against the literature. <br />
<br />
a) Read the manual annotation guidelines on the GO Consortium website.<br><br />
http://www.geneontology.org/GO.annotation.shtml<br />
<br />
b) Contact the GO Consortium to ask about annotation camps and mentoring.<br><br />
[insert description of camps and mentoring]<br />
<br />
2. Sequence based manual annotation.<br />
<br />
The process of manual annotation based on sequence similarity involves the manual review of a host of sequence based search data including: BLAST-type searches, domain based searches (InterPro,Pfam, TIGRFAMs, PROSITE, etc.), SignalP, TMHMM, paralagous families, COGs, etc. The annotator evalutates this information by looking at alignments, scores, etc. while taking into consideration the genomic context of the gene product being annotated including neighboring genes, possible operons, syntenic regions, pathway and system resconstruction, etc.<br />
<br />
== PAMGO example ==<br />
<br />
Here is an example of how a new group has started working with the GO Consortium. <br />
<br />
'''<br />
The Plant-Associated Microbe Gene Ontology (PAMGO) Group'''<br />
<br />
In 2003 the genome sequence of the tomato pathogen Pseudomonas syringae pv. tomato DC3000 was published. This project was a collaboration between Robin Buell at the The Institute for Genomic Research (TIGR) and Alan Collmer of Cornell University. As part of the annotation of P. syringae TIGR provided some GO assignments to the P. syringae proteins. Dissussion between Alan Collmer and Brett Tyler at the NSF Plant Genome Research Program Awardees Meeting that fall revealed a shared awareness of the potential power of the GO and led to the formation of the Plant-Associated Microbe Gene Ontology (PAMGO) working group. Brett Tyler coordinated the effort to bring together PIs from genome projects representing the major groups of microbial pathogens: Bacteria, Fungi, Oomycetes, and Nematodes. The PAMGO group recognized the potential power of the GO to greatly facilitate research in areas common to all these pathogens by providing a robust framework for comparing functions across species. Since TIGR is a member of the GO consortium, the new PAMGO group entered into collaboration with TIGR staff Michelle Gwinn-Giglio and Linda Hannick to develop terms specific for interactions between pathogens and their hosts.<br />
<br><br><br />
<br />
During 2004 the PAMGO Interest Group worked to develop high level terms to describe processes relevant to plant-microbe associations, which would provide a framework for the later development of more detailed terms. Candace Collmer (Wells College) while on sabbatical leave, and Michelle Gwinn-Giglio (TIGR) led the effort. This activity began with a full-day workshop on April 23, 2004 at TIGR of all the PAMGO participants. The workshop participants defined a set of high level terms and relationships that would be as general as possible, not only for pathogens of all kingdoms, but for the whole range of host-microbe interactions from mutualism to parasitism, and for all hosts, not only plants. Further refinement of the terms and their definitions occurred by email, and on June 2, 2004 the proposed terms were submitted to the GO community for discussion. On Aug 22-23, 2004 Candace and Alan Collmer and Michelle Gwinn-Giglio presented the proposal at a GO content meeting focused on pathogenesis, metabolism, and the cell cycle at the Carnegie Institution, Stanford, CA and on Oct. 15-16, 2004 Michelle Gwinn-Giglio presented three modified options to a GO Consortium Meeting in Chicago. These high level terms generated much debate, both at the original workshop, and within the wider GO community, because of the varied ways in which different communities use words such as "Symbiosis" and "Pathogenesis", and the difficulty of defining the term "Pathogenesis" consistently, given that some organisms may or may not cause disease depending on the physical environment and the physiological or genetic status of the host. This discussion highlighted the varied usage of these terms and stimulated user communities to think about how these terms should be used. A final version was agreed upon and resubmitted to GO on Dec 14, 2004 and made part of the active ontologies on Jan 31, 2005.<br />
<br><br><br />
In addition to the term development activites in 2004, the PAMGO group was also busy writing a grant to the NSF/USDA Microbial Genome Sequencing Program to fund their GO development work. Fortunately, the grant was awarded and provides 3 years of funding (Fall 2005-Fall 2008) for PAMGO to continue the development of more granular terms under the initial PAMGO term set. The PAMGO group is now actively working on terms that will describe the myriad ways that pathogens affect the metabolism of their hosts. A PAMGO jamboree was held in July 2006 where more than 100 new terms were developed.<br><br><br />
<br />
Using the PAMGO terms, as well as the rest of the GO ontologies, PAMGO annotators are assigning GO terms to the proteins from the PAMGO organisms that have a role in interacting with their hosts. It is anticipated that PAMGO will begin sending in association files of these annotations at the end of this year.<br><br><br />
<br />
<br />
'''PAMGO people and pathogens:'''<br />
<br />
'''Virginia Bioinformatics Institute'''<br />
<br />
Phytophthora sojae (Oomycete)<br><br />
Phytophthora ramorum (Oomycete)<br><br />
Brett Tyler<br><br />
Trudy Torto-Alalibo<br><br />
Marcus Chibucos<br><br />
Rays Jiang<br><br />
<br />
Agrobacterium tumefaciens (Bacterium)<br><br />
Joao Setubal<br><br />
Joshua Shallom<br><br />
Tsai-Tien Tseng<br><br />
<br />
<br />
'''Cornell University'''<br />
<br />
Pseudomonas syringae pv. tomato DC3000 (Bacterium)<br><br />
Pseudomonas syringae pv. phaseolicola 1448A (Bacterium)<br><br />
Pseudomonas syringae pv. syringae B728A (Bacterium)<br><br />
Alan Collmer<br><br />
Magdalen Lindeberg<br><br />
Candace Collmer (Wells College, September-May)<br><br />
<br />
<br />
'''University of Wisconsin'''<br />
<br />
Erwinia chrysanthemi 3937 (Bacterium)<br><br />
Nicole Perna<br><br />
Jeremy Glasner<br><br />
Bryan Biehl<br><br />
<br />
<br />
'''North Carolina State University'''<br />
<br />
Magnaporthe grisea (Fungus)<br><br />
Meloidogyne hapla (Nematode)<br><br />
Ralph Dean<br><br />
David Bird<br><br />
Thomas Mitchell<br><br />
Shaowu Meng<br><br />
<br />
<br />
'''The Institute for Genomic Research'''<br />
<br />
Michelle Gwinn-Giglio<br><br />
Linda Hannick<br><br />
Robin Buell<br><br />
Owen White<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Beginning_Annotation_SOP&diff=6924Beginning Annotation SOP2006-10-16T17:50:13Z<p>Mlgwinn: /* SOP for starting annotation */</p>
<hr />
<div>This page is a place to build the SOP on beginning annotation. <br />
<br />
<br />
== These are the guidelines that the PIs gave me: ==<br />
<br />
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful. <br />
<br />
As far as the documentation; you might start with this outline... <br />
<br />
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit. <br />
<br />
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be <br />
used to frame the inquiries of annotation groups and to support these groups in many contexts. <br />
<br />
<br />
<br />
== SOP for starting annotation ==<br />
<br />
'''Automatic Annotation'''<br />
<br />
A. Automatic GO annotation tools<br />
<br />
There are several GO-related annotation tools that have been developed by many groups. Look at the annotation tools on the GO website:<br />
<br />
http://www.geneontology.org/GO.tools.annotation.shtml<br />
<br />
Please write to the GO-Friends mailing list if you have a specific annotation tool needs. All the tool developers are there and will help you to choose a good to tool, or may modify a tool to include the functionality that you need. Mail go-friends at geneontology.org.<br />
<br />
B. Automatic annotation based on GO mapping files and GO-annotated protein datasets for those users with database infrastructure in place.<br />
<br />
1) sequence-based methods<br />
<br />
blast2go<br />
You may also like to try BLAST2GO to find GO annotations to sequences similar to yours.<br />
<br><br />
http://www.geneontology.org/GO.tools.other.shtml#blast2go<br />
<br><br />
Use GOst<br><br />
http://www.godatabase.org/cgi-bin/gost/gost.cgi<br />
<br><br />
<br />
2) Domain-based comparison methods<br />
<br />
Interproscan<br />
Run your sequences through [[InterProScan]] either online or by downloading and running the application on your own computer. <br><br />
http://www.ebi.ac.uk/InterProScan/<br />
<br />
3) other<br />
<br />
keyword2go - a mapping of Swiss-Prot keywords to GO<br />
ec2go - a mapping of EC numbers to GO<br />
see additional mappings page on go website (link here)<br />
<br />
C. Annotation Services for those without a pre-existing database infrastructure:<br />
<br />
1) TIGR's Annotation Engine Service for prokaryotic genomes. This free service provides automatic annotation and database infrastructure to anyone with a prokaryotic DNA sequence they wish to annotate. More information can be found at: www.tigr.org/AnnotationEngine/<br />
In addition, TIGR offers a 3-day Prokaryotic Annotation and Analysis course. This course complements the Annotation Engine service in that it provides detailed information on TIGR's annotation pipeline and use of the free manual annotation tool Manatee. More info can be found at: www.tigr.org/AnnotationClass/<br />
<br />
2) GenDB www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/<br />
<br />
3) The public repositories<br />
<a href="http://www.ebi.ac.uk/Submissions/"> EBI Submissions, including EMBL-bank </a><br><br />
<a href="http://www.ncbi.nlm.nih.gov/Genbank/submit.html">Genbank Submissions</a><br><br />
<a href="http://www.ddbj.nig.ac.jp/sub-e.html">DDBJ Submission</a><br><br />
(EMBL-Bank, GenBank and DDBJ exchange data amongst themselves so you can use any of these submission interfaces and<br />
have your data appear in all three resources.)<br />
Once your sequences have been processed and passed along the pipeline to all the related databases you will be able to retrieve:<br><br />
a) Unique stable identifiers such as UniProt or RefSeq for your sequences.<br />
b) Some level of automatic GO annotation to your sequences. (Publically available.) <br />
<br><br />
'''(I am hoping that I can insert a picture here that shows where sequences go in and where annotated sequences come out so that people can choose their favourite provider and be sure that they know what they are getting and what they are missing out on by choosing to download at that point.)'''<br />
<br />
D. GOblet<br />
<br><br />
http://goblet.molgen.mpg.de/<br />
<br><br />
<br />
<br />
'''Manual Annotation'''<br />
<br />
1. Literature based manual annotation - Check and improve your annotations against the literature. <br />
<br />
1) Read the manual annotation guidelines on the GO Consortium website.<br><br />
http://www.geneontology.org/GO.annotation.shtml<br />
<br />
2) Contact the GO Consortium to ask about annotation camps and mentoring.<br><br />
[insert description of camps and mentoring]<br />
<br />
2. Sequence based manual annotation.<br />
<br />
The process of manual annotation based on sequence similarity involves the manual review of a host of sequence based search data including: BLAST-type searches, domain based searches (InterPro,Pfam, TIGRFAMs, PROSITE, etc.), SignalP, TMHMM, paralagous families, COGs, etc. The annotator evalutates this information by looking at alignments, scores, etc. while taking into consideration the genomic context of the gene product being annotated including neighboring genes, possible operons, syntenic regions, pathway and system resconstruction, etc.<br />
<br />
== PAMGO example ==<br />
<br />
Here is an example of how a new group has started working with the GO Consortium. <br />
<br />
'''<br />
The Plant-Associated Microbe Gene Ontology (PAMGO) Group'''<br />
<br />
In 2003 the genome sequence of the tomato pathogen Pseudomonas syringae pv. tomato DC3000 was published. This project was a collaboration between Robin Buell at the The Institute for Genomic Research (TIGR) and Alan Collmer of Cornell University. As part of the annotation of P. syringae TIGR provided some GO assignments to the P. syringae proteins. Dissussion between Alan Collmer and Brett Tyler at the NSF Plant Genome Research Program Awardees Meeting that fall revealed a shared awareness of the potential power of the GO and led to the formation of the Plant-Associated Microbe Gene Ontology (PAMGO) working group. Brett Tyler coordinated the effort to bring together PIs from genome projects representing the major groups of microbial pathogens: Bacteria, Fungi, Oomycetes, and Nematodes. The PAMGO group recognized the potential power of the GO to greatly facilitate research in areas common to all these pathogens by providing a robust framework for comparing functions across species. Since TIGR is a member of the GO consortium, the new PAMGO group entered into collaboration with TIGR staff Michelle Gwinn-Giglio and Linda Hannick to develop terms specific for interactions between pathogens and their hosts.<br />
<br><br><br />
<br />
During 2004 the PAMGO Interest Group worked to develop high level terms to describe processes relevant to plant-microbe associations, which would provide a framework for the later development of more detailed terms. Candace Collmer (Wells College) while on sabbatical leave, and Michelle Gwinn-Giglio (TIGR) led the effort. This activity began with a full-day workshop on April 23, 2004 at TIGR of all the PAMGO participants. The workshop participants defined a set of high level terms and relationships that would be as general as possible, not only for pathogens of all kingdoms, but for the whole range of host-microbe interactions from mutualism to parasitism, and for all hosts, not only plants. Further refinement of the terms and their definitions occurred by email, and on June 2, 2004 the proposed terms were submitted to the GO community for discussion. On Aug 22-23, 2004 Candace and Alan Collmer and Michelle Gwinn-Giglio presented the proposal at a GO content meeting focused on pathogenesis, metabolism, and the cell cycle at the Carnegie Institution, Stanford, CA and on Oct. 15-16, 2004 Michelle Gwinn-Giglio presented three modified options to a GO Consortium Meeting in Chicago. These high level terms generated much debate, both at the original workshop, and within the wider GO community, because of the varied ways in which different communities use words such as "Symbiosis" and "Pathogenesis", and the difficulty of defining the term "Pathogenesis" consistently, given that some organisms may or may not cause disease depending on the physical environment and the physiological or genetic status of the host. This discussion highlighted the varied usage of these terms and stimulated user communities to think about how these terms should be used. A final version was agreed upon and resubmitted to GO on Dec 14, 2004 and made part of the active ontologies on Jan 31, 2005.<br />
<br><br><br />
In addition to the term development activites in 2004, the PAMGO group was also busy writing a grant to the NSF/USDA Microbial Genome Sequencing Program to fund their GO development work. Fortunately, the grant was awarded and provides 3 years of funding (Fall 2005-Fall 2008) for PAMGO to continue the development of more granular terms under the initial PAMGO term set. The PAMGO group is now actively working on terms that will describe the myriad ways that pathogens affect the metabolism of their hosts. A PAMGO jamboree was held in July 2006 where more than 100 new terms were developed.<br><br><br />
<br />
Using the PAMGO terms, as well as the rest of the GO ontologies, PAMGO annotators are assigning GO terms to the proteins from the PAMGO organisms that have a role in interacting with their hosts. It is anticipated that PAMGO will begin sending in association files of these annotations at the end of this year.<br><br><br />
<br />
<br />
'''PAMGO people and pathogens:'''<br />
<br />
'''Virginia Bioinformatics Institute'''<br />
<br />
Phytophthora sojae (Oomycete)<br><br />
Phytophthora ramorum (Oomycete)<br><br />
Brett Tyler<br><br />
Trudy Torto-Alalibo<br><br />
Marcus Chibucos<br><br />
Rays Jiang<br><br />
<br />
Agrobacterium tumefaciens (Bacterium)<br><br />
Joao Setubal<br><br />
Joshua Shallom<br><br />
Tsai-Tien Tseng<br><br />
<br />
<br />
'''Cornell University'''<br />
<br />
Pseudomonas syringae pv. tomato DC3000 (Bacterium)<br><br />
Pseudomonas syringae pv. phaseolicola 1448A (Bacterium)<br><br />
Pseudomonas syringae pv. syringae B728A (Bacterium)<br><br />
Alan Collmer<br><br />
Magdalen Lindeberg<br><br />
Candace Collmer (Wells College, September-May)<br><br />
<br />
<br />
'''University of Wisconsin'''<br />
<br />
Erwinia chrysanthemi 3937 (Bacterium)<br><br />
Nicole Perna<br><br />
Jeremy Glasner<br><br />
Bryan Biehl<br><br />
<br />
<br />
'''North Carolina State University'''<br />
<br />
Magnaporthe grisea (Fungus)<br><br />
Meloidogyne hapla (Nematode)<br><br />
Ralph Dean<br><br />
David Bird<br><br />
Thomas Mitchell<br><br />
Shaowu Meng<br><br />
<br />
<br />
'''The Institute for Genomic Research'''<br />
<br />
Michelle Gwinn-Giglio<br><br />
Linda Hannick<br><br />
Robin Buell<br><br />
Owen White<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Beginning_Annotation_SOP&diff=6923Beginning Annotation SOP2006-10-16T17:47:08Z<p>Mlgwinn: /* SOP for starting annotation */</p>
<hr />
<div>This page is a place to build the SOP on beginning annotation. <br />
<br />
<br />
== These are the guidelines that the PIs gave me: ==<br />
<br />
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful. <br />
<br />
As far as the documentation; you might start with this outline... <br />
<br />
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit. <br />
<br />
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be <br />
used to frame the inquiries of annotation groups and to support these groups in many contexts. <br />
<br />
<br />
<br />
== SOP for starting annotation ==<br />
<br />
Automatic Annotation<br />
<br />
A. Automatic GO annotation tools<br />
<br />
There are several GO-related annotation tools that have been developed by many groups. Look at the annotation tools on the GO website:<br />
<br />
http://www.geneontology.org/GO.tools.annotation.shtml<br />
<br />
Please write to the GO-Friends mailing list if you have a specific annotation tool needs. All the tool developers are there and will help you to choose a good to tool, or may modify a tool to include the functionality that you need. Mail go-friends at geneontology.org.<br />
<br />
B. Automatic annotation based on GO mapping files and GO-annotated protein datasets for those users with database infrastructure in place.<br />
<br />
1) sequence-based methods<br />
<br />
blast2go<br />
You may also like to try BLAST2GO to find GO annotations to sequences similar to yours.<br />
<br><br />
http://www.geneontology.org/GO.tools.other.shtml#blast2go<br />
<br><br />
Use GOst<br><br />
http://www.godatabase.org/cgi-bin/gost/gost.cgi<br />
<br><br />
<br />
2) Domain-based comparison methods<br />
<br />
Interproscan<br />
Run your sequences through [[InterProScan]] either online or by downloading and running the application on your own computer. <br><br />
http://www.ebi.ac.uk/InterProScan/<br />
<br />
3) other<br />
<br />
keyword2go - a mapping of Swiss-Prot keywords to GO<br />
ec2go - a mapping of EC numbers to GO<br />
see additional mappings page on go website (link here)<br />
<br />
C. Annotation Services<br />
<br />
1) TIGR's Annotation Engine Service for prokaryotic genomes. This free service provides automatic annotation and database infrastructure to anyone with a prokaryotic DNA sequence they wish to annotate. More information can be found at: www.tigr.org/AnnotationEngine/<br />
In addition, TIGR offers a 3-day Prokaryotic Annotation and Analysis course. This course complements the Annotation Engine service in that it provides detailed information on TIGR's annotation pipeline and use of the free manual annotation tool Manatee. More info can be found at: www.tigr.org/AnnotationClass/<br />
<br />
2) GenDB www.cebitec.uni-bielefeld.de/groups/brf/software/gendb_info/<br />
<br />
D. GOblet<br />
<br><br />
http://goblet.molgen.mpg.de/<br />
<br><br />
<br />
E. For those who do not have any database infrastructure you can use the public repositories to aid in this process:<br />
<br />
Submit your sequences to one of the large public repositories.<br><br />
<a href="http://www.ebi.ac.uk/Submissions/"> EBI Submissions, including EMBL-bank </a><br><br />
<a href="http://www.ncbi.nlm.nih.gov/Genbank/submit.html">Genbank Submissions</a><br><br />
<a href="http://www.ddbj.nig.ac.jp/sub-e.html">DDBJ Submission</a><br><br />
<br />
(EMBL-Bank, GenBank and DDBJ exchange data amongst themselves so you can use any of these submission interfaces and<br />
have your data appear in all three resources.)<br />
<br />
Once your sequences have been processed and passed along the pipeline to all the related databases you will be able to retrieve:<br><br />
1) Unique stable identifiers such as UniProt or RefSeq for your sequences.<br />
2) Some level of automatic GO annotation to your sequences. (Publically available.) <br />
<br><br />
'''(I am hoping that I can insert a picture here that shows where sequences go in and where annotated sequences come out so that people can choose their favourite provider and be sure that they know what they are getting and what they are missing out on by choosing to download at that point.)'''<br />
<br />
<br />
Manual Annotation<br />
<br />
1. Literature based manual annotation - Check and improve your annotations against the literature. <br />
<br />
1) Read the manual annotation guidelines on the GO Consortium website.<br><br />
http://www.geneontology.org/GO.annotation.shtml<br />
<br />
2) Contact the GO Consortium to ask about annotation camps and mentoring.<br><br />
[insert description of camps and mentoring]<br />
<br />
2. Sequence based manual annotation.<br />
<br />
The process of manual annotation based on sequence similarity involves the manual review of a host of sequence based search data including: BLAST-type searches, domain based searches (InterPro,Pfam, TIGRFAMs, PROSITE, etc.), SignalP, TMHMM, paralagous families, COGs, etc. The annotator evalutates this information by looking at alignments, scores, etc. while taking into consideration the genomic context of the gene product being annotated including neighboring genes, possible operons, syntenic regions, pathway and system resconstruction, etc.<br />
<br />
== PAMGO example ==<br />
<br />
Here is an example of how a new group has started working with the GO Consortium. <br />
<br />
'''<br />
The Plant-Associated Microbe Gene Ontology (PAMGO) Group'''<br />
<br />
In 2003 the genome sequence of the tomato pathogen Pseudomonas syringae pv. tomato DC3000 was published. This project was a collaboration between Robin Buell at the The Institute for Genomic Research (TIGR) and Alan Collmer of Cornell University. As part of the annotation of P. syringae TIGR provided some GO assignments to the P. syringae proteins. Dissussion between Alan Collmer and Brett Tyler at the NSF Plant Genome Research Program Awardees Meeting that fall revealed a shared awareness of the potential power of the GO and led to the formation of the Plant-Associated Microbe Gene Ontology (PAMGO) working group. Brett Tyler coordinated the effort to bring together PIs from genome projects representing the major groups of microbial pathogens: Bacteria, Fungi, Oomycetes, and Nematodes. The PAMGO group recognized the potential power of the GO to greatly facilitate research in areas common to all these pathogens by providing a robust framework for comparing functions across species. Since TIGR is a member of the GO consortium, the new PAMGO group entered into collaboration with TIGR staff Michelle Gwinn-Giglio and Linda Hannick to develop terms specific for interactions between pathogens and their hosts.<br />
<br><br><br />
<br />
During 2004 the PAMGO Interest Group worked to develop high level terms to describe processes relevant to plant-microbe associations, which would provide a framework for the later development of more detailed terms. Candace Collmer (Wells College) while on sabbatical leave, and Michelle Gwinn-Giglio (TIGR) led the effort. This activity began with a full-day workshop on April 23, 2004 at TIGR of all the PAMGO participants. The workshop participants defined a set of high level terms and relationships that would be as general as possible, not only for pathogens of all kingdoms, but for the whole range of host-microbe interactions from mutualism to parasitism, and for all hosts, not only plants. Further refinement of the terms and their definitions occurred by email, and on June 2, 2004 the proposed terms were submitted to the GO community for discussion. On Aug 22-23, 2004 Candace and Alan Collmer and Michelle Gwinn-Giglio presented the proposal at a GO content meeting focused on pathogenesis, metabolism, and the cell cycle at the Carnegie Institution, Stanford, CA and on Oct. 15-16, 2004 Michelle Gwinn-Giglio presented three modified options to a GO Consortium Meeting in Chicago. These high level terms generated much debate, both at the original workshop, and within the wider GO community, because of the varied ways in which different communities use words such as "Symbiosis" and "Pathogenesis", and the difficulty of defining the term "Pathogenesis" consistently, given that some organisms may or may not cause disease depending on the physical environment and the physiological or genetic status of the host. This discussion highlighted the varied usage of these terms and stimulated user communities to think about how these terms should be used. A final version was agreed upon and resubmitted to GO on Dec 14, 2004 and made part of the active ontologies on Jan 31, 2005.<br />
<br><br><br />
In addition to the term development activites in 2004, the PAMGO group was also busy writing a grant to the NSF/USDA Microbial Genome Sequencing Program to fund their GO development work. Fortunately, the grant was awarded and provides 3 years of funding (Fall 2005-Fall 2008) for PAMGO to continue the development of more granular terms under the initial PAMGO term set. The PAMGO group is now actively working on terms that will describe the myriad ways that pathogens affect the metabolism of their hosts. A PAMGO jamboree was held in July 2006 where more than 100 new terms were developed.<br><br><br />
<br />
Using the PAMGO terms, as well as the rest of the GO ontologies, PAMGO annotators are assigning GO terms to the proteins from the PAMGO organisms that have a role in interacting with their hosts. It is anticipated that PAMGO will begin sending in association files of these annotations at the end of this year.<br><br><br />
<br />
<br />
'''PAMGO people and pathogens:'''<br />
<br />
'''Virginia Bioinformatics Institute'''<br />
<br />
Phytophthora sojae (Oomycete)<br><br />
Phytophthora ramorum (Oomycete)<br><br />
Brett Tyler<br><br />
Trudy Torto-Alalibo<br><br />
Marcus Chibucos<br><br />
Rays Jiang<br><br />
<br />
Agrobacterium tumefaciens (Bacterium)<br><br />
Joao Setubal<br><br />
Joshua Shallom<br><br />
Tsai-Tien Tseng<br><br />
<br />
<br />
'''Cornell University'''<br />
<br />
Pseudomonas syringae pv. tomato DC3000 (Bacterium)<br><br />
Pseudomonas syringae pv. phaseolicola 1448A (Bacterium)<br><br />
Pseudomonas syringae pv. syringae B728A (Bacterium)<br><br />
Alan Collmer<br><br />
Magdalen Lindeberg<br><br />
Candace Collmer (Wells College, September-May)<br><br />
<br />
<br />
'''University of Wisconsin'''<br />
<br />
Erwinia chrysanthemi 3937 (Bacterium)<br><br />
Nicole Perna<br><br />
Jeremy Glasner<br><br />
Bryan Biehl<br><br />
<br />
<br />
'''North Carolina State University'''<br />
<br />
Magnaporthe grisea (Fungus)<br><br />
Meloidogyne hapla (Nematode)<br><br />
Ralph Dean<br><br />
David Bird<br><br />
Thomas Mitchell<br><br />
Shaowu Meng<br><br />
<br />
<br />
'''The Institute for Genomic Research'''<br />
<br />
Michelle Gwinn-Giglio<br><br />
Linda Hannick<br><br />
Robin Buell<br><br />
Owen White<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Beginning_Annotation_SOP&diff=6922Beginning Annotation SOP2006-10-16T17:42:40Z<p>Mlgwinn: /* PAMGO example */</p>
<hr />
<div>This page is a place to build the SOP on beginning annotation. <br />
<br />
<br />
== These are the guidelines that the PIs gave me: ==<br />
<br />
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful. <br />
<br />
As far as the documentation; you might start with this outline... <br />
<br />
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit. <br />
<br />
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be <br />
used to frame the inquiries of annotation groups and to support these groups in many contexts. <br />
<br />
<br />
<br />
== SOP for starting annotation ==<br />
<br />
Automatic Annotation<br />
<br />
A. Automatic GO annotation tools<br />
<br />
There are several GO-related annotation tools that have been developed by many groups. Look at the annotation tools on the GO website:<br />
<br />
http://www.geneontology.org/GO.tools.annotation.shtml<br />
<br />
Please write to the GO-Friends mailing list if you have a specific annotation tool needs. All the tool developers are there and will help you to choose a good to tool, or may modify a tool to include the functionality that you need. Mail go-friends at geneontology.org.<br />
<br />
B. Automatic annotation based on GO mapping files and GO-annotated protein datasets for those users with database infrastructure in place.<br />
<br />
1) sequence-based methods<br />
<br />
blast2go<br />
You may also like to try BLAST2GO to find GO annotations to sequences similar to yours.<br />
<br><br />
http://www.geneontology.org/GO.tools.other.shtml#blast2go<br />
<br><br />
Use GOst<br><br />
http://www.godatabase.org/cgi-bin/gost/gost.cgi<br />
<br><br />
<br />
2) Domain-based comparison methods<br />
<br />
Interproscan<br />
Run your sequences through [[InterProScan]] either online or by downloading and running the application on your own computer. <br><br />
http://www.ebi.ac.uk/InterProScan/<br />
<br />
3) other<br />
<br />
keyword2go - a mapping of Swiss-Prot keywords to GO<br />
ec2go - a mapping of EC numbers to GO<br />
see additional mappings page on go website (link here)<br />
<br />
C. Annotation Services<br />
<br />
1) TIGR's Annotation Engine Service for prokaryotic genomes. This free service provides automatic annotation and database infrastructure to anyone with a prokaryotic DNA sequence they wish to annotate. www.tigr.org/AnnotationEngine<br />
<br />
2) GenDB<br />
<br />
D. GOblet<br />
<br><br />
http://goblet.molgen.mpg.de/<br />
<br><br />
<br />
E. If you do not have any database infrastructure you can use the public repositories.<br />
<br />
'''A) Submit your sequences to one of the large public repositories.''' <br><br />
<a href="http://www.ebi.ac.uk/Submissions/"> EBI Submissions, including EMBL-bank </a><br><br />
<a href="http://www.ncbi.nlm.nih.gov/Genbank/submit.html">Genbank Submissions</a><br><br />
<a href="http://www.ddbj.nig.ac.jp/sub-e.html">DDBJ Submission</a><br><br />
<br />
(EMBL-Bank, GenBank and DDBJ exchange data amongst themselves so you can use any of these submission interfaces and<br />
have your data appear in all three resources.)<br />
<br />
Once your sequences have been processed and passed along the pipeline to all the related databases you will be able to retrieve:<br><br />
<br />
1) Unique stable identifiers such as UniProt or RefSeq for your sequences.<br />
<br />
2) Some level of automatic GO annotation to your sequences. (Publically available.) <br />
<br><br />
'''(I am hoping that I can insert a picture here that shows where sequences go in and where annotated sequences come out so that people can choose their favourite provider and be sure that they know what they are getting and what they are missing out on by choosing to download at that point.)'''<br />
<br />
<br />
Manual Annotation<br />
<br />
1. Literature based manual annotation - Check and improve your annotations against the literature. <br />
<br />
1) Read the manual annotation guidelines on the GO Consortium website.<br><br />
http://www.geneontology.org/GO.annotation.shtml<br />
<br />
2) Contact the GO Consortium to ask about annotation camps and mentoring.<br><br />
[insert description of camps and mentoring]<br />
<br />
2. Sequence based manual annotation.<br />
<br />
The process of manual annotation based on sequence similarity involves the manual review of a host of sequence based search data including: BLAST-type searches, domain based searches (InterPro,Pfam, TIGRFAMs, PROSITE, etc.), SignalP, TMHMM, paralagous families, COGs, etc. The annotator evalutates this information by looking at alignments, scores, etc. while taking into consideration the genomic context of the gene product being annotated including neighboring genes, possible operons, syntenic regions, pathway and system resconstruction, etc.<br />
<br />
== PAMGO example ==<br />
<br />
Here is an example of how a new group has started working with the GO Consortium. <br />
<br />
'''<br />
The Plant-Associated Microbe Gene Ontology (PAMGO) Group'''<br />
<br />
In 2003 the genome sequence of the tomato pathogen Pseudomonas syringae pv. tomato DC3000 was published. This project was a collaboration between Robin Buell at the The Institute for Genomic Research (TIGR) and Alan Collmer of Cornell University. As part of the annotation of P. syringae TIGR provided some GO assignments to the P. syringae proteins. Dissussion between Alan Collmer and Brett Tyler at the NSF Plant Genome Research Program Awardees Meeting that fall revealed a shared awareness of the potential power of the GO and led to the formation of the Plant-Associated Microbe Gene Ontology (PAMGO) working group. Brett Tyler coordinated the effort to bring together PIs from genome projects representing the major groups of microbial pathogens: Bacteria, Fungi, Oomycetes, and Nematodes. The PAMGO group recognized the potential power of the GO to greatly facilitate research in areas common to all these pathogens by providing a robust framework for comparing functions across species. Since TIGR is a member of the GO consortium, the new PAMGO group entered into collaboration with TIGR staff Michelle Gwinn-Giglio and Linda Hannick to develop terms specific for interactions between pathogens and their hosts.<br />
<br><br><br />
<br />
During 2004 the PAMGO Interest Group worked to develop high level terms to describe processes relevant to plant-microbe associations, which would provide a framework for the later development of more detailed terms. Candace Collmer (Wells College) while on sabbatical leave, and Michelle Gwinn-Giglio (TIGR) led the effort. This activity began with a full-day workshop on April 23, 2004 at TIGR of all the PAMGO participants. The workshop participants defined a set of high level terms and relationships that would be as general as possible, not only for pathogens of all kingdoms, but for the whole range of host-microbe interactions from mutualism to parasitism, and for all hosts, not only plants. Further refinement of the terms and their definitions occurred by email, and on June 2, 2004 the proposed terms were submitted to the GO community for discussion. On Aug 22-23, 2004 Candace and Alan Collmer and Michelle Gwinn-Giglio presented the proposal at a GO content meeting focused on pathogenesis, metabolism, and the cell cycle at the Carnegie Institution, Stanford, CA and on Oct. 15-16, 2004 Michelle Gwinn-Giglio presented three modified options to a GO Consortium Meeting in Chicago. These high level terms generated much debate, both at the original workshop, and within the wider GO community, because of the varied ways in which different communities use words such as "Symbiosis" and "Pathogenesis", and the difficulty of defining the term "Pathogenesis" consistently, given that some organisms may or may not cause disease depending on the physical environment and the physiological or genetic status of the host. This discussion highlighted the varied usage of these terms and stimulated user communities to think about how these terms should be used. A final version was agreed upon and resubmitted to GO on Dec 14, 2004 and made part of the active ontologies on Jan 31, 2005.<br />
<br><br><br />
In addition to the term development activites in 2004, the PAMGO group was also busy writing a grant to the NSF/USDA Microbial Genome Sequencing Program to fund their GO development work. Fortunately, the grant was awarded and provides 3 years of funding (Fall 2005-Fall 2008) for PAMGO to continue the development of more granular terms under the initial PAMGO term set. The PAMGO group is now actively working on terms that will describe the myriad ways that pathogens affect the metabolism of their hosts. A PAMGO jamboree was held in July 2006 where more than 100 new terms were developed.<br><br><br />
<br />
Using the PAMGO terms, as well as the rest of the GO ontologies, PAMGO annotators are assigning GO terms to the proteins from the PAMGO organisms that have a role in interacting with their hosts. It is anticipated that PAMGO will begin sending in association files of these annotations at the end of this year.<br><br><br />
<br />
<br />
'''PAMGO people and pathogens:'''<br />
<br />
'''Virginia Bioinformatics Institute'''<br />
<br />
Phytophthora sojae (Oomycete)<br><br />
Phytophthora ramorum (Oomycete)<br><br />
Brett Tyler<br><br />
Trudy Torto-Alalibo<br><br />
Marcus Chibucos<br><br />
Rays Jiang<br><br />
<br />
Agrobacterium tumefaciens (Bacterium)<br><br />
Joao Setubal<br><br />
Joshua Shallom<br><br />
Tsai-Tien Tseng<br><br />
<br />
<br />
'''Cornell University'''<br />
<br />
Pseudomonas syringae pv. tomato DC3000 (Bacterium)<br><br />
Pseudomonas syringae pv. phaseolicola 1448A (Bacterium)<br><br />
Pseudomonas syringae pv. syringae B728A (Bacterium)<br><br />
Alan Collmer<br><br />
Magdalen Lindeberg<br><br />
Candace Collmer (Wells College, September-May)<br><br />
<br />
<br />
'''University of Wisconsin'''<br />
<br />
Erwinia chrysanthemi 3937 (Bacterium)<br><br />
Nicole Perna<br><br />
Jeremy Glasner<br><br />
Bryan Biehl<br><br />
<br />
<br />
'''North Carolina State University'''<br />
<br />
Magnaporthe grisea (Fungus)<br><br />
Meloidogyne hapla (Nematode)<br><br />
Ralph Dean<br><br />
David Bird<br><br />
Thomas Mitchell<br><br />
Shaowu Meng<br><br />
<br />
<br />
'''The Institute for Genomic Research'''<br />
<br />
Michelle Gwinn-Giglio<br><br />
Linda Hannick<br><br />
Robin Buell<br><br />
Owen White<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Beginning_Annotation_SOP&diff=6921Beginning Annotation SOP2006-10-16T17:41:42Z<p>Mlgwinn: /* PAMGO example */</p>
<hr />
<div>This page is a place to build the SOP on beginning annotation. <br />
<br />
<br />
== These are the guidelines that the PIs gave me: ==<br />
<br />
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful. <br />
<br />
As far as the documentation; you might start with this outline... <br />
<br />
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit. <br />
<br />
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be <br />
used to frame the inquiries of annotation groups and to support these groups in many contexts. <br />
<br />
<br />
<br />
== SOP for starting annotation ==<br />
<br />
Automatic Annotation<br />
<br />
A. Automatic GO annotation tools<br />
<br />
There are several GO-related annotation tools that have been developed by many groups. Look at the annotation tools on the GO website:<br />
<br />
http://www.geneontology.org/GO.tools.annotation.shtml<br />
<br />
Please write to the GO-Friends mailing list if you have a specific annotation tool needs. All the tool developers are there and will help you to choose a good to tool, or may modify a tool to include the functionality that you need. Mail go-friends at geneontology.org.<br />
<br />
B. Automatic annotation based on GO mapping files and GO-annotated protein datasets for those users with database infrastructure in place.<br />
<br />
1) sequence-based methods<br />
<br />
blast2go<br />
You may also like to try BLAST2GO to find GO annotations to sequences similar to yours.<br />
<br><br />
http://www.geneontology.org/GO.tools.other.shtml#blast2go<br />
<br><br />
Use GOst<br><br />
http://www.godatabase.org/cgi-bin/gost/gost.cgi<br />
<br><br />
<br />
2) Domain-based comparison methods<br />
<br />
Interproscan<br />
Run your sequences through [[InterProScan]] either online or by downloading and running the application on your own computer. <br><br />
http://www.ebi.ac.uk/InterProScan/<br />
<br />
3) other<br />
<br />
keyword2go - a mapping of Swiss-Prot keywords to GO<br />
ec2go - a mapping of EC numbers to GO<br />
see additional mappings page on go website (link here)<br />
<br />
C. Annotation Services<br />
<br />
1) TIGR's Annotation Engine Service for prokaryotic genomes. This free service provides automatic annotation and database infrastructure to anyone with a prokaryotic DNA sequence they wish to annotate. www.tigr.org/AnnotationEngine<br />
<br />
2) GenDB<br />
<br />
D. GOblet<br />
<br><br />
http://goblet.molgen.mpg.de/<br />
<br><br />
<br />
E. If you do not have any database infrastructure you can use the public repositories.<br />
<br />
'''A) Submit your sequences to one of the large public repositories.''' <br><br />
<a href="http://www.ebi.ac.uk/Submissions/"> EBI Submissions, including EMBL-bank </a><br><br />
<a href="http://www.ncbi.nlm.nih.gov/Genbank/submit.html">Genbank Submissions</a><br><br />
<a href="http://www.ddbj.nig.ac.jp/sub-e.html">DDBJ Submission</a><br><br />
<br />
(EMBL-Bank, GenBank and DDBJ exchange data amongst themselves so you can use any of these submission interfaces and<br />
have your data appear in all three resources.)<br />
<br />
Once your sequences have been processed and passed along the pipeline to all the related databases you will be able to retrieve:<br><br />
<br />
1) Unique stable identifiers such as UniProt or RefSeq for your sequences.<br />
<br />
2) Some level of automatic GO annotation to your sequences. (Publically available.) <br />
<br><br />
'''(I am hoping that I can insert a picture here that shows where sequences go in and where annotated sequences come out so that people can choose their favourite provider and be sure that they know what they are getting and what they are missing out on by choosing to download at that point.)'''<br />
<br />
<br />
Manual Annotation<br />
<br />
1. Literature based manual annotation - Check and improve your annotations against the literature. <br />
<br />
1) Read the manual annotation guidelines on the GO Consortium website.<br><br />
http://www.geneontology.org/GO.annotation.shtml<br />
<br />
2) Contact the GO Consortium to ask about annotation camps and mentoring.<br><br />
[insert description of camps and mentoring]<br />
<br />
2. Sequence based manual annotation.<br />
<br />
The process of manual annotation based on sequence similarity involves the manual review of a host of sequence based search data including: BLAST-type searches, domain based searches (InterPro,Pfam, TIGRFAMs, PROSITE, etc.), SignalP, TMHMM, paralagous families, COGs, etc. The annotator evalutates this information by looking at alignments, scores, etc. while taking into consideration the genomic context of the gene product being annotated including neighboring genes, possible operons, syntenic regions, pathway and system resconstruction, etc.<br />
<br />
== PAMGO example ==<br />
<br />
Here is an example of how a new group has started working with the GO Consortium. <br />
<br />
'''<br />
The Plant-Associated Microbe Gene Ontology (PAMGO) Group'''<br />
<br />
In 2003 the genome sequence of the tomato pathogen Pseudomonas syringae pv. tomato DC3000 was published. This project was a collaboration between Robin Buell at the The Institute for Genomic Research (TIGR) and Alan Collmer of Cornell University. As part of the annotation of P. syringae TIGR provided some GO assignments to the P. syringae proteins. Dissussion between Alan Collmer and Brett Tyler at the NSF Plant Genome Research Program Awardees Meeting that fall revealed a shared awareness of the potential power of the GO and led to the formation of the Plant-Associated Microbe Gene Ontology (PAMGO) working group. Brett Tyler coordinated the effort to bring together PIs from genome projects representing the major groups of microbial pathogens: Bacteria, Fungi, Oomycetes, and Nematodes. The PAMGO group recognized the potential power of the GO to greatly facilitate research in areas common to all these pathogens by providing a robust framework for comparing functions across species. Since TIGR is a member of the GO consortium, the new PAMGO group entered into collaboration with TIGR staff Michelle Gwinn-Giglio and Linda Hannick to develop terms specific for interactions between pathogens and their hosts.<br />
<br><br><br />
<br />
During 2004 the PAMGO Interest Group worked to develop high level terms to describe processes relevant to plant-microbe associations, which would provide a framework for the later development of more detailed terms. Candace Collmer (Wells College) while on sabbatical leave, and Michelle Gwinn-Giglio (TIGR) led the effort. This activity began with a full-day workshop on April 23, 2004 at TIGR of all the PAMGO participants. The workshop participants defined a set of high level terms and relationships that would be as general as possible, not only for pathogens of all kingdoms, but for the whole range of host-microbe interactions from mutualism to parasitism, and for all hosts, not only plants. Further refinement of the terms and their definitions occurred by email, and on June 2, 2004 the proposed terms were submitted to the GO community for discussion. On Aug 22-23, 2004 Candace and Alan Collmer and Michelle Gwinn-Giglio presented the proposal at a GO content meeting focused on pathogenesis, metabolism, and the cell cycle at the Carnegie Institution, Stanford, CA and on Oct. 15-16, 2004 Michelle Gwinn-Giglio presented three modified options to a GO Consortium Meeting in Chicago. These high level terms generated much debate, both at the original workshop, and within the wider GO community, because of the varied ways in which different communities use words such as "Symbiosis" and "Pathogenesis", and the difficulty of defining the term "Pathogenesis" consistently, given that some organisms may or may not cause disease depending on the physical environment and the physiological or genetic status of the host. This discussion highlighted the varied usage of these terms and stimulated user communities to think about how these terms should be used. A final version was agreed upon and resubmitted to GO on Dec 14, 2004 and made part of the active ontologies on Jan 31, 2005.<br />
<br><br><br />
In addition to the term development activites in 2004, the PAMGO group was also busy writing a grant to the NSF/USDA Microbial Genome Sequencing Program to fund their GO development work. Fortunately, the grant was awarded and provides 3 years of funding (Fall 2005-Fall 2008) for PAMGO to continue the development of more granular terms under the initial PAMGO term set. The PAMGO group is now actively working on terms that will describe the myriad ways that pathogens affect the metabolism of their hosts. A PAMGO jamboree was held in July 2006 where more than 100 new terms were developed.<br><br><br />
<br />
Using the PAMGO terms, as well as the rest of the GO ontologies, PAMGO annotators are assigning GO terms to the proteins from the PAMGO organisms that have a role in interacting with their hosts. It is anticipated that PAMGO will begin sending in association files of these annotations at the end of this year.<br><br><br />
'''<br />
PAMGO people and pathogens:'''<br />
<br />
'''Virginia Bioinformatics Institute'''<br />
<br />
Phytophthora sojae (Oomycete)<br><br />
Phytophthora ramorum (Oomycete)<br><br />
Brett Tyler<br><br />
Trudy Torto-Alalibo<br><br />
Marcus Chibucos<br><br />
Rays Jiang<br><br />
<br />
Agrobacterium tumefaciens (Bacterium)<br><br />
Joao Setubal<br><br />
Joshua Shallom<br><br />
Tsai-Tien Tseng<br><br />
<br />
'''Cornell University'''<br />
<br />
Pseudomonas syringae pv. tomato DC3000 (Bacterium)<br><br />
Pseudomonas syringae pv. phaseolicola 1448A (Bacterium)<br><br />
Pseudomonas syringae pv. syringae B728A (Bacterium)<br><br />
Alan Collmer<br><br />
Magdalen Lindeberg<br><br />
Candace Collmer (Wells College, September-May)<br><br />
<br />
'''University of Wisconsin'''<br />
<br />
Erwinia chrysanthemi 3937 (Bacterium)<br><br />
Nicole Perna<br><br />
Jeremy Glasner<br><br />
Bryan Biehl<br><br />
<br />
<br />
'''North Carolina State University'''<br />
<br />
Magnaporthe grisea (Fungus)<br><br />
Meloidogyne hapla (Nematode)<br><br />
Ralph Dean<br><br />
David Bird<br><br />
Thomas Mitchell<br><br />
Shaowu Meng<br><br />
<br />
'''The Institute for Genomic Research'''<br />
<br />
Michelle Gwinn-Giglio<br><br />
Linda Hannick<br><br />
Robin Buell<br><br />
Owen White<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Beginning_Annotation_SOP&diff=6920Beginning Annotation SOP2006-10-16T17:40:44Z<p>Mlgwinn: /* PAMGO example */</p>
<hr />
<div>This page is a place to build the SOP on beginning annotation. <br />
<br />
<br />
== These are the guidelines that the PIs gave me: ==<br />
<br />
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful. <br />
<br />
As far as the documentation; you might start with this outline... <br />
<br />
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit. <br />
<br />
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be <br />
used to frame the inquiries of annotation groups and to support these groups in many contexts. <br />
<br />
<br />
<br />
== SOP for starting annotation ==<br />
<br />
Automatic Annotation<br />
<br />
A. Automatic GO annotation tools<br />
<br />
There are several GO-related annotation tools that have been developed by many groups. Look at the annotation tools on the GO website:<br />
<br />
http://www.geneontology.org/GO.tools.annotation.shtml<br />
<br />
Please write to the GO-Friends mailing list if you have a specific annotation tool needs. All the tool developers are there and will help you to choose a good to tool, or may modify a tool to include the functionality that you need. Mail go-friends at geneontology.org.<br />
<br />
B. Automatic annotation based on GO mapping files and GO-annotated protein datasets for those users with database infrastructure in place.<br />
<br />
1) sequence-based methods<br />
<br />
blast2go<br />
You may also like to try BLAST2GO to find GO annotations to sequences similar to yours.<br />
<br><br />
http://www.geneontology.org/GO.tools.other.shtml#blast2go<br />
<br><br />
Use GOst<br><br />
http://www.godatabase.org/cgi-bin/gost/gost.cgi<br />
<br><br />
<br />
2) Domain-based comparison methods<br />
<br />
Interproscan<br />
Run your sequences through [[InterProScan]] either online or by downloading and running the application on your own computer. <br><br />
http://www.ebi.ac.uk/InterProScan/<br />
<br />
3) other<br />
<br />
keyword2go - a mapping of Swiss-Prot keywords to GO<br />
ec2go - a mapping of EC numbers to GO<br />
see additional mappings page on go website (link here)<br />
<br />
C. Annotation Services<br />
<br />
1) TIGR's Annotation Engine Service for prokaryotic genomes. This free service provides automatic annotation and database infrastructure to anyone with a prokaryotic DNA sequence they wish to annotate. www.tigr.org/AnnotationEngine<br />
<br />
2) GenDB<br />
<br />
D. GOblet<br />
<br><br />
http://goblet.molgen.mpg.de/<br />
<br><br />
<br />
E. If you do not have any database infrastructure you can use the public repositories.<br />
<br />
'''A) Submit your sequences to one of the large public repositories.''' <br><br />
<a href="http://www.ebi.ac.uk/Submissions/"> EBI Submissions, including EMBL-bank </a><br><br />
<a href="http://www.ncbi.nlm.nih.gov/Genbank/submit.html">Genbank Submissions</a><br><br />
<a href="http://www.ddbj.nig.ac.jp/sub-e.html">DDBJ Submission</a><br><br />
<br />
(EMBL-Bank, GenBank and DDBJ exchange data amongst themselves so you can use any of these submission interfaces and<br />
have your data appear in all three resources.)<br />
<br />
Once your sequences have been processed and passed along the pipeline to all the related databases you will be able to retrieve:<br><br />
<br />
1) Unique stable identifiers such as UniProt or RefSeq for your sequences.<br />
<br />
2) Some level of automatic GO annotation to your sequences. (Publically available.) <br />
<br><br />
'''(I am hoping that I can insert a picture here that shows where sequences go in and where annotated sequences come out so that people can choose their favourite provider and be sure that they know what they are getting and what they are missing out on by choosing to download at that point.)'''<br />
<br />
<br />
Manual Annotation<br />
<br />
1. Literature based manual annotation - Check and improve your annotations against the literature. <br />
<br />
1) Read the manual annotation guidelines on the GO Consortium website.<br><br />
http://www.geneontology.org/GO.annotation.shtml<br />
<br />
2) Contact the GO Consortium to ask about annotation camps and mentoring.<br><br />
[insert description of camps and mentoring]<br />
<br />
2. Sequence based manual annotation.<br />
<br />
The process of manual annotation based on sequence similarity involves the manual review of a host of sequence based search data including: BLAST-type searches, domain based searches (InterPro,Pfam, TIGRFAMs, PROSITE, etc.), SignalP, TMHMM, paralagous families, COGs, etc. The annotator evalutates this information by looking at alignments, scores, etc. while taking into consideration the genomic context of the gene product being annotated including neighboring genes, possible operons, syntenic regions, pathway and system resconstruction, etc.<br />
<br />
== PAMGO example ==<br />
<br />
Here is an example of how a new group has started working with the GO Consortium. <br />
<br />
'''<br />
The Plant-Associated Microbe Gene Ontology (PAMGO) Group'''<br />
<br />
In 2003 the genome sequence of the tomato pathogen Pseudomonas syringae pv. tomato DC3000 was published. This project was a collaboration between Robin Buell at the The Institute for Genomic Research (TIGR) and Alan Collmer of Cornell University. As part of the annotation of P. syringae TIGR provided some GO assignments to the P. syringae proteins. Dissussion between Alan Collmer and Brett Tyler at the NSF Plant Genome Research Program Awardees Meeting that fall revealed a shared awareness of the potential power of the GO and led to the formation of the Plant-Associated Microbe Gene Ontology (PAMGO) working group. Brett Tyler coordinated the effort to bring together PIs from genome projects representing the major groups of microbial pathogens: Bacteria, Fungi, Oomycetes, and Nematodes. The PAMGO group recognized the potential power of the GO to greatly facilitate research in areas common to all these pathogens by providing a robust framework for comparing functions across species. Since TIGR is a member of the GO consortium, the new PAMGO group entered into collaboration with TIGR staff Michelle Gwinn-Giglio and Linda Hannick to develop terms specific for interactions between pathogens and their hosts.<br />
<br><br><br />
<br />
During 2004 the PAMGO Interest Group worked to develop high level terms to describe processes relevant to plant-microbe associations, which would provide a framework for the later development of more detailed terms. Candace Collmer (Wells College) while on sabbatical leave, and Michelle Gwinn-Giglio (TIGR) led the effort. This activity began with a full-day workshop on April 23, 2004 at TIGR of all the PAMGO participants. The workshop participants defined a set of high level terms and relationships that would be as general as possible, not only for pathogens of all kingdoms, but for the whole range of host-microbe interactions from mutualism to parasitism, and for all hosts, not only plants. Further refinement of the terms and their definitions occurred by email, and on June 2, 2004 the proposed terms were submitted to the GO community for discussion. On Aug 22-23, 2004 Candace and Alan Collmer and Michelle Gwinn-Giglio presented the proposal at a GO content meeting focused on pathogenesis, metabolism, and the cell cycle at the Carnegie Institution, Stanford, CA and on Oct. 15-16, 2004 Michelle Gwinn-Giglio presented three modified options to a GO Consortium Meeting in Chicago. These high level terms generated much debate, both at the original workshop, and within the wider GO community, because of the varied ways in which different communities use words such as "Symbiosis" and "Pathogenesis", and the difficulty of defining the term "Pathogenesis" consistently, given that some organisms may or may not cause disease depending on the physical environment and the physiological or genetic status of the host. This discussion highlighted the varied usage of these terms and stimulated user communities to think about how these terms should be used. A final version was agreed upon and resubmitted to GO on Dec 14, 2004 and made part of the active ontologies on Jan 31, 2005.<br />
<br><br><br />
In addition to the term development activites in 2004, the PAMGO group was also busy writing a grant to the NSF/USDA Microbial Genome Sequencing Program to fund their GO development work. Fortunately, the grant was awarded and provides 3 years of funding (Fall 2005-Fall 2008) for PAMGO to continue the development of more granular terms under the initial PAMGO term set. The PAMGO group is now actively working on terms that will describe the myriad ways that pathogens affect the metabolism of their hosts. A PAMGO jamboree was held in July 2006 where more than 100 new terms were developed.<br><br><br />
<br />
Using the PAMGO terms, as well as the rest of the GO ontologies, PAMGO annotators are assigning GO terms to the proteins from the PAMGO organisms that have a role in interacting with their hosts. It is anticipated that PAMGO will begin sending in association files of these annotations at the end of this year.<br><br><br />
'''<br />
PAMGO people and pathogens:'''<br />
<br />
'''Virginia Bioinformatics Institute'''<br />
<br />
Phytophthora sojae (Oomycete)<br><br />
Phytophthora ramorum (Oomycete)<br><br />
Brett Tyler<br><br />
Trudy Torto-Alalibo<br><br />
Marcus Chibucos<br><br />
Rays Jiang<br><br />
<br />
Agrobacterium tumefaciens (Bacterium)<br><br />
Joao Setubal<br><br />
Joshua Shallom<br><br />
Tsai-Tien Tseng<br><br />
<br />
'''Cornell University'''<br />
<br />
Pseudomonas syringae pv. tomato DC3000 (Bacterium)<br><br />
Pseudomonas syringae pv. phaseolicola 1448A (Bacterium)<br><br />
Pseudomonas syringae pv. syringae B728A (Bacterium)<br><br />
Alan Collmer<br><br />
Magdalen Lindeberg<br><br />
Candace Collmer (Wells College, September-May)<br><br />
<br />
'''University of Wisconsin'''<br />
<br />
Erwinia chrysanthemi 3937 (Bacterium)<br><br />
Nicole Perna<br><br />
Jeremy Glasner<br><br />
Bryan Biehl<br><br />
'''<br />
North Carolina State University'''<br />
<br />
Magnaporthe grisea (Fungus)<br><br />
Meloidogyne hapla (Nematode)<br><br />
Ralph Dean<br><br />
David Bird<br><br />
Thomas Mitchell<br><br />
Shaowu Meng<br><br />
<br />
'''The Institute for Genomic Research'''<br />
<br />
Michelle Gwinn-Giglio<br><br />
Linda Hannick<br><br />
Robin Buell<br><br />
Owen White<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Beginning_Annotation_SOP&diff=6919Beginning Annotation SOP2006-10-16T17:40:10Z<p>Mlgwinn: /* PAMGO example */</p>
<hr />
<div>This page is a place to build the SOP on beginning annotation. <br />
<br />
<br />
== These are the guidelines that the PIs gave me: ==<br />
<br />
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful. <br />
<br />
As far as the documentation; you might start with this outline... <br />
<br />
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit. <br />
<br />
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be <br />
used to frame the inquiries of annotation groups and to support these groups in many contexts. <br />
<br />
<br />
<br />
== SOP for starting annotation ==<br />
<br />
Automatic Annotation<br />
<br />
A. Automatic GO annotation tools<br />
<br />
There are several GO-related annotation tools that have been developed by many groups. Look at the annotation tools on the GO website:<br />
<br />
http://www.geneontology.org/GO.tools.annotation.shtml<br />
<br />
Please write to the GO-Friends mailing list if you have a specific annotation tool needs. All the tool developers are there and will help you to choose a good to tool, or may modify a tool to include the functionality that you need. Mail go-friends at geneontology.org.<br />
<br />
B. Automatic annotation based on GO mapping files and GO-annotated protein datasets for those users with database infrastructure in place.<br />
<br />
1) sequence-based methods<br />
<br />
blast2go<br />
You may also like to try BLAST2GO to find GO annotations to sequences similar to yours.<br />
<br><br />
http://www.geneontology.org/GO.tools.other.shtml#blast2go<br />
<br><br />
Use GOst<br><br />
http://www.godatabase.org/cgi-bin/gost/gost.cgi<br />
<br><br />
<br />
2) Domain-based comparison methods<br />
<br />
Interproscan<br />
Run your sequences through [[InterProScan]] either online or by downloading and running the application on your own computer. <br><br />
http://www.ebi.ac.uk/InterProScan/<br />
<br />
3) other<br />
<br />
keyword2go - a mapping of Swiss-Prot keywords to GO<br />
ec2go - a mapping of EC numbers to GO<br />
see additional mappings page on go website (link here)<br />
<br />
C. Annotation Services<br />
<br />
1) TIGR's Annotation Engine Service for prokaryotic genomes. This free service provides automatic annotation and database infrastructure to anyone with a prokaryotic DNA sequence they wish to annotate. www.tigr.org/AnnotationEngine<br />
<br />
2) GenDB<br />
<br />
D. GOblet<br />
<br><br />
http://goblet.molgen.mpg.de/<br />
<br><br />
<br />
E. If you do not have any database infrastructure you can use the public repositories.<br />
<br />
'''A) Submit your sequences to one of the large public repositories.''' <br><br />
<a href="http://www.ebi.ac.uk/Submissions/"> EBI Submissions, including EMBL-bank </a><br><br />
<a href="http://www.ncbi.nlm.nih.gov/Genbank/submit.html">Genbank Submissions</a><br><br />
<a href="http://www.ddbj.nig.ac.jp/sub-e.html">DDBJ Submission</a><br><br />
<br />
(EMBL-Bank, GenBank and DDBJ exchange data amongst themselves so you can use any of these submission interfaces and<br />
have your data appear in all three resources.)<br />
<br />
Once your sequences have been processed and passed along the pipeline to all the related databases you will be able to retrieve:<br><br />
<br />
1) Unique stable identifiers such as UniProt or RefSeq for your sequences.<br />
<br />
2) Some level of automatic GO annotation to your sequences. (Publically available.) <br />
<br><br />
'''(I am hoping that I can insert a picture here that shows where sequences go in and where annotated sequences come out so that people can choose their favourite provider and be sure that they know what they are getting and what they are missing out on by choosing to download at that point.)'''<br />
<br />
<br />
Manual Annotation<br />
<br />
1. Literature based manual annotation - Check and improve your annotations against the literature. <br />
<br />
1) Read the manual annotation guidelines on the GO Consortium website.<br><br />
http://www.geneontology.org/GO.annotation.shtml<br />
<br />
2) Contact the GO Consortium to ask about annotation camps and mentoring.<br><br />
[insert description of camps and mentoring]<br />
<br />
2. Sequence based manual annotation.<br />
<br />
The process of manual annotation based on sequence similarity involves the manual review of a host of sequence based search data including: BLAST-type searches, domain based searches (InterPro,Pfam, TIGRFAMs, PROSITE, etc.), SignalP, TMHMM, paralagous families, COGs, etc. The annotator evalutates this information by looking at alignments, scores, etc. while taking into consideration the genomic context of the gene product being annotated including neighboring genes, possible operons, syntenic regions, pathway and system resconstruction, etc.<br />
<br />
== PAMGO example ==<br />
<br />
Here is an example of how a new group has started working with the GO Consortium. <br />
<br />
'''<br />
The Plant-Associated Microbe Gene Ontology (PAMGO) Group'''<br />
<br />
In 2003 the genome sequence of the tomato pathogen Pseudomonas syringae pv. tomato DC3000 was published. This project was a collaboration between Robin Buell at the The Institute for Genomic Research (TIGR) and Alan Collmer of Cornell University. As part of the annotation of P. syringae TIGR provided some GO assignments to the P. syringae proteins. Dissussion between Alan Collmer and Brett Tyler at the NSF Plant Genome Research Program Awardees Meeting that fall revealed a shared awareness of the potential power of the GO and led to the formation of the Plant-Associated Microbe Gene Ontology (PAMGO) working group. Brett Tyler coordinated the effort to bring together PIs from genome projects representing the major groups of microbial pathogens: Bacteria, Fungi, Oomycetes, and Nematodes. The PAMGO group recognized the potential power of the GO to greatly facilitate research in areas common to all these pathogens by providing a robust framework for comparing functions across species. Since TIGR is a member of the GO consortium, the new PAMGO group entered into collaboration with TIGR staff Michelle Gwinn-Giglio and Linda Hannick to develop terms specific for interactions between pathogens and their hosts.<br />
<br><br><br />
<br />
During 2004 the PAMGO Interest Group worked to develop high level terms to describe processes relevant to plant-microbe associations, which would provide a framework for the later development of more detailed terms. Candace Collmer (Wells College) while on sabbatical leave, and Michelle Gwinn-Giglio (TIGR) led the effort. This activity began with a full-day workshop on April 23, 2004 at TIGR of all the PAMGO participants. The workshop participants defined a set of high level terms and relationships that would be as general as possible, not only for pathogens of all kingdoms, but for the whole range of host-microbe interactions from mutualism to parasitism, and for all hosts, not only plants. Further refinement of the terms and their definitions occurred by email, and on June 2, 2004 the proposed terms were submitted to the GO community for discussion. On Aug 22-23, 2004 Candace and Alan Collmer and Michelle Gwinn-Giglio presented the proposal at a GO content meeting focused on pathogenesis, metabolism, and the cell cycle at the Carnegie Institution, Stanford, CA and on Oct. 15-16, 2004 Michelle Gwinn-Giglio presented three modified options to a GO Consortium Meeting in Chicago. These high level terms generated much debate, both at the original workshop, and within the wider GO community, because of the varied ways in which different communities use words such as "Symbiosis" and "Pathogenesis", and the difficulty of defining the term "Pathogenesis" consistently, given that some organisms may or may not cause disease depending on the physical environment and the physiological or genetic status of the host. This discussion highlighted the varied usage of these terms and stimulated user communities to think about how these terms should be used. A final version was agreed upon and resubmitted to GO on Dec 14, 2004 and made part of the active ontologies on Jan 31, 2005.<br />
<br><br><br />
In addition to the term development activites in 2004, the PAMGO group was also busy writing a grant to the NSF/USDA Microbial Genome Sequencing Program to fund their GO development work. Fortunately, the grant was awarded and provides 3 years of funding (Fall 2005-Fall 2008) for PAMGO to continue the development of more granular terms under the initial PAMGO term set. The PAMGO group is now actively working on terms that will describe the myriad ways that pathogens affect the metabolism of their hosts. A PAMGO jamboree was held in July 2006 where more than 100 new terms were developed.<br><br><br />
<br />
Using the PAMGO terms, as well as the rest of the GO ontologies, PAMGO annotators are assigning GO terms to the proteins from the PAMGO organisms that have a role in interacting with their hosts. It is anticipated that PAMGO will begin sending in association files of these annotations at the end of this year.<br />
'''<br />
PAMGO people and pathogens:'''<br />
<br />
'''Virginia Bioinformatics Institute'''<br />
<br />
Phytophthora sojae (Oomycete)<br><br />
Phytophthora ramorum (Oomycete)<br><br />
Brett Tyler<br><br />
Trudy Torto-Alalibo<br><br />
Marcus Chibucos<br><br />
Rays Jiang<br><br />
<br />
Agrobacterium tumefaciens (Bacterium)<br><br />
Joao Setubal<br><br />
Joshua Shallom<br><br />
Tsai-Tien Tseng<br><br />
<br />
'''Cornell University'''<br />
<br />
Pseudomonas syringae pv. tomato DC3000 (Bacterium)<br><br />
Pseudomonas syringae pv. phaseolicola 1448A (Bacterium)<br><br />
Pseudomonas syringae pv. syringae B728A (Bacterium)<br><br />
Alan Collmer<br><br />
Magdalen Lindeberg<br><br />
Candace Collmer (Wells College, September-May)<br><br />
<br />
'''University of Wisconsin'''<br />
<br />
Erwinia chrysanthemi 3937 (Bacterium)<br><br />
Nicole Perna<br><br />
Jeremy Glasner<br><br />
Bryan Biehl<br><br />
'''<br />
North Carolina State University'''<br />
<br />
Magnaporthe grisea (Fungus)<br><br />
Meloidogyne hapla (Nematode)<br><br />
Ralph Dean<br><br />
David Bird<br><br />
Thomas Mitchell<br><br />
Shaowu Meng<br><br />
<br />
'''The Institute for Genomic Research'''<br />
<br />
Michelle Gwinn-Giglio<br><br />
Linda Hannick<br><br />
Robin Buell<br><br />
Owen White<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Beginning_Annotation_SOP&diff=6918Beginning Annotation SOP2006-10-16T17:39:06Z<p>Mlgwinn: /* PAMGO example */</p>
<hr />
<div>This page is a place to build the SOP on beginning annotation. <br />
<br />
<br />
== These are the guidelines that the PIs gave me: ==<br />
<br />
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful. <br />
<br />
As far as the documentation; you might start with this outline... <br />
<br />
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit. <br />
<br />
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be <br />
used to frame the inquiries of annotation groups and to support these groups in many contexts. <br />
<br />
<br />
<br />
== SOP for starting annotation ==<br />
<br />
Automatic Annotation<br />
<br />
A. Automatic GO annotation tools<br />
<br />
There are several GO-related annotation tools that have been developed by many groups. Look at the annotation tools on the GO website:<br />
<br />
http://www.geneontology.org/GO.tools.annotation.shtml<br />
<br />
Please write to the GO-Friends mailing list if you have a specific annotation tool needs. All the tool developers are there and will help you to choose a good to tool, or may modify a tool to include the functionality that you need. Mail go-friends at geneontology.org.<br />
<br />
B. Automatic annotation based on GO mapping files and GO-annotated protein datasets for those users with database infrastructure in place.<br />
<br />
1) sequence-based methods<br />
<br />
blast2go<br />
You may also like to try BLAST2GO to find GO annotations to sequences similar to yours.<br />
<br><br />
http://www.geneontology.org/GO.tools.other.shtml#blast2go<br />
<br><br />
Use GOst<br><br />
http://www.godatabase.org/cgi-bin/gost/gost.cgi<br />
<br><br />
<br />
2) Domain-based comparison methods<br />
<br />
Interproscan<br />
Run your sequences through [[InterProScan]] either online or by downloading and running the application on your own computer. <br><br />
http://www.ebi.ac.uk/InterProScan/<br />
<br />
3) other<br />
<br />
keyword2go - a mapping of Swiss-Prot keywords to GO<br />
ec2go - a mapping of EC numbers to GO<br />
see additional mappings page on go website (link here)<br />
<br />
C. Annotation Services<br />
<br />
1) TIGR's Annotation Engine Service for prokaryotic genomes. This free service provides automatic annotation and database infrastructure to anyone with a prokaryotic DNA sequence they wish to annotate. www.tigr.org/AnnotationEngine<br />
<br />
2) GenDB<br />
<br />
D. GOblet<br />
<br><br />
http://goblet.molgen.mpg.de/<br />
<br><br />
<br />
E. If you do not have any database infrastructure you can use the public repositories.<br />
<br />
'''A) Submit your sequences to one of the large public repositories.''' <br><br />
<a href="http://www.ebi.ac.uk/Submissions/"> EBI Submissions, including EMBL-bank </a><br><br />
<a href="http://www.ncbi.nlm.nih.gov/Genbank/submit.html">Genbank Submissions</a><br><br />
<a href="http://www.ddbj.nig.ac.jp/sub-e.html">DDBJ Submission</a><br><br />
<br />
(EMBL-Bank, GenBank and DDBJ exchange data amongst themselves so you can use any of these submission interfaces and<br />
have your data appear in all three resources.)<br />
<br />
Once your sequences have been processed and passed along the pipeline to all the related databases you will be able to retrieve:<br><br />
<br />
1) Unique stable identifiers such as UniProt or RefSeq for your sequences.<br />
<br />
2) Some level of automatic GO annotation to your sequences. (Publically available.) <br />
<br><br />
'''(I am hoping that I can insert a picture here that shows where sequences go in and where annotated sequences come out so that people can choose their favourite provider and be sure that they know what they are getting and what they are missing out on by choosing to download at that point.)'''<br />
<br />
<br />
Manual Annotation<br />
<br />
1. Literature based manual annotation - Check and improve your annotations against the literature. <br />
<br />
1) Read the manual annotation guidelines on the GO Consortium website.<br><br />
http://www.geneontology.org/GO.annotation.shtml<br />
<br />
2) Contact the GO Consortium to ask about annotation camps and mentoring.<br><br />
[insert description of camps and mentoring]<br />
<br />
2. Sequence based manual annotation.<br />
<br />
The process of manual annotation based on sequence similarity involves the manual review of a host of sequence based search data including: BLAST-type searches, domain based searches (InterPro,Pfam, TIGRFAMs, PROSITE, etc.), SignalP, TMHMM, paralagous families, COGs, etc. The annotator evalutates this information by looking at alignments, scores, etc. while taking into consideration the genomic context of the gene product being annotated including neighboring genes, possible operons, syntenic regions, pathway and system resconstruction, etc.<br />
<br />
== PAMGO example ==<br />
<br />
Here is an example of how a new group has started working with the GO Consortium. <br />
<br />
'''<br />
The Plant-Associated Microbe Gene Ontology (PAMGO) Group'''<br />
<br />
In 2003 the genome sequence of the tomato pathogen Pseudomonas syringae pv. tomato DC3000 was published. This project was a collaboration between Robin Buell at the The Institute for Genomic Research (TIGR) and Alan Collmer of Cornell University. As part of the annotation of P. syringae TIGR provided some GO assignments to the P. syringae proteins. Dissussion between Alan Collmer and Brett Tyler at the NSF Plant Genome Research Program Awardees Meeting that fall revealed a shared awareness of the potential power of the GO and led to the formation of the Plant-Associated Microbe Gene Ontology (PAMGO) working group. Brett Tyler coordinated the effort to bring together PIs from genome projects representing the major groups of microbial pathogens: Bacteria, Fungi, Oomycetes, and Nematodes. The PAMGO group recognized the potential power of the GO to greatly facilitate research in areas common to all these pathogens by providing a robust framework for comparing functions across species. Since TIGR is a member of the GO consortium, the new PAMGO group entered into collaboration with TIGR staff Michelle Gwinn-Giglio and Linda Hannick to develop terms specific for interactions between pathogens and their hosts.<br />
<br><br><br />
<br />
During 2004 the PAMGO Interest Group worked to develop high level terms to describe processes relevant to plant-microbe associations, which would provide a framework for the later development of more detailed terms. Candace Collmer (Wells College) while on sabbatical leave, and Michelle Gwinn-Giglio (TIGR) led the effort. This activity began with a full-day workshop on April 23, 2004 at TIGR of all the PAMGO participants. The workshop participants defined a set of high level terms and relationships that would be as general as possible, not only for pathogens of all kingdoms, but for the whole range of host-microbe interactions from mutualism to parasitism, and for all hosts, not only plants. Further refinement of the terms and their definitions occurred by email, and on June 2, 2004 the proposed terms were submitted to the GO community for discussion. On Aug 22-23, 2004 Candace and Alan Collmer and Michelle Gwinn-Giglio presented the proposal at a GO content meeting focused on pathogenesis, metabolism, and the cell cycle at the Carnegie Institution, Stanford, CA and on Oct. 15-16, 2004 Michelle Gwinn-Giglio presented three modified options to a GO Consortium Meeting in Chicago. These high level terms generated much debate, both at the original workshop, and within the wider GO community, because of the varied ways in which different communities use words such as "Symbiosis" and "Pathogenesis", and the difficulty of defining the term "Pathogenesis" consistently, given that some organisms may or may not cause disease depending on the physical environment and the physiological or genetic status of the host. This discussion highlighted the varied usage of these terms and stimulated user communities to think about how these terms should be used. A final version was agreed upon and resubmitted to GO on Dec 14, 2004 and made part of the active ontologies on Jan 31, 2005.<br />
<br><br><br />
In addition to the term development activites in 2004, the PAMGO group was also busy writing a grant to the NSF/USDA Microbial Genome Sequencing Program to fund their GO development work. Fortunately, the grant was awarded and provides 3 years of funding (Fall 2005-Fall 2008) for PAMGO to continue the development of more granular terms under the initial PAMGO term set. The PAMGO group is now actively working on terms that will describe the myriad ways that pathogens affect the metabolism of their hosts. A PAMGO jamboree was held in July 2006 more than 100 new terms were developed. Using the PAMGO terms, as well as the rest of the GO ontologies, PAMGO annotators are assigning GO terms to the proteins from the PAMGO organisms that have a role in interacting with their hosts. It is anticipated that PAMGO will begin sending in association files of these annotations at the end of this year.<br />
'''<br />
PAMGO people and pathogens:'''<br />
<br />
'''Virginia Bioinformatics Institute'''<br />
<br />
Phytophthora sojae (Oomycete)<br><br />
Phytophthora ramorum (Oomycete)<br><br />
Brett Tyler<br><br />
Trudy Torto-Alalibo<br><br />
Marcus Chibucos<br><br />
Rays Jiang<br><br />
<br />
Agrobacterium tumefaciens (Bacterium)<br><br />
Joao Setubal<br><br />
Joshua Shallom<br><br />
Tsai-Tien Tseng<br><br />
<br />
'''Cornell University'''<br />
<br />
Pseudomonas syringae pv. tomato DC3000 (Bacterium)<br><br />
Pseudomonas syringae pv. phaseolicola 1448A (Bacterium)<br><br />
Pseudomonas syringae pv. syringae B728A (Bacterium)<br><br />
Alan Collmer<br><br />
Magdalen Lindeberg<br><br />
Candace Collmer (Wells College, September-May)<br><br />
<br />
'''University of Wisconsin'''<br />
<br />
Erwinia chrysanthemi 3937 (Bacterium)<br><br />
Nicole Perna<br><br />
Jeremy Glasner<br><br />
Bryan Biehl<br><br />
'''<br />
North Carolina State University'''<br />
<br />
Magnaporthe grisea (Fungus)<br><br />
Meloidogyne hapla (Nematode)<br><br />
Ralph Dean<br><br />
David Bird<br><br />
Thomas Mitchell<br><br />
Shaowu Meng<br><br />
<br />
'''The Institute for Genomic Research'''<br />
<br />
Michelle Gwinn-Giglio<br><br />
Linda Hannick<br><br />
Robin Buell<br><br />
Owen White<br></div>Mlgwinnhttps://wiki.geneontology.org/index.php?title=Beginning_Annotation_SOP&diff=6917Beginning Annotation SOP2006-10-16T17:36:35Z<p>Mlgwinn: /* SOP for starting annotation */</p>
<hr />
<div>This page is a place to build the SOP on beginning annotation. <br />
<br />
<br />
== These are the guidelines that the PIs gave me: ==<br />
<br />
The initial step would be to create a document that outlines the annotation process. In addition, a case study, such as how the Chicken genome came to be annotated—what order events happened in, how the timing worked, what software was used, how they interacted with their GOA mentors, and so on—would be very useful. <br />
<br />
As far as the documentation; you might start with this outline... <br />
<br />
First, a brief statement about how the annotation process starts once the genes or gene products are defined (i.e. unique, stable IDs/ identifiers from UniProt or RefSeq are available for their sequences). Then, the document should include steps for doing GO annotations by various methods including automated methods such as InterProScan approach or by incorporating experimentally based annotations of orthologs; and curated methods such as assigning literature (experimentally) based GO annotations. The document should provide pointers to the existing documentation wherever possible. Thirdly, there should be information on the gene association file format and how to submit. <br />
<br />
Once this documentation [essentially a 'standard operating procedure' not a detailed how-to] is defined, it can then be <br />
used to frame the inquiries of annotation groups and to support these groups in many contexts. <br />
<br />
<br />
<br />
== SOP for starting annotation ==<br />
<br />
Automatic Annotation<br />
<br />
A. Automatic GO annotation tools<br />
<br />
There are several GO-related annotation tools that have been developed by many groups. Look at the annotation tools on the GO website:<br />
<br />
http://www.geneontology.org/GO.tools.annotation.shtml<br />
<br />
Please write to the GO-Friends mailing list if you have a specific annotation tool needs. All the tool developers are there and will help you to choose a good to tool, or may modify a tool to include the functionality that you need. Mail go-friends at geneontology.org.<br />
<br />
B. Automatic annotation based on GO mapping files and GO-annotated protein datasets for those users with database infrastructure in place.<br />
<br />
1) sequence-based methods<br />
<br />
blast2go<br />
You may also like to try BLAST2GO to find GO annotations to sequences similar to yours.<br />
<br><br />
http://www.geneontology.org/GO.tools.other.shtml#blast2go<br />
<br><br />
Use GOst<br><br />
http://www.godatabase.org/cgi-bin/gost/gost.cgi<br />
<br><br />
<br />
2) Domain-based comparison methods<br />
<br />
Interproscan<br />
Run your sequences through [[InterProScan]] either online or by downloading and running the application on your own computer. <br><br />
http://www.ebi.ac.uk/InterProScan/<br />
<br />
3) other<br />
<br />
keyword2go - a mapping of Swiss-Prot keywords to GO<br />
ec2go - a mapping of EC numbers to GO<br />
see additional mappings page on go website (link here)<br />
<br />
C. Annotation Services<br />
<br />
1) TIGR's Annotation Engine Service for prokaryotic genomes. This free service provides automatic annotation and database infrastructure to anyone with a prokaryotic DNA sequence they wish to annotate. www.tigr.org/AnnotationEngine<br />
<br />
2) GenDB<br />
<br />
D. GOblet<br />
<br><br />
http://goblet.molgen.mpg.de/<br />
<br><br />
<br />
E. If you do not have any database infrastructure you can use the public repositories.<br />
<br />
'''A) Submit your sequences to one of the large public repositories.''' <br><br />
<a href="http://www.ebi.ac.uk/Submissions/"> EBI Submissions, including EMBL-bank </a><br><br />
<a href="http://www.ncbi.nlm.nih.gov/Genbank/submit.html">Genbank Submissions</a><br><br />
<a href="http://www.ddbj.nig.ac.jp/sub-e.html">DDBJ Submission</a><br><br />
<br />
(EMBL-Bank, GenBank and DDBJ exchange data amongst themselves so you can use any of these submission interfaces and<br />
have your data appear in all three resources.)<br />
<br />
Once your sequences have been processed and passed along the pipeline to all the related databases you will be able to retrieve:<br><br />
<br />
1) Unique stable identifiers such as UniProt or RefSeq for your sequences.<br />
<br />
2) Some level of automatic GO annotation to your sequences. (Publically available.) <br />
<br><br />
'''(I am hoping that I can insert a picture here that shows where sequences go in and where annotated sequences come out so that people can choose their favourite provider and be sure that they know what they are getting and what they are missing out on by choosing to download at that point.)'''<br />
<br />
<br />
Manual Annotation<br />
<br />
1. Literature based manual annotation - Check and improve your annotations against the literature. <br />
<br />
1) Read the manual annotation guidelines on the GO Consortium website.<br><br />
http://www.geneontology.org/GO.annotation.shtml<br />
<br />
2) Contact the GO Consortium to ask about annotation camps and mentoring.<br><br />
[insert description of camps and mentoring]<br />
<br />
2. Sequence based manual annotation.<br />
<br />
The process of manual annotation based on sequence similarity involves the manual review of a host of sequence based search data including: BLAST-type searches, domain based searches (InterPro,Pfam, TIGRFAMs, PROSITE, etc.), SignalP, TMHMM, paralagous families, COGs, etc. The annotator evalutates this information by looking at alignments, scores, etc. while taking into consideration the genomic context of the gene product being annotated including neighboring genes, possible operons, syntenic regions, pathway and system resconstruction, etc.<br />
<br />
== PAMGO example ==<br />
<br />
Here is an example of how a new group has started working with the GO Consortium. <br />
<br />
'''<br />
The Plant-Associated Microbe Gene Ontology (PAMGO) Group'''<br />
<br />
In 2003 the genome sequence of the tomato pathogen Pseudomonas syringae pv. tomato DC3000 was published. This project was a collaboration between Robin Buell at the The Institute for Genomic Research (TIGR) and Alan Collmer of Cornell University. As part of the annotation of P. syringae TIGR provided some GO assignments to the P. syringae proteins. Dissussion between Alan Collmer and Brett Tyler at the NSF Plant Genome Research Program Awardees Meeting that fall revealed a shared awareness of the potential power of the GO and led to the formation of the Plant-Associated Microbe Gene Ontology (PAMGO) working group. Brett Tyler coordinated the effort to bring together PIs from genome projects representing the major groups of microbial pathogens: Bacteria, Fungi, Oomycetes, and Nematodes. The PAMGO group recognized the potential power of the GO to greatly facilitate research in areas common to all these pathogens by providing a robust framework for comparing functions across species. Since TIGR is a member of the GO consortium, the new PAMGO group entered into collaboration with TIGR staff Michelle Gwinn-Giglio and Linda Hannick to develop terms specific for interactions between pathogens and their hosts.<br />
<br><br><br />
<br />
During 2004 the PAMGO Interest Group worked to develop high level terms to describe processes relevant to plant-microbe associations, which would provide a framework for the later development of more detailed terms. Candace Collmer (Wells College) while on sabbatical leave, and Michelle Gwinn-Giglio (TIGR) led the effort. This activity began with a full-day workshop on April 23, 2004 at TIGR of all the PAMGO participants. The workshop participants defined a set of high level terms and relationships that would be as general as possible, not only for pathogens of all kingdoms, but for the whole range of host-microbe interactions from mutualism to parasitism, and for all hosts, not only plants. Further refinement of the terms and their definitions occurred by email, and on June 2, 2004 the proposed terms were submitted to the GO community for discussion. On Aug 22-23, 2004 Candace and Alan Collmer and Michelle Gwinn-Giglio presented the proposal at a GO content meeting focused on pathogenesis, metabolism, and the cell cycle at the Carnegie Institution, Stanford, CA and on Oct. 15-16, 2004 Michelle Gwinn-Giglio presented three modified options to a GO Consortium Meeting in Chicago. These high level terms generated much debate, both at the original workshop, and within the wider GO community, because of the varied ways in which different communities use words such as "Symbiosis" and "Pathogenesis", and the difficulty of defining the term "Pathogenesis" consistently, given that some organisms may or may not cause disease depending on the physical environment and the physiological or genetic status of the host. This discussion highlighted the varied usage of these terms and stimulated user communities to think about how these terms should be used. A final version was agreed upon and resubmitted to GO on Dec 14, 2004 and made part of the active ontologies on Jan 31, 2005.<br />
<br><br><br />
In addition to the term development activites in 2004, the PAMGO group was also busy writing a grant to the NSF/USDA Microbial Genome Sequencing Program to fund their GO development work. Fortunately, the grant was awarded and provides 3 years of funding (Fall 2005-Fall 2008) for PAMGO to continue the development of more granular terms under the initial PAMGO term set. The PAMGO group is now actively working on terms that will describe the myriad ways that pathogens affect the metabolism of their hosts. A PAMGO jamboree is scheduled for summer 2006 where it is expected that these additional terms will be entered into the active ontologies. Using the PAMGO terms, as well as the rest of the GO ontologies, PAMGO annotators are assigning GO terms to the proteins from the PAMGO organisms that have a role in interacting with their hosts. It is anticipated that PAMGO will begin sending in association files of these annotations at the end of this year.<br />
'''<br />
PAMGO people and pathogens:'''<br />
<br />
'''Virginia Bioinformatics Institute'''<br />
<br />
Phytophthora sojae (Oomycete)<br><br />
Phytophthora ramorum (Oomycete)<br><br />
Brett Tyler<br><br />
Trudy Torto-Alalibo<br><br />
Marcus Chibucos<br><br />
Rays Jiang<br><br />
<br />
Agrobacterium tumefaciens (Bacterium)<br><br />
Joao Setubal<br><br />
Joshua Shallom<br><br />
<br />
'''Cornell University'''<br />
<br />
Pseudomonas syringae pv. tomato DC3000 (Bacterium)<br><br />
Pseudomonas syringae pv. phaseolicola 1448A (Bacterium)<br><br />
Pseudomonas syringae pv. syringae B728A (Bacterium)<br><br />
Alan Collmer<br><br />
Magdalen Lindeberg<br><br />
Candace Collmer (Wells College, September-May)<br><br />
<br />
'''University of Wisconsin'''<br />
<br />
Erwinia chrysanthemi 3937 (Bacterium)<br><br />
Nicole Perna<br><br />
Jeremy Glasner<br><br />
'''<br />
North Carolina State University'''<br />
<br />
Magnaporthe grisea (Fungus)<br><br />
Meloidogyne hapla (Nematode)<br><br />
Ralph Dean<br><br />
David Bird<br><br />
Thomas Mitchell<br><br />
Shaowu Meng<br><br />
<br />
'''The Institute for Genomic Research'''<br />
<br />
Michelle Gwinn-Giglio<br><br />
Linda Hannick<br><br />
Robin Buell<br><br />
Owen White<br></div>Mlgwinn