https://wiki.geneontology.org/api.php?action=feedcontributions&user=Dhowe&feedformat=atomGO Wiki - User contributions [en]2024-03-29T07:48:30ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=ZFIN_December_2017&diff=66125ZFIN December 20172017-12-13T00:16:24Z<p>Dhowe: </p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 12, 2017 =<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are made available to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:200px;" | Position Type<br />
! style="background:lightgray; width:250px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Sabrina Toro<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Curatorial <br/>GO lead<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 each; 0.6 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical<br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
<br />
[[File:GOC_AnnualReport_Stats_20171212.jpg|1000px]]<br />
<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncurated data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF and gp2protein files were generated and manually checked into the GO SVN repository on a weekly basis until March 2017. After that date, GAF files were made available for direct pull by GOC. <br />
<br />
GPI files were generated and made available for direct pull by GOC. <br />
<br />
Danio rerio annotations were reviewed and updated in the context of the Signaling project and in the context of ontology work. <br />
<br />
Sabrina Toro took part in the Signaling project and attended the Signaling workshop in Cambridge in October, 2017.<br />
<br />
Sabrina Toro attends the bimonthly annotation advocacy conference calls, as well as the bimonthly meetings on the development of the Noctua tool. <br />
Doug Howe and Sabrina Toro attended the GO meeting in Corvallis in June, 2017. ZFIN curators joined them for the subsequent Noctua workshop. <br />
Sabrina Toro attended the GO meeting in Cambridge in October, 2017.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2017&diff=66124ZFIN December 20172017-12-13T00:10:24Z<p>Dhowe: </p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 12, 2017 =<br />
<br />
=BEING UPDATED...NOT YET COMPLETE=<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are made available to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:200px;" | Position Type<br />
! style="background:lightgray; width:250px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Sabrina Toro<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Curatorial <br/>GO lead<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 each; 0.6 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical<br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
<br />
[[File:GOC_AnnualReport_Stats_20171212.jpg|1000px]]<br />
<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncurated data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF and gp2protein files were generated and manually checked into the GO SVN repository on a weekly basis until March 2017. After that date, GAF files were made available for direct pull by GOC. <br />
<br />
GPI files were generated and made available for direct pull by GOC. <br />
<br />
Danio rerio annotations were reviewed and updated in the context of the Signaling project and in the context of ontology work. <br />
<br />
Sabrina Toro took part in the Signaling project and attended the Signaling workshop in Cambridge in October, 2017.<br />
<br />
Sabrina Toro attends the bimonthly annotation advocacy conference calls, as well as the bimonthly meetings on the development of the Noctua tool. <br />
Doug Howe and Sabrina Toro attended the GO meeting in Corvallis in June, 2017. ZFIN curators joined them for the subsequent Noctua workshop. <br />
Sabrina Toro attended the GO meeting in Cambridge in October, 2017.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2017&diff=66123ZFIN December 20172017-12-13T00:04:41Z<p>Dhowe: </p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 12, 2017 =<br />
<br />
=BEING UPDATED...NOT YET COMPLETE=<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are made available to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:200px;" | Position Type<br />
! style="background:lightgray; width:250px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Sabrina Toro<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Curatorial <br/>GO lead<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 each; 0.6 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical<br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
<br />
[[File:GOC_AnnualReport_Stats_20171212.jpg|1000px]]<br />
<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncharted data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF and gp2protein files were generated and manually checked into the GO SVN repository on a weekly basis until March 2017. After that date, GAF files were made available for direct pull by GOC. <br />
<br />
GPI files were generated and made available for direct pull by GOC. <br />
<br />
Danio rerio annotations were reviewed and updated in the context of the Signaling project and in the context of ontology work. <br />
<br />
Sabrina Toro took part in the Signaling project and attended the Signaling workshop in Cambridge in October, 2017.<br />
<br />
Sabrina Toro attends the bimonthly annotation advocacy conference calls, as well as the bimonthly meetings on the development of the Noctua tool. <br />
Doug Howe and Sabrina Toro attended the GO meeting in Corvallis in June, 2017. ZFIN curators joined them for the subsequent Noctua workshop. <br />
Sabrina Toro attended the GO meeting in Cambridge in October, 2017.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2017&diff=66117ZFIN December 20172017-12-12T18:17:07Z<p>Dhowe: Created page with "Category:ZFIN Category:Reports = Zebrafish Model Organism Database Summary, December 12, 2017 = =BEING UPDATED...NOT YET COMPLETE= = Overview = ZFIN is the Zebrafi..."</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 12, 2017 =<br />
<br />
=BEING UPDATED...NOT YET COMPLETE=<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are checked in to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:200px;" | Position Type<br />
! style="background:lightgray; width:250px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Sabrina Toro<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Curatorial <br/>GO lead<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 each; 0.6 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical<br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
<br />
[[File:Screen_Shot_2016-12-22_at_2.19.13_PM.png]]<br />
<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncharted data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF files are currently checked into the GO SVN repository on a weekly basis. We rely largely on QC reports that come from the GO GAF validation steps after file check-in. We also have internal processes that monitor annotations for use of obsolete or secondary GO term usage in annotations. Sabrina Toro, a ZFIN curator, continues with the primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.<br />
<br />
Doug and Sabrina attended the GO meeting and subsequent Noctua workshop given at USC in November, 2016.<br />
<br />
We are in consultation with Seth and Chris to begin planning steps towards adoption of Noctua for GO curation at ZFIN.</div>Dhowehttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=646702017 Cambridge GOC Meeting Logistics2017-08-01T19:22:56Z<p>Dhowe: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
To be added<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<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 />
==Meeting Dinner==<br />
* Dinner will be on Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, 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 />
| Moni Munoz-Torres<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<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 />
| Yes<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-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 />
| 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 />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Maybe<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 />
|Alice Shypitsyna <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 />
| <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 />
<br />
NOT attending:<br />
<br />
Peter D'Eustachio<br /><br />
Doug Howe<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. 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 />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=646692017 Cambridge GOC Meeting Logistics2017-08-01T19:21:26Z<p>Dhowe: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
To be added<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<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 />
==Meeting Dinner==<br />
* Dinner will be on Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, 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 />
| Moni Munoz-Torres<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<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 />
| Yes<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-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 />
| 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 />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Maybe<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 />
|Alice Shypitsyna <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 />
| <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 />
<br />
NOT attending:<br />
<br />
Peter D'Eustachio<br />
Doug Howe<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. 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 />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=646682017 Cambridge GOC Meeting Logistics2017-08-01T19:20:57Z<p>Dhowe: /* Attendees */ Doug not attending in person, maybe attending remotely with lots of AMP Energy soda...</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
To be added<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<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 />
==Meeting Dinner==<br />
* Dinner will be on Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, 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 />
| Moni Munoz-Torres<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<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 />
| Yes<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-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 />
| 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 />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Maybe<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 />
|Alice Shypitsyna <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 />
| <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 />
<br />
NOT attending:<br />
<br />
Peter D'Eustachio<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. 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 />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=GOCAM_Project&diff=64027GOCAM Project2017-06-03T20:33:47Z<p>Dhowe: /* Calls to discuss LEGO annotaiton */ typo</p>
<hr />
<div>[[Category:LEGO]]<br />
<br />
==Background==<br />
Please see Paul T's [http://wiki.geneontology.org/images/1/12/Paul's_LEGO_white_paper_March_2010.pdf LEGO white paper] from March 2010.<br />
<br />
==Recurring BlueJeans meeting - Mondays 8:30 am PST==<br />
*https://bluejeans.com/969313231<br />
<br />
==LEGO annotation tool (Noctua)== <br />
http://noctua.berkeleybop.org/<br />
<br />
==Specifications and documents==<br />
*[https://docs.google.com/document/d/18ihslb7prB6CWtu2yjF-pMHZBTY1-AdXJAu-ZyuyXS4/edit LEGO Curation Documentation - 2015 LEGO Jamboree]<br />
*Google Doc [https://docs.google.com/document/d/1OsE19zh8KE_2wT3-8oJysqEGqy-fahnhcjthO34IWP4/edit?usp=sharing LEGO Specification Proposal] from 2014 - an attempt to define all LEGO elements. It was presented at the 2014 GOC ([http://wiki.geneontology.org/images/b/bb/LEGO_specfication.pdf slides])<br />
*[http://wiki.geneontology.org/index.php/LEGO_Model_Draft_Specification LEGO Model Draft Specification] from 2011 (out of date)<br />
<br />
==Link to the LEGO model repository==<br />
<br />
<br />
==2015 LEGO Jamboree meeting==<br />
<br />
http://wiki.geneontology.org/index.php/2015_LEGO_Jamboree_Logistics<br />
==Calls to discuss LEGO annotation==<br />
first and third Mondays of each month.<br />
<br />
http://wiki.geneontology.org/index.php/LEGO_January_4,_2016</div>Dhowehttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=639812017 Corvallis GOC Meeting Agenda2017-05-30T21:42:36Z<p>Dhowe: /* Attendees */</p>
<hr />
<div>=Thursday June 1=<br />
==8-9am Breakfast and setup==<br />
==Welcome, schedule and logistics==<br />
*Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
*Introductions<br />
==Overview of Objectives for Upcoming Year==<br />
*Aim1: Provide a comprehensive model of biological knowledge focused on human biology<br />
**Ontology<br />
***MF refactoring completed<br />
***BP refactoring underway, including annotation qualifiers<br />
**Annotation<br />
***N# of pathways annotated according to prioritized list (Paul S to provide)<br />
***Complete the incorporation of new annotation groups/sources: SynGO, SIGNOR<br />
*Aim 2: Provide the “hub” for a broad community of scientists to extend and modify the GO<br />
**Pipeline transition completed (**almost** -- chris)<br />
**Noctua rolled out to all GO curation groups<br />
***Evidence issues resolved in Noctua<br />
**Documentation for ontology request guidelines completed<br />
*Aim 3: Apply biological knowledge obtained in model organisms to human biology<br />
**PAINT annotations going directly into GO database (not via MODs)<br />
**PAINT annotation completed for all families with experimental annotations<br />
**Established alert system for ongoing review of annotated families<br />
*Aim 4: Maintain the integrity and quality of new and existing annotations<br />
**Ongoing annotation consistency exercises (conference calls and github) will now include a write-up (or blog) as case studies to be published on the web site.<br />
**An automated rule-based annotation QA system will be put into place that will be refined/extended based on input from the consistency exercises and PAINT curators<br />
**Establishment of an agreed upon policy for when annotations will be removed (and put this policy into action)<br />
*Am 5: Enable the scientific community to make full use of the GO data resources<br />
**Fixed existing problems with enrichment analysis<br />
**Website?<br />
**Outreach?<br />
<br />
==Infrastructure (Aim 2—Provide a “hub”)==<br />
===Pipeline Migration (Seth & Chris 20 mins) (Goal 2.a)===<br />
===New APIs (Seth & Chris 10 mins)===<br />
===TermGenie replacement* (Dan 20 mins)===<br />
*https://github.com/geneontology/go-ontology/issues/13472<br />
<br />
==12-1pm Lunch==<br />
===Graph Store update (Eric 10 mins)===<br />
===Licensing and GO (Seth 20 mins)===<br />
*Where we currently stand with licensing and possible issues<br />
*What others do with our data<br />
===GO and Related Projects===<br />
*Planteome (Chris, Seth, and Pankaj): How GO and Planteome contribute to one another<br />
*SIGNOR (Chris and Paul T) and SynGO (Ruth?) annotation incorporation (Goal 1.b.ii)<br />
**https://github.com/geneontology/noctua/issues/413<br />
**https://github.com/geneontology/noctua/issues/418<br />
*AGR<br />
**Parts of GO infrastructure being re-used by AGR (Chris)<br />
***db-xrefs.yaml<br />
**Data Formats (Chris)<br />
***BGI and GPI<br />
***Gene association JSON<br />
**Ribbon demo (Suzi)<br />
*Other Projects<br />
**BioCaddie and db-xrefs.yaml (Chris)<br />
**Monarch (Chris)<br />
**Panther?<br />
==3-3:30pm snacks==<br />
===Identifiers (Chris)===<br />
*Replacing double MGI (Chris)<br />
**https://github.com/geneontology/go-site/issues/346<br />
**https://github.com/geneontology/go-site/pull/338 (AGR)<br />
==Ontology (Aim 1—a comprehensive model of biological knowledge)==<br />
===Update on Ontology Editing: David + Chris 20min===<br />
*Design Pattern Updates: David OS + Chris 20 mins<br />
*Ontology Documentation: Moni 10 mins (Goal 2.c)<br />
*Curator notes and propagation<br />
**https://github.com/geneontology/go-ontology/issues/13384<br />
*Proposal: text mining github tickets for ontology terms (Chris, Kimberley)<br />
===MF refactoring (Paul, DavidOS 30 mins) (Goal 1.a.i)===<br />
*Issues: https://github.com/geneontology/molecular_function_refactoring/issues<br />
*Emphasis on practical implications for LEGO curation (templates).<br />
===ECO===<br />
*Mapping to classic GO evidence codes. The official mapping of IMP to ECO is insufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
**https://github.com/evidenceontology/evidenceontology/issues/117<br />
*There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g.<br />
**https://github.com/evidenceontology/evidenceontology/issues/123#issuecomment-281041854<br />
<br />
===Noctua and SIGNOR2 (Chris & Paul T)===<br />
*https://github.com/geneontology/noctua/issues/413<br />
*Additional document - https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit#<br />
<br />
===Straw man BP refactor Chris (Goal 1.a.ii)===<br />
<br />
==6:00pm onwards mixer==<br />
<br />
=Friday June 2=<br />
==8-9am Breakfast==<br />
==Ontology continued…==<br />
===The fate of simple processes===<br />
*What do we consider a single-step process and what is their future?<br />
**GH ticket about single step processes https://github.com/geneontology/go-ontology/issues/12859<br />
**Is this a single step process? https://github.com/geneontology/go-ontology/issues/13012<br />
*The distinction between cellular processes and processes, do we need it?<br />
**GH ticket about cellular processes: https://github.com/geneontology/go-ontology/issues/12849<br />
<br />
==Annotation (Aims 1, 3, & 4—integrity and quality)==<br />
===Noctua Update (Seth & Chris 10 mins)===<br />
===Noctua rollout to curation groups (Goal 2.b)===<br />
*Current plan:<br />
**SGD (June, July)<br />
**WormBase (August, September)<br />
**Swiss-Prot (October)<br />
**Others? Issues?<br />
===GAFs and GPADs from Noctua models (David and Seth, 30 mins)===<br />
* Where do we stand?<br />
**https://github.com/geneontology/noctua/issues/418<br />
**Challenges with complex models (evidence) (Goal 2.b.i)<br />
**All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly (PRO to supply a GPI file).<br />
**GP-CC Should we allow direct GO part_of CC assertion (rather than via GO <-- enabled_by MF occurs_in --> CC). This is more accurate in some cases e.g. for membrane components.<br />
===Use of Qualifiers in Legacy Annotations (needs to come before pipeline??)===<br />
*RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)<br />
*New qualifiers for biological processes<br />
*Incorporate expanded list of GP-GO term relations into annotation tools and files<br />
*Regulation and causality<br />
<br />
==12-1pm Lunch==<br />
<br />
===Focused Pathway annotation (Goal 1.b.i)===<br />
===Contacts for Curation Groups (Pascale & David)===<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
===PAINT update (Chris, Karen, Suzi, Pascale and Huaiyu)===<br />
*Analysis of the PAINT annotations (Karen and Huaiyu).<br />
*Plan for production services/pipeline for PAINT annotations (Chris)<br />
*Reverse flow (Goal 3.a)<br />
*Completion of all families with exp. evidence (Goal 3.b)<br />
*Initial implementation of alert system: what are the requirements? (Goal 3.c)<br />
===Annotation QC issues===<br />
====Consistency exercises (written case studies - Goal 4.a)====<br />
<br />
====GO Rules System (Eric) (Goal 4.b)====<br />
<br />
====QA from PAINT - automated rule-based annotation QA (Pascale) (Goal 4.b)====<br />
<br />
====How do annotation groups handle obsoleting/deprecating GO annotations? (led by someone from SGD or Val?) (Goal 4.c)====<br />
<br />
====Consistent use of the type field in GAFs and GPAD (Chris)====<br />
*E.g. https://github.com/geneontology/go-annotation/issues/1554<br />
<br />
==3:30pm Networking and Recreational outing==<br />
<br />
==6:00pm — Dinner==<br />
<br />
==Saturday June 3==<br />
==8-9am Breakfast==<br />
==Annotation continued…==<br />
===Annotation QC issues continued…===<br />
====HTP papers (Helen, Pascale & Sylvain)====<br />
*See notes /list of papers:<br />
<br />
====Transcription-Factor decision tree (Ruth - 20 mins)====<br />
*https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
====Modified protein binding (Pascale & Sylvain)====<br />
*https://github.com/geneontology/go-ontology/issues/12787<br />
===Annotation of Viral Processes===<br />
*13214<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
*Transcription, translation of viral genome<br />
*DOS proposal for multi-organism annotation (reviving old proposal) - poss allowing non-canonical function to be separable<br />
<br />
==12-1pm Lunch==<br />
==Community relations (Aim 5—enabling the community)==<br />
===Enrichment Analysis (Val & Seth) (Goal 5.a)===<br />
*by default have the enrichment tool run directly on the GO annotation dataset<br />
*by default enable loading a background<br />
*currently missing a substantial number of annotations (e.g. fission yeast)<br />
*Via ontobio python library (Chris)<br />
**Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb<br />
===Website? (Goal 5.b)===<br />
===Outreach? (Goal 5.c)===<br />
<br />
==3-5:30-pm Networking and Recreation==<br />
<br />
==5:30pm POSTERS and mixer==<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<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 bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
| Y (1)<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|-<br />
| David OS<br />
| EBI<br />
| Y<br />
| Y<br />
| N<br />
| AM<br />
| N<br />
|-<br />
| Malcolm Fisher<br />
| Xenbase<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:Remote: Bluegenes<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
|-<br />
|Harold Drabkin<br />
|MGI<br />
|-<br />
|Mary Dolan<br />
|MGI<br />
|-<br />
|Li Ni<br />
|MGI<br />
|-<br />
|Karen Christie<br />
|MGI<br />
|-<br />
|Dmitry Sitnikov<br />
|MGI<br />
|-<br />
|}<br />
<br />
[[Category: GO Consortium Meetings]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=637062017 Corvallis GOC Meeting Agenda2017-05-04T18:34:20Z<p>Dhowe: /* Attendees */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this? <br />
<br />
==Update on Ontology Editing==<br />
<br />
* David + Chris 20min<br />
* Design Pattern Updates: David OS + Chris 20 mins<br />
* Ontology Documentation: Moni 10 mins<br />
* [https://github.com/geneontology/go-ontology/issues/13384 Curator notes and propagation]<br />
* Proposal: text mining github tickets for ontology terms<br />
<br />
==MF refactoring (Paul, DavidOS) ==<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
<br />
David + others? 30 min<br />
<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
<br />
== Use of Qualifiers in Legacy Annotations ==<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
** [https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit# Additional document]<br />
* [https://gist.github.com/cmungall/4ed28123c3db832a7d99cbdd8e8a5920 Straw man BP refactor] Chris<br />
<br />
==Annotation of Viral Processes==<br />
*[https://github.com/geneontology/go-ontology/issues/13214 13214]<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
**Transcription, translation of viral genome<br />
<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Helen, Pascale & Sylvain<br />
<br />
See notes /list of papers:<br />
<br />
=== Transcription-Factor decision tree===<br />
Ruth (20mins?)<br />
<br />
https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
<br />
== PAINT update==<br />
Pascale and Huaiyu<br />
<br />
* Analysis of the PAINT annotation.<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<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 bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ceri Van Slyke<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=636852017 Corvallis GOC Meeting Agenda2017-05-02T20:19:19Z<p>Dhowe: /* Attendees */ added a few new ZFIN attendees for the Noctua workshop</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this? <br />
<br />
==Update on Ontology Editing==<br />
<br />
David + Chris 20min<br />
<br />
==MF refactoring (Paul, DavidOS) ==<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
<br />
David + others? 30 min<br />
<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
<br />
== Use of Qualifiers in Legacy Annotations ==<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
<br />
==Annotation of Viral Processes==<br />
*[https://github.com/geneontology/go-ontology/issues/13214 13214]<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
**Transcription, translation of viral genome<br />
<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Pascale & Sylvain<br />
<br />
See notes /list of papers:<br />
<br />
=== Transcription-Factor decision tree===<br />
Ruth (20mins?)<br />
<br />
https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations? <br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<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 bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| <br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2016&diff=62843ZFIN December 20162016-12-22T22:34:35Z<p>Dhowe: Completed ZFIN annual report</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 21, 2016 =<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are checked in to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:200px;" | Position Type<br />
! style="background:lightgray; width:250px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Sabrina Toro<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Curatorial <br/>GO lead<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 each; 0.6 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical<br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
<br />
[[File:Screen_Shot_2016-12-22_at_2.19.13_PM.png]]<br />
<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncharted data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF files are currently checked into the GO SVN repository on a weekly basis. We rely largely on QC reports that come from the GO GAF validation steps after file check-in. We also have internal processes that monitor annotations for use of obsolete or secondary GO term usage in annotations. Sabrina Toro, a ZFIN curator, continues with the primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.<br />
<br />
Doug and Sabrina attended the GO meeting and subsequent Noctua workshop given at USC in November, 2016.<br />
<br />
We are in consultation with Seth and Chris to begin planning steps towards adoption of Noctua for GO curation at ZFIN.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2016&diff=62842ZFIN December 20162016-12-22T22:33:59Z<p>Dhowe: /* DRAFT - NOT YET COMPLETED */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 14, 2016 =<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are checked in to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:200px;" | Position Type<br />
! style="background:lightgray; width:250px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Sabrina Toro<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Curatorial <br/>GO lead<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 each; 0.6 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical<br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
<br />
[[File:Screen_Shot_2016-12-22_at_2.19.13_PM.png]]<br />
<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncharted data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF files are currently checked into the GO SVN repository on a weekly basis. We rely largely on QC reports that come from the GO GAF validation steps after file check-in. We also have internal processes that monitor annotations for use of obsolete or secondary GO term usage in annotations. Sabrina Toro, a ZFIN curator, continues with the primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.<br />
<br />
Doug and Sabrina attended the GO meeting and subsequent Noctua workshop given at USC in November, 2016.<br />
<br />
We are in consultation with Seth and Chris to begin planning steps towards adoption of Noctua for GO curation at ZFIN.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2016&diff=62841ZFIN December 20162016-12-22T22:33:47Z<p>Dhowe: /* Annotation Progress */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 14, 2016 =<br />
=DRAFT - NOT YET COMPLETED=<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are checked in to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:200px;" | Position Type<br />
! style="background:lightgray; width:250px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Sabrina Toro<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Curatorial <br/>GO lead<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 each; 0.6 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical<br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
<br />
[[File:Screen_Shot_2016-12-22_at_2.19.13_PM.png]]<br />
<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncharted data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF files are currently checked into the GO SVN repository on a weekly basis. We rely largely on QC reports that come from the GO GAF validation steps after file check-in. We also have internal processes that monitor annotations for use of obsolete or secondary GO term usage in annotations. Sabrina Toro, a ZFIN curator, continues with the primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.<br />
<br />
Doug and Sabrina attended the GO meeting and subsequent Noctua workshop given at USC in November, 2016.<br />
<br />
We are in consultation with Seth and Chris to begin planning steps towards adoption of Noctua for GO curation at ZFIN.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2016&diff=62840ZFIN December 20162016-12-22T22:33:26Z<p>Dhowe: /* Annotation Progress */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 14, 2016 =<br />
=DRAFT - NOT YET COMPLETED=<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are checked in to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:200px;" | Position Type<br />
! style="background:lightgray; width:250px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Sabrina Toro<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Curatorial <br/>GO lead<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 each; 0.6 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical<br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
<br />
[[File:Screen_Shot_2016-12-22_at_2.19.13_PM.png]]<br />
<br />
DATA TO BE ADDED FOR 2016<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncharted data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF files are currently checked into the GO SVN repository on a weekly basis. We rely largely on QC reports that come from the GO GAF validation steps after file check-in. We also have internal processes that monitor annotations for use of obsolete or secondary GO term usage in annotations. Sabrina Toro, a ZFIN curator, continues with the primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.<br />
<br />
Doug and Sabrina attended the GO meeting and subsequent Noctua workshop given at USC in November, 2016.<br />
<br />
We are in consultation with Seth and Chris to begin planning steps towards adoption of Noctua for GO curation at ZFIN.</div>Dhowehttps://wiki.geneontology.org/index.php?title=File:Screen_Shot_2016-12-22_at_2.19.13_PM.png&diff=62839File:Screen Shot 2016-12-22 at 2.19.13 PM.png2016-12-22T22:30:28Z<p>Dhowe: ZFIN GO annotation summary table, 2015-2016, for the 2016 annual report.</p>
<hr />
<div>ZFIN GO annotation summary table, 2015-2016, for the 2016 annual report.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2016&diff=62738ZFIN December 20162016-12-14T23:25:53Z<p>Dhowe: /* Other Highlights */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 14, 2016 =<br />
=DRAFT - NOT YET COMPLETED=<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are checked in to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:200px;" | Position Type<br />
! style="background:lightgray; width:250px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Sabrina Toro<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Curatorial <br/>GO lead<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 each; 0.6 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical<br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[File:|ZFIN curation stats from X, 2015 to Y, 2016]]<br />
<br />
DATA TO BE ADDED FOR 2016<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncharted data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF files are currently checked into the GO SVN repository on a weekly basis. We rely largely on QC reports that come from the GO GAF validation steps after file check-in. We also have internal processes that monitor annotations for use of obsolete or secondary GO term usage in annotations. Sabrina Toro, a ZFIN curator, continues with the primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.<br />
<br />
Doug and Sabrina attended the GO meeting and subsequent Noctua workshop given at USC in November, 2016.<br />
<br />
We are in consultation with Seth and Chris to begin planning steps towards adoption of Noctua for GO curation at ZFIN.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2016&diff=62737ZFIN December 20162016-12-14T23:23:38Z<p>Dhowe: /* Staff: */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 14, 2016 =<br />
=DRAFT - NOT YET COMPLETED=<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are checked in to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:200px;" | Position Type<br />
! style="background:lightgray; width:250px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Sabrina Toro<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Curatorial <br/>GO lead<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 each; 0.6 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical<br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[File:|ZFIN curation stats from X, 2015 to Y, 2016]]<br />
<br />
DATA TO BE ADDED FOR 2016<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncharted data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF files are currently checked into the GO SVN repository on a weekly basis. We rely largely on QC reports that come from the GO GAF validation steps after file check-in. We also have internal processes that monitor annotations for use of obsolete or secondary GO term usage in annotations. Sabrina Toro, a ZFIN curator, continues with the primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2016&diff=62736ZFIN December 20162016-12-14T23:22:04Z<p>Dhowe: updated staff count and FTE</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 14, 2016 =<br />
=DRAFT - NOT YET COMPLETED=<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are checked in to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Sabrina Toro<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Curatorial <br/>GO lead<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 each; 0.6 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical<br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[File:|ZFIN curation stats from X, 2015 to Y, 2016]]<br />
<br />
DATA TO BE ADDED FOR 2016<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncharted data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF files are currently checked into the GO SVN repository on a weekly basis. We rely largely on QC reports that come from the GO GAF validation steps after file check-in. We also have internal processes that monitor annotations for use of obsolete or secondary GO term usage in annotations. Sabrina Toro, a ZFIN curator, continues with the primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2016&diff=62730ZFIN December 20162016-12-14T21:54:14Z<p>Dhowe: Adding first draft of ZFIN 2016 report...not yet complete.</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 14, 2016 =<br />
=DRAFT - NOT YET COMPLETED=<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use. These data are checked in to the central GO Consortium repository on a weekly basis.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |9 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.9 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[File:|ZFIN curation stats from X, 2015 to Y, 2016]]<br />
<br />
DATA TO BE ADDED FOR 2016<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in focused annotation efforts such as those spearheaded by members of the GO consortium, or when we do "back curation" to find important uncharted data when we release new curation capabilities.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF files are currently checked into the GO SVN repository on a weekly basis. We rely largely on QC reports that come from the GO GAF validation steps after file check-in. We also have internal processes that monitor annotations for use of obsolete or secondary GO term usage in annotations. Sabrina Toro, a ZFIN curator, continues with the primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug</div>Dhowehttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Logistics&diff=622522016 Los Angeles GOC Meeting Logistics2016-10-24T18:44:07Z<p>Dhowe: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Los Angeles, November 4-6, 2016=<br />
<br />
* Location: <br />
** University of Southern California<br />
<br />
==Registration==<br />
* Please register at: https://www.regonline.com/registration/Checkin.aspx?EventID=1890594<br />
<br />
==Consortium dinner Friday November 4==<br />
<br />
<br />
==Planned Schedule== <br />
<br />
* '''Friday November 4''': <br />
:* Meeting will run from 9am to 5pm.<br />
:* Consortium Dinner will follow.<br />
<br />
*'''Saturday November 5''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Sunday November 6''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
*'''Monday November 7''': <br />
:* Noctua training workshop will run from 9 am to 3 pm<br />
<br />
==Meeting Venue and Directions==<br />
* University of Southern California, Ray I. Irani Hall, room 101.<br />
** Campus Map: type "RRI" in the search box - http://web-app.usc.edu/maps/<br />
** Walk from hotel: Cross the street (Figueroa) at the light just north of the hotel, and continue almost straight across campus<br />
** Driving from off-campus: Enter campus from Vermont Street (west side), and pay for parking in Parking Structure A ("PSA" on map), which is right across from RRI. Or park right next to the Radisson Hotel and walk with the others (this is cheaper and probably easier on Saturday and Sunday).<br />
<br />
<br />
===Arriving===<br />
* International Flights<br />
** LAX<br />
** Recommend Uber (pick up on Departures level, one floor above ground) or Taxi<br />
* Some domestic flights<br />
** Burbank airport, slightly closer and more convenient than LAX<br />
<br />
===Meeting Dinner===<br />
* Dinner will be on the 4th, starting at 6:30pm, at McKays in the Trophy Room: http://mckays.usc.edu/<br />
* Here are the dinner choices for that evening<br />
** Appetizer:<br />
*** Soup of the Day<br />
*** Garden Green Salad<br />
*** Cajun Fried Calamari (Crispy Calamari Fries Served with House Remoulade & Lemon)<br />
** Main<br />
*** Montego Bay Chicken (Half of a Farm Raised Chicken, Char-Grilled & Brushed with Authentic Jerk Marinade Over Chorizo-Calypso Rice)<br />
*** Sake Salmon (Fresh Atlantic Salmon Glazed with Rice Wine & Miso Stir-Fried Vegetables, Forbidden Rice)<br />
*** Flat Iron Steak (10oz Flat Iron Steak Grilled to Perfection with Maytag Mashed Potatoes Seasonal Vegetables & Red Wine Demi Glace)<br />
*** Boneless Short Rib (12-Hour, Cabernet Braised Short Rib over Smoked Cheddar, Red Pepper Grits Seasonal Vegetables)<br />
*** Cavatappi Arrabbiata (Corkcrew Pasta Tossed in Garlic Crème Sauce with Fried Roasted Tomatoes, Salmon Belly & Carlsbad Mussels)<br />
*** Thai Curry Noodles (vegan/vegetarian; gluten-free) (Sautéed Garden Vegetables in a Rich-Red Curry Broth, Served with Flat Stir-Fried Noodles)<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, 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 attend the Noctua/LEGO workshop the day after the meeting, Monday, November 7th?<br />
|-<br />
| Shur-Jen Wang<br />
| Rat Genome Database<br />
| Yes<br />
| No<br />
| No<br />
<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Suzanna Lewis<br />
| LBNL<br />
|Yes<br />
|Yes<br />
|Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Laboratory<br />
|Yes<br />
|Yes<br />
|Yes<br />
|-<br />
| Paul Sternberg<br />
| Caltech<br />
|Yes<br />
|<br />
|Yes<br />
|-<br />
| Chris Mungall<br />
| LBNL<br />
| Yes<br />
|<br />
| No (previously organized meeting)<br />
|-<br />
| Seth Carbon<br />
| LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Stacia Engel<br />
| Stanford, SGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| WB, Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Christian Pich<br />
| ZFIN<br />
| No<br />
| No<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes (note food: vegetarian or fish only)<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR<br />
| Yes<br />
|Yes<br />
| Yes<br />
|-<br />
| Donghui<br />
| TAIR<br />
| Yes<br />
|Yes<br />
|No<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
|Yes<br />
|Yes<br />
|Yes<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
|Yes<br />
|Yes<br />
|No<br />
|-<br />
| David Hill<br />
| The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Not sure<br />
|-<br />
| Karen Christie<br />
| The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Mary Dolan<br />
| The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
|-<br />
| Li Ni<br />
| The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Dmitry Sitnikov<br />
| The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Yes<br />
| <br />
| No<br />
|-<br />
| Fiona McCarthy<br />
| AgBase<br />
| No<br />
|<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| No<br />
|Yes (note: vegetarian or fish only)<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Olivia Lang<br />
| SGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Yes<br />
|<br />
| No<br />
|-<br />
|-<br />
| Helen Parkinson<br />
| EBI<br />
| No<br />
|<br />
| No<br />
|-<br />
|-<br />
| David Osumi-Sutherland<br />
| EBI<br />
| Yes<br />
|<br />
| No (It's my daughter's birthday!)<br />
|-<br />
|-<br />
| Val Wood<br />
| PomBase<br />
| Yes<br />
|<br />
| Yes<br />
|-<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
|<br />
| Yes<br />
|-<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
|Yes<br />
|Yes<br />
| No<br />
|-<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
| No<br />
|-<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
|-<br />
| Jim Hu<br />
| TAMU<br />
| Yes<br />
| Yes<br />
| No<br />
|-<br />
|-<br />
| Debby Siegele<br />
| TAMU<br />
| Yes<br />
| Yes<br />
| No<br />
|-<br />
|-<br />
| Suzi Aleksander<br />
| TAMU<br />
| Yes<br />
| Yes<br />
| Yes <br />
|-<br />
|-<br />
| Jim Balhoff<br />
| RTI<br />
| Yes<br />
| Yes<br />
| No<br />
|- <br />
|Xiaosong Huang<br />
| USC<br />
| Yes<br />
|<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB <br />
|Yes<br />
|Yes<br />
|Yes<br />
|-<br />
| Chris Grove<br />
| WB<br />
| No<br />
| No<br />
| Yes<br />
|-<br />
| Raymond Lee<br />
| WB<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Marc Feuermann<br />
| Swiss-Prot<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Sylvain Poux<br />
| Swiss-Prot<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Malcolm Fisher<br />
| Xenbase<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Marcus Chibucos<br />
| ECO, IGS<br />
| Yes<br />
| Yes<br />
| No<br />
|}<br />
<br />
NOT attending:<br />
<br />
Moni Munoz-Torres - Previous commitment to attend http://www.icg-11.org/<br />
<br />
Melanie Courtot<br />
<br />
Paola Roncaglia<br />
<br />
==Accommodations==<br />
* PLEASE BOOK USING CODE "GOCON" BY OCTOBER 13 TO ENSURE RATE<br />
* Make hotel reservations with your personal access code “GOCON” either <br />
** online https://www.radisson.com/los-angeles-hotel-ca-90007/cafiguer<br />
** by phone from US 1.800.333.3333, international call +1.213.748.4141<br />
* We have arranged for a group rate at the Radisson Hotel across the street from the USC campus.<br />
* Make sure to book by October 13, as there may be no availability after that date<br />
** the weekend of November 5-6 there will be two big football games at the Coliseum<br />
* Individuals will pay on own for all charges<br />
<br />
== Local activities ==<br />
* walking distance:<br />
** Exposition Park - https://en.wikipedia.org/wiki/Exposition_Park_(Los_Angeles)<br />
*** Natural History Museum - http://www.nhm.org <br />
*** California Science Center - http://californiasciencecenter.org<br />
* Downtown LA<br />
** LA Live - https://www.lalive.com/<br />
** MOCA - http://www.moca.org/<br />
** Little Tokyo - http://www.littletokyola.org<br />
<br />
[[Category: GO Consortium Meetings]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=2016_Geneva_GOC_Meeting_Logistics&diff=598632016 Geneva GOC Meeting Logistics2016-01-28T20:00:21Z<p>Dhowe: /* Registration */</p>
<hr />
<div>=GOC Meeting, Geneva Switzerland, April 15-16, 2016=<br />
<br />
* Location: <br />
*Friday: Campus Biotech Geneva (CBG), 9 Chemin des Mines<br />
*Saturday: Campus Medical Universitaire (CMU), 1 rue Michel-Servet<br />
<br />
==Planned Schedule== <br />
<br />
* '''Friday April 15''': <br />
:* Meeting will run from 9am to 5pm.<br />
:* Consortium Dinner will follow.<br />
<br />
*'''Saturday April 16''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
==Meeting Venue and Directions==<br />
<br />
===Arriving===<br />
<br />
<br />
===Meeting Dinner===<br />
<br />
<br />
===Registration===<br />
(based on 30 attendees)<br />
Between 100 - 150 CHF (depending on room available on Saturday). This includes Friday night dinner.<br />
<br />
==Registration==<br />
Please add your name to the table if you intend to attend the meeting, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
|-<br />
| Paul Thomas<br />
| USC<br />
|-<br />
| Suzanna Lewis<br />
| LBNL<br />
|-<br />
| Judy Blake<br />
| Jackson Laboratory<br />
|-<br />
| Mike Cherry<br />
| Stanford<br />
|-<br />
| Pascale Gaudet<br />
| GO Central /SIB Swiss Institute of Bioinformatics<br />
|-<br />
| Sandra Orchard (Fri only)<br />
| EMBL-EBI<br />
|-<br />
| Birgit Meldal (Fri only)<br />
| EMBL-EBI<br />
|-<br />
| Marcus Chibucos (Fri only)<br />
| ECO/University of Maryland School of Medicine/IGS<br />
|-<br />
| Petra Fey<br />
| dictyBase/Northwestern University<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
|-<br />
| Stacia Engel<br />
| Stanford, SGD<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
|-<br />
| Melanie Courtot<br />
| EMBL-EBI<br />
|-<br />
| Helen Parkinson<br />
| EMBL-EBI<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
|-<br />
| Aleks Shypitsyna<br />
| EMBL-EBI<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
|-<br />
|-)<br />
|}<br />
===Fees===<br />
TBD<br />
===How to Register===<br />
<br />
==Accommodations==<br />
<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]]<br />
[[Category: Consortium Meeting Logistics]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=2015_LEGO_Jamboree_Logistics&diff=592322015 LEGO Jamboree Logistics2015-11-30T20:29:10Z<p>Dhowe: /* Remote Attendees */ Added Doug and Sabrina to list of remote attendees</p>
<hr />
<div>[[Category:Consortium Meeting Logistics]]<br />
== Dates ==<br />
* December 8-10, 2015<br />
** Start 9am December 8<br />
** End at noon December 10, optionally continue through 4pm or so.<br />
<br />
== Venue ==<br />
<br />
Geneva, Switzerland<br><br />
Campus Biotech<br><br />
<br />
== Participants ==<br />
Please use this link to register: <br />
https://goo.gl/1t1ybJ<br />
<br />
==Hotels==<br />
<br />
== Agenda ==<br />
<br />
===Tuesday, December 8th===<br />
<br />
====Schedule====<br />
*10am Seminar: Using LEGO to Represent Biological Knowledge - Paul T. and Chris<br />
**For a more general audience<br />
*11am Workshop Begins: More specific introduction to LEGO for curators<br />
*Lunch<br />
*1:30pm? Hands-on with Noctua<br />
**Creating simple annatons in Noctua<br />
*** A simple enzyme paper ''Pfkl''-- http://www.ncbi.nlm.nih.gov/pubmed/?term=6244280<br />
*** A regulation paper ''Pfkl''-- http://www.ncbi.nlm.nih.gov/pubmed/6446714<br />
<br />
====Discussion and Action Items====<br />
<br />
===Wednesday, December 9th===<br />
====Schedule====<br />
*Continuing on with annotation examples and suggested papers from participants:<br />
*Annotating causal relationships and downstream effects<br />
**TAIR annotation consistency exercise: [http://www.ncbi.nlm.nih.gov/pubmed/26124109 The MYB36 transcription factor orchestrates Casparian strip formation.]<br />
*Annotations involving specific isoforms and feedforward circuits<br />
**WormBase: [http://www.ncbi.nlm.nih.gov/pubmed/25148942 MIG-10 (Lamellipodin) stabilizes invading cell adhesion to basement membrane and is a negative transcriptional target of EGL-43 in C. elegans.]<br />
<br />
====Discussion and Action Items====<br />
<br />
===Thursday, December 10th===<br />
====Schedule====<br />
*Future plans and thoughts<br />
**Seeding models<br />
**Plans for going forward<br />
<br />
====Discussion and Action Items====<br />
<br />
<br />
==Remote Attendees==<br />
Doug Howe - ZFIN - sorry I can't be there in person! If you are able to webcast any portions, I'd be happy to drink lots of coffee on my end.<br />
Sabrina Toro - ZFIN<br />
<br />
==Group photo==</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2015&diff=58601ZFIN December 20152015-10-06T18:39:40Z<p>Dhowe: /* Ontology Development Contributions */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, September 30, 2015 =<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |9 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.9 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[File:zfinannotsummary2015.png|ZFIN curation stats from Dec 10, 2014 to Sept. 30, 2015]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
Several term requests from Ceri:<br />
response to sodium azide<br />
cellular response to sodium azide<br />
<br />
Researched and submitted request for terms related to "alarm substance" in teleost both via TermGenie and GO tracker. Requested template for development of structure.<br />
GO TermGenie request for templates and new terms. These are all pending.<br />
https://github.com/geneontology/termgenie/issues/71#issuecomment-112330898<br />
response to chondroitin 4'-sulfate<br />
response to chondroitin 6'-sulfate<br />
response to schreckstoff<br />
<br />
GO term request:<br />
https://github.com/geneontology/go-ontology/issues/12077<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF file quality control is now routinely done via the OWL Tools scripts run as a job on the GO Jenkins. Sabrina Toro, a ZFIN curator, has now taken on primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2015&diff=58546ZFIN December 20152015-09-30T23:07:53Z<p>Dhowe: /* Zebrafish Model Organism Database Summary, December 2015 */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, September 30, 2015 =<br />
<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |9 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.9 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[File:zfinannotsummary2015.png|ZFIN curation stats from Dec 10, 2014 to Sept. 30, 2015]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF file quality control is now routinely done via the OWL Tools scripts run as a job on the GO Jenkins. Sabrina Toro, a ZFIN curator, has now taken on primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2015&diff=58545ZFIN December 20152015-09-30T22:42:16Z<p>Dhowe: updated the stats chart...prior version had an error in the calculation of %change</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 2015 =<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |9 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.9 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[File:zfinannotsummary2015.png|ZFIN curation stats from Dec 10, 2014 to Sept. 30, 2015]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF file quality control is now routinely done via the OWL Tools scripts run as a job on the GO Jenkins. Sabrina Toro, a ZFIN curator, has now taken on primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.</div>Dhowehttps://wiki.geneontology.org/index.php?title=File:Zfinannotsummary2015.png&diff=58544File:Zfinannotsummary2015.png2015-09-30T22:40:43Z<p>Dhowe: ZFIN annotation summary, Dec 2014 - Sept 2015</p>
<hr />
<div>ZFIN annotation summary, Dec 2014 - Sept 2015</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2015&diff=58543ZFIN December 20152015-09-30T22:36:20Z<p>Dhowe: /* NOTE THIS DOCUMENT IS STILL BEING WORKED ON..NOT YET READY FOR 2015 REPORT */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 2015 =<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |9 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.9 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[File:Zfinannotationstats2015.png|ZFIN curation stats from Dec 10, 2014 to Sept. 30, 2015]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF file quality control is now routinely done via the OWL Tools scripts run as a job on the GO Jenkins. Sabrina Toro, a ZFIN curator, has now taken on primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2015&diff=58542ZFIN December 20152015-09-30T22:35:36Z<p>Dhowe: /* Annotation Progress */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 2015 =<br />
=NOTE THIS DOCUMENT IS STILL BEING WORKED ON..NOT YET READY FOR 2015 REPORT=<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |9 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.9 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[File:Zfinannotationstats2015.png|ZFIN curation stats from Dec 10, 2014 to Sept. 30, 2015]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF file quality control is now routinely done via the OWL Tools scripts run as a job on the GO Jenkins. Sabrina Toro, a ZFIN curator, has now taken on primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2015&diff=58541ZFIN December 20152015-09-30T22:34:26Z<p>Dhowe: /* Annotation Progress */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 2015 =<br />
=NOTE THIS DOCUMENT IS STILL BEING WORKED ON..NOT YET READY FOR 2015 REPORT=<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |9 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.9 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[<br />
File:Zfinannotationstats2015.png|ZFIN curation stats from Dec 10, 2014 to Sept. 30, 2015<br />
]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF file quality control is now routinely done via the OWL Tools scripts run as a job on the GO Jenkins. Sabrina Toro, a ZFIN curator, has now taken on primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.</div>Dhowehttps://wiki.geneontology.org/index.php?title=File:Zfinannotationstats2015.png&diff=58540File:Zfinannotationstats2015.png2015-09-30T22:33:06Z<p>Dhowe: ZFIN 2015 Annotation stats (Dec 2014-Sept 2015)</p>
<hr />
<div>ZFIN 2015 Annotation stats (Dec 2014-Sept 2015)</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2015&diff=58539ZFIN December 20152015-09-30T22:27:40Z<p>Dhowe: /* Annotation Progress */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 2015 =<br />
=NOTE THIS DOCUMENT IS STILL BEING WORKED ON..NOT YET READY FOR 2015 REPORT=<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |9 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.9 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[<br />
File:Screen_Shot_2015-09-30_at_2.20.58_PM.png|ZFIN curation stats from Dec 10, 2014 to Sept. 30, 2015<br />
]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF file quality control is now routinely done via the OWL Tools scripts run as a job on the GO Jenkins. Sabrina Toro, a ZFIN curator, has now taken on primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.</div>Dhowehttps://wiki.geneontology.org/index.php?title=File:Screen_Shot_2015-09-30_at_2.20.58_PM.png&diff=58538File:Screen Shot 2015-09-30 at 2.20.58 PM.png2015-09-30T22:12:40Z<p>Dhowe: ZFIN curation stats Dec., 10, 2014-Sept. 30, 2015</p>
<hr />
<div>ZFIN curation stats Dec., 10, 2014-Sept. 30, 2015</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2015&diff=58537ZFIN December 20152015-09-30T22:11:00Z<p>Dhowe: /* Annotation Progress */</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 2015 =<br />
=NOTE THIS DOCUMENT IS STILL BEING WORKED ON..NOT YET READY FOR 2015 REPORT=<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |9 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.9 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
[[<br />
File:GOC Annual Report Stats 20150930.jpg|thumbnail|ZFIN curation stats from Dec 10, 2014 to Sept. 30, 2015<br />
]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF file quality control is now routinely done via the OWL Tools scripts run as a job on the GO Jenkins. Sabrina Toro, a ZFIN curator, has now taken on primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2015&diff=58534ZFIN December 20152015-09-30T18:23:02Z<p>Dhowe: First update of the 2015 report..not yet complete..still need to add stats table and any ontology development contributions.</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 2015 =<br />
=NOTE THIS DOCUMENT IS STILL BEING WORKED ON..NOT YET READY FOR 2015 REPORT=<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |9 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.9 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GOC NHGRI grant.<br />
<br />
= Annotation Progress =<br />
<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF file quality control is now routinely done via the OWL Tools scripts run as a job on the GO Jenkins. Sabrina Toro, a ZFIN curator, has now taken on primary responsibility for weekly submission of our GAF and gp2protein files in consultation with Doug.</div>Dhowehttps://wiki.geneontology.org/index.php?title=April_2015_GOC_Teleconference_Agenda_and_Logistics&diff=56543April 2015 GOC Teleconference Agenda and Logistics2015-03-31T01:14:40Z<p>Dhowe: /* Attendees */ added Sabrina and doug from Zfin</p>
<hr />
<div>[[Category:GO_Consortium_Meetings]]<br />
<br />
==Logistics==<br />
* Call runs April 1, from 11am to 12:30pm EDT<br />
* Call-in information / screen sharing: We will use Bluejeans teleconferencing software for audio and video and WILL NOT use the GO conference line. We will use Bluejeans for screen sharing also. If attendees have a question they should post it on the chat window and they will answered in order.<br />
** Link for the Bluejeans meeting: https://bluejeans.com/626682538<br />
<br />
==Agenda==<br />
===Introduction (11:00 - 11:05) (GO PI's)===<br />
===Discussion of priorities for calendar year 2015 (11:05 - 11:30) (GO PI's)===<br />
<br />
===Talk by Paul Pavlidis, UBC (11:30 - 12:05)===<br />
====The use of GO in data analysis: can we raise the bar?====<br />
* [http://pavlab.chibi.ubc.ca Paul Pavlidis's lab website]<br />
<br />
===Other agenda items (12:05 - 12:30)===<br />
* Update on AmiGO/GO website Behave testing framework (Mary/Seth/Chris)<br />
* Annotating complexes as objects, producing a separate GAF for complexes, educating users about these annotations<br />
* Training curators on LEGO<br />
<br />
==Attendees==<br />
Please sign up so we know who can attend.<br />
<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
|-<br />
| Rama Balakrishnan<br />
| Stanford University, SGD<br />
|-<br />
|David Hill<br />
|Jackson Labs, MGI<br />
|-<br />
|Kimberly<br />
|Cal Tech, Wormbase<br />
|-<br />
|Paul Thomas<br />
|USC<br />
|-<br />
|Huaiyu Mi<br />
|USC<br />
|-<br />
| Moni Munoz-Torres<br />
| Lawrence Berkeley National Lab, BBOP<br />
|-<br />
| Seth Carbon<br />
| Lawrence Berkeley National Lab, BBOP<br />
|-<br />
| Chris Mungall<br />
| Lawrence Berkeley National Lab, BBOP<br />
|-<br />
| Tanya Berardini<br />
| Phoenix Bioinformatics, TAIR<br />
|-<br />
| Eva Huala<br />
| Phoenix Bioinformatics, TAIR<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
|-<br />
|}</div>Dhowehttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_February_10,_2015&diff=56007Annotation Conf. Call, February 10, 20152015-02-10T17:21:08Z<p>Dhowe: Added Sabrina to list of CalTech demo tool names</p>
<hr />
<div><br />
<br />
=Agenda=<br />
<br />
==Jenkins reports==<br />
http://build.berkeleybop.org/view/GAF/<br />
<br />
==RNA Central==<br />
Please send the identifiers for RNA gene products that is being used internally by your MOD for GO annotation. This will provide the initial mappings so that we can then switch over to using the RNACentral IDs. Contact RNA Central using this form - http://rnacentral.org/contact<br />
<br />
==Demo of CalTech annotation tool==<br />
We will use CalTech's annotation tool for our curation consistency exercises. This tool allows us to highlight a sentence and enter specific GO terms/evidence etc. Kimberly will give a demo of how it works. If you want an account in this tool, please put your name down here on this wiki page so Kimberly can send one email to her programmer requesting for accounts.<br />
* Petra<br />
* Val<br />
* Bob<br />
* Aleks (EBI)<br />
* Penelope (EBI)<br />
* Dmitry (MGI)<br />
* David H (MGI)<br />
* Stacia (SGD)<br />
* Tanya (TAIR)<br />
* Donghui (TAIR)<br />
* Leonore (TAIR)<br />
* Doug (ZFIN)<br />
* Sabrina (ZFIN)<br />
<br />
==Annotation Consistency Exercise - February 24, 2015==<br />
Here is a link to the paper that I've chosen for the first annotation consistency exercise/discussion:<br />
<br />
http://www.ncbi.nlm.nih.gov/pubmed/25569233<br />
<br />
It describes studies on C. elegans bcl-7 (http://www.wormbase.org/species/c_elegans/gene/WBGene00016192) and human BCL7B (http://www.uniprot.org/uniprot/Q9BQE9).<br />
<br />
The main thing I'd like to focus on for the annotation exercise is what Biological Process annotations curators make, noting that, at the moment, the all-encompassing Biological Process terms might not yet exist for what is described in the paper. In particular, I'd like to discuss annotating to a process vs. regulation of a process, and the use of annotation extensions to provide more context for the BP terms. <br />
<br />
I don't want people to get too hung up on the C. elegans biology, but I've included some links to entries on the anatomy terms and phenotypes described in the paper, in case they're helpful:<br />
*Seam cells<br />
**http://www.wormatlas.org/hermaphrodite/seam%20cells/mainframe.htm<br />
**http://www.wormatlas.org/hermaphrodite/seam%20cells/Images/Seamfig3leg.htm<br />
*Egl phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000006<br />
*Pvl phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000697<br />
*Burst phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000038<br />
*Alae morphology phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0001412<br />
<br />
Note that the paper starts with gross anatomical defects and then progresses to a more detailed characterization of the phenotype. This is fairly typical.<br />
<br />
--Kimberly<br />
<br />
<br />
<br />
<br />
[[Category:Annotation Working Group]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call,_February_10,_2015&diff=56006Annotation Conf. Call, February 10, 20152015-02-10T17:11:16Z<p>Dhowe: Added Doug to list of people wanting demo accounts on CalTech annotation tool</p>
<hr />
<div><br />
<br />
=Agenda=<br />
<br />
==Jenkins reports==<br />
http://build.berkeleybop.org/view/GAF/<br />
<br />
==RNA Central==<br />
Please send the identifiers for RNA gene products that is being used internally by your MOD for GO annotation. This will provide the initial mappings so that we can then switch over to using the RNACentral IDs. Contact RNA Central using this form - http://rnacentral.org/contact<br />
<br />
==Demo of CalTech annotation tool==<br />
We will use CalTech's annotation tool for our curation consistency exercises. This tool allows us to highlight a sentence and enter specific GO terms/evidence etc. Kimberly will give a demo of how it works. If you want an account in this tool, please put your name down here on this wiki page so Kimberly can send one email to her programmer requesting for accounts.<br />
* Petra<br />
* Val<br />
* Bob<br />
* Aleks (EBI)<br />
* Penelope (EBI)<br />
* Dmitry (MGI)<br />
* David H (MGI)<br />
* Stacia (SGD)<br />
* Tanya (TAIR)<br />
* Donghui (TAIR)<br />
* Leonore (TAIR)<br />
* Doug (ZFIN)<br />
<br />
==Annotation Consistency Exercise - February 24, 2015==<br />
Here is a link to the paper that I've chosen for the first annotation consistency exercise/discussion:<br />
<br />
http://www.ncbi.nlm.nih.gov/pubmed/25569233<br />
<br />
It describes studies on C. elegans bcl-7 (http://www.wormbase.org/species/c_elegans/gene/WBGene00016192) and human BCL7B (http://www.uniprot.org/uniprot/Q9BQE9).<br />
<br />
The main thing I'd like to focus on for the annotation exercise is what Biological Process annotations curators make, noting that, at the moment, the all-encompassing Biological Process terms might not yet exist for what is described in the paper. In particular, I'd like to discuss annotating to a process vs. regulation of a process, and the use of annotation extensions to provide more context for the BP terms. <br />
<br />
I don't want people to get too hung up on the C. elegans biology, but I've included some links to entries on the anatomy terms and phenotypes described in the paper, in case they're helpful:<br />
*Seam cells<br />
**http://www.wormatlas.org/hermaphrodite/seam%20cells/mainframe.htm<br />
**http://www.wormatlas.org/hermaphrodite/seam%20cells/Images/Seamfig3leg.htm<br />
*Egl phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000006<br />
*Pvl phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000697<br />
*Burst phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0000038<br />
*Alae morphology phenotype<br />
**http://www.wormbase.org/species/all/phenotype/WBPhenotype:0001412<br />
<br />
Note that the paper starts with gross anatomical defects and then progresses to a more detailed characterization of the phenotype. This is fairly typical.<br />
<br />
--Kimberly<br />
<br />
<br />
<br />
<br />
[[Category:Annotation Working Group]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_December_2014&diff=55564ZFIN December 20142014-12-11T00:03:53Z<p>Dhowe: Added annual report for ZFIN</p>
<hr />
<div>[[Category:ZFIN]] [[Category:Reports]]<br />
= Zebrafish Model Organism Database Summary, December 2014 =<br />
= Overview =<br />
ZFIN is the Zebrafish Model Organism Database (zfin.org). We serve as the distributor for all GO annotations for the zebrafish, Danio rerio. We make annotations during curation of published papers, and we also load gene_association files from external sources that include Danio rerio annotations. Those are then captured in the ZFIN database, and represented in our gene_association.zfin file for anyone to download and use.<br />
<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |7 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.7 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |4 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |3 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GO.<br />
<br />
= Annotation Progress =<br />
[[File:ZFIN%202014%20annotation%20stats.png]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of the current literature focusing first on new mutants, phenotypes, expression, and Human disease models. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers.<br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications and seminal early publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations from function to process or component terms provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =<br />
GAF file quality control is now done via the OWL Tools scripts locally before submission to the GO SVN.</div>Dhowehttps://wiki.geneontology.org/index.php?title=File:ZFIN_2014_annotation_stats.png&diff=55562File:ZFIN 2014 annotation stats.png2014-12-10T23:44:15Z<p>Dhowe: These are the stats I used in the Dec. 2014 Annual Report for ZFIN.</p>
<hr />
<div>These are the stats I used in the Dec. 2014 Annual Report for ZFIN.</div>Dhowehttps://wiki.geneontology.org/index.php?title=2014_Barcelona_Meeting_Logistics&diff=547622014 Barcelona Meeting Logistics2014-10-02T17:59:52Z<p>Dhowe: /* Remote Attendees */</p>
<hr />
<div>== Dates ==<br />
October 13-15, 2014<br />
We are planning to meet for 3 full days. <br />
<br />
== Agenda ==<br />
* [[2014 Barcelona GOC Meeting Agenda]]<br />
<br />
== Meeting Info ==<br />
=== Venue ===<br />
CRG, Barcelona<br />
<br />
PRBB (Charles Darwin Room)<br />
Calle Dr. Aiguader, 88<br />
08003, Barcelona<br />
Spain<br />
<br />
Website: http://pasteur.crg.es/portal/page/portal/Internet/<br />
<br />
<br />
<br />
=== Registration ===<br />
Please use this form to register : [https://docs.google.com/forms/d/1Q8nudtqusn7OrcJO1IC7KZPLUy2Rijkr_k6tI6OQUbI/edit?c=0&w=1#| Registration Form ]<br />
<br />
====Registered participants as of Sept 3====<br />
* Attrill Helen Louise FlyBase<br />
* Balakrishnan Rama Stanford University<br />
* Berardini Tanya TAIR<br />
* Blake Judith Jackson Laboratory<br />
* Carbon Seth BBOP (LBL)<br />
* Cherry Mike Stanford University<br />
* D'Eustachio Peter NYU School of Medicine<br />
* Feuermann Marc SIB- Swiss Institute of Bioinformatics<br />
* Fey Petra Northwestern University<br />
* Gaudet Pascale SIB Swiss Institute of Bioinformatics<br />
* Hill David The Jackson Laboratory<br />
* Huala Eva Phoenix Bioinformatics<br />
* Huntley Rachael EMBL-EBI (H4-Barcelona Hotel; arrive Barc. 12th@2pm; depart Barc. 15th@10pm)<br />
* Li Donghui TAIR<br />
* Lomax Jane EMBL-EBI<br />
* Lovering Ruth University College London (H4-Barcelona Hotel; arrive Barc. 12th@2:20pm; depart Barc. 16th@12:50pm)<br />
* Mi Huaiyu USC<br />
* Muller Hans-Michael Caltech<br />
* Mungall Chris LBNL<br />
* Munoz-Torres Monica Lawrence Berkeley National Laboratory<br />
* O'Donovan Claire EMBL-EBI (H4-Barcelona Hotel; arrive Barc. 12th@2pm; depart Barc. 15th@10pm)<br />
* Osumi-Sutherland David Jon EBI<br />
* Petri Victoria Medical College of Wisconsin/HMGC/RGD<br />
* Roncaglia Paola EMBL-EBI (H4-Barcelona Hotel; arrive Barc. 12th@2:50pm; depart Barc. 16th@10:40am) <br />
* Sawford Tony EMBL-EBI (H4-Barcelona Hotel; arrive Barc. 12th@2pm; depart Barc. 15th@10pm)<br />
* Shimoyama Mary Rat Genome Database<br />
* Sternberg Paul California Institute of Technology<br />
* Tweedie Susan University of Cambridge<br />
* Van Auken Kimberly Caltech (H4-Barcelona Hotel; arrive Barc. 11th@7:10pm; depart Barc. 16th@10:45am)<br />
* Wood Valerie University of Cambridge<br />
* Zahn Monique SIB Swiss Institute of Bioinformatics<br />
<br />
== Traveling to Barcelona and the CRG ==<br />
'''Getting to Barcelona'''<br />
http://wikitravel.org/en/Barcelona#Get_in<br />
<br />
'''Metro'''<br />
Ciutadella/Vila Olímpica station<br />
<br />
=== Lodging ===<br />
==== Recommended option ====<br />
We have reserved a block of rooms at the [H4-Barcelona Hotel | http://www.hotel4barcelona.com/es/ ] under "GO Meeting Group"<br />
Please fill the hotel reservation form and email it grupos.hotel4barcelona@besthotels.es or fax it at +34 933 293 724 [http://wiki.geneontology.org/images/0/06/GO-MEETING_Hotel_booking-reservation_form_vf.pdf]<br />
<br />
* '''Rate per Night:'''<br />
** Single : 95.00 Euro / night (10% taxes included), Breakfast buffet included<br />
** Double / Twin : 105.00 Euro / night (10% taxes included), Breakfast buffet included<br />
<br />
'''Please note: this rate is guaranteed until July 16th only'''. After this day the rate could be increased & availability is not guaranteed. <br />
<br />
==== Other hotel options ====<br />
* *OPTION 2. Hotel H10 Marina Barcelona* <br />
http://www.hotelh10marinabarcelona.com/ <br />
** SINGLE 115 € <br />
** DOUBLE 135 € <br />
<br />
** Buffet breakfast with more than 150 products included in the price. <br />
** Local tourist tax not included = 1,21€ per person/night <br />
** 10% VAT included <br />
<br />
* *OPTION 3. W-Barcelona* <br />
http://www.w-barcelona.es/ <br />
** SINGLE 295 € <br />
** DOUBLE 320 € <br />
<br />
** Breakfast included<br />
** Local tourist tax not included = 2,48€ per person/night <br />
** Local VAT not included (approx. 10%) <br />
<br />
* *OPTION 4. Residencia Campus del Mar (*residence for students*)* <br />
http://www.resa.es/Residencias/Campus-del-Mar/ubicacion <br />
** SINGLE 68 € <br />
** DOUBLE 98 € <br />
<br />
** Breakfast included <br />
** All the rooms have private bathroom and kitchen <br />
** 10% VAT included <br />
<br />
* *OPTION 5. Hotel H10 Port Vell****s <br />
www.hotelh10portvell.com <br />
SINGLE 125 € <br />
DOUBLE 145 € <br />
<br />
** Breakfast included. <br />
** Local tourist tax not included = 1,21€ per person/night <br />
** VAT included <br />
<br />
<br />
=== Conference Dinner ===<br />
Arenal Restaurant<br />
http://www.arenalrestaurant.com/<br />
(5 minutes walk from venue)<br />
Menu prices per person:<br />
* 40,70€ (VAT included) with alcoholic drinks.<br />
* 38,50€ (VAT included) without alcoholic drinks.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== Remote Attendees ===<br />
Doug Howe, ZFIN, 2nd & 3rd days only<br />
<br />
Sabrina Toro, ZFIN<br />
<br />
== Local Information ==<br />
=== Restaurants ===<br />
* RESTAURANT BESTIAL 0,3 Km from venue <br />
http://www.eltenedor.es/restaurante/bestial/1506 <br />
<br />
* RESTAURANT PEZ VELA 3 Km from venue<br />
http://www.eltenedor.es/restaurante/pez-vela/11409 <br />
<br />
* BAR CASA TOMAS (best "dobles mixtas" = French fries with a 'ali oli' sauce and red spicy sauce) <br />
Major de Sarria 49<br />
<br />
* LA PARADETA (restaurant serving fish and sea food)<br />
C/Riego 27 (Sants neighborhood)<br />
<br />
* PLA DE LA GARSA (restaurant serving local cheese and cured meat)<br />
Assaonadors 13<br />
<br />
* LA VINATERIA DEL CALL <br />
Sant Domünec del Call 9 (In Gothic neighborhood)<br />
<br />
* MADRID-BARCELONA (typical dishes; near Plaza Catalunya)<br />
Arago 282<br />
<br />
* BOADAS (mythic cocktail near Plaza Catalunya)<br />
c/Tallers 1<br />
<br />
* CAELUM (desserts moade in Spanish monasteries for coffee/tea time)<br />
c/De la Palla 8<br />
<br />
<br />
=== Weather ===<br />
Average high in October: 23 C / 72 F<br />
Average low: 15 C / 60 F<br />
<br />
=== Things to do ===<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=2014_Barcelona_Meeting_Logistics&diff=547612014 Barcelona Meeting Logistics2014-10-02T17:59:26Z<p>Dhowe: /* Remote Attendees */</p>
<hr />
<div>== Dates ==<br />
October 13-15, 2014<br />
We are planning to meet for 3 full days. <br />
<br />
== Agenda ==<br />
* [[2014 Barcelona GOC Meeting Agenda]]<br />
<br />
== Meeting Info ==<br />
=== Venue ===<br />
CRG, Barcelona<br />
<br />
PRBB (Charles Darwin Room)<br />
Calle Dr. Aiguader, 88<br />
08003, Barcelona<br />
Spain<br />
<br />
Website: http://pasteur.crg.es/portal/page/portal/Internet/<br />
<br />
<br />
<br />
=== Registration ===<br />
Please use this form to register : [https://docs.google.com/forms/d/1Q8nudtqusn7OrcJO1IC7KZPLUy2Rijkr_k6tI6OQUbI/edit?c=0&w=1#| Registration Form ]<br />
<br />
====Registered participants as of Sept 3====<br />
* Attrill Helen Louise FlyBase<br />
* Balakrishnan Rama Stanford University<br />
* Berardini Tanya TAIR<br />
* Blake Judith Jackson Laboratory<br />
* Carbon Seth BBOP (LBL)<br />
* Cherry Mike Stanford University<br />
* D'Eustachio Peter NYU School of Medicine<br />
* Feuermann Marc SIB- Swiss Institute of Bioinformatics<br />
* Fey Petra Northwestern University<br />
* Gaudet Pascale SIB Swiss Institute of Bioinformatics<br />
* Hill David The Jackson Laboratory<br />
* Huala Eva Phoenix Bioinformatics<br />
* Huntley Rachael EMBL-EBI (H4-Barcelona Hotel; arrive Barc. 12th@2pm; depart Barc. 15th@10pm)<br />
* Li Donghui TAIR<br />
* Lomax Jane EMBL-EBI<br />
* Lovering Ruth University College London (H4-Barcelona Hotel; arrive Barc. 12th@2:20pm; depart Barc. 16th@12:50pm)<br />
* Mi Huaiyu USC<br />
* Muller Hans-Michael Caltech<br />
* Mungall Chris LBNL<br />
* Munoz-Torres Monica Lawrence Berkeley National Laboratory<br />
* O'Donovan Claire EMBL-EBI (H4-Barcelona Hotel; arrive Barc. 12th@2pm; depart Barc. 15th@10pm)<br />
* Osumi-Sutherland David Jon EBI<br />
* Petri Victoria Medical College of Wisconsin/HMGC/RGD<br />
* Roncaglia Paola EMBL-EBI (H4-Barcelona Hotel; arrive Barc. 12th@2:50pm; depart Barc. 16th@10:40am) <br />
* Sawford Tony EMBL-EBI (H4-Barcelona Hotel; arrive Barc. 12th@2pm; depart Barc. 15th@10pm)<br />
* Shimoyama Mary Rat Genome Database<br />
* Sternberg Paul California Institute of Technology<br />
* Tweedie Susan University of Cambridge<br />
* Van Auken Kimberly Caltech (H4-Barcelona Hotel; arrive Barc. 11th@7:10pm; depart Barc. 16th@10:45am)<br />
* Wood Valerie University of Cambridge<br />
* Zahn Monique SIB Swiss Institute of Bioinformatics<br />
<br />
== Traveling to Barcelona and the CRG ==<br />
'''Getting to Barcelona'''<br />
http://wikitravel.org/en/Barcelona#Get_in<br />
<br />
'''Metro'''<br />
Ciutadella/Vila Olímpica station<br />
<br />
=== Lodging ===<br />
==== Recommended option ====<br />
We have reserved a block of rooms at the [H4-Barcelona Hotel | http://www.hotel4barcelona.com/es/ ] under "GO Meeting Group"<br />
Please fill the hotel reservation form and email it grupos.hotel4barcelona@besthotels.es or fax it at +34 933 293 724 [http://wiki.geneontology.org/images/0/06/GO-MEETING_Hotel_booking-reservation_form_vf.pdf]<br />
<br />
* '''Rate per Night:'''<br />
** Single : 95.00 Euro / night (10% taxes included), Breakfast buffet included<br />
** Double / Twin : 105.00 Euro / night (10% taxes included), Breakfast buffet included<br />
<br />
'''Please note: this rate is guaranteed until July 16th only'''. After this day the rate could be increased & availability is not guaranteed. <br />
<br />
==== Other hotel options ====<br />
* *OPTION 2. Hotel H10 Marina Barcelona* <br />
http://www.hotelh10marinabarcelona.com/ <br />
** SINGLE 115 € <br />
** DOUBLE 135 € <br />
<br />
** Buffet breakfast with more than 150 products included in the price. <br />
** Local tourist tax not included = 1,21€ per person/night <br />
** 10% VAT included <br />
<br />
* *OPTION 3. W-Barcelona* <br />
http://www.w-barcelona.es/ <br />
** SINGLE 295 € <br />
** DOUBLE 320 € <br />
<br />
** Breakfast included<br />
** Local tourist tax not included = 2,48€ per person/night <br />
** Local VAT not included (approx. 10%) <br />
<br />
* *OPTION 4. Residencia Campus del Mar (*residence for students*)* <br />
http://www.resa.es/Residencias/Campus-del-Mar/ubicacion <br />
** SINGLE 68 € <br />
** DOUBLE 98 € <br />
<br />
** Breakfast included <br />
** All the rooms have private bathroom and kitchen <br />
** 10% VAT included <br />
<br />
* *OPTION 5. Hotel H10 Port Vell****s <br />
www.hotelh10portvell.com <br />
SINGLE 125 € <br />
DOUBLE 145 € <br />
<br />
** Breakfast included. <br />
** Local tourist tax not included = 1,21€ per person/night <br />
** VAT included <br />
<br />
<br />
=== Conference Dinner ===<br />
Arenal Restaurant<br />
http://www.arenalrestaurant.com/<br />
(5 minutes walk from venue)<br />
Menu prices per person:<br />
* 40,70€ (VAT included) with alcoholic drinks.<br />
* 38,50€ (VAT included) without alcoholic drinks.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
=== Remote Attendees ===<br />
Doug Howe, ZFIN, 2nd & 3rd days only<br />
Sabrina Toro, ZFIN<br />
<br />
== Local Information ==<br />
=== Restaurants ===<br />
* RESTAURANT BESTIAL 0,3 Km from venue <br />
http://www.eltenedor.es/restaurante/bestial/1506 <br />
<br />
* RESTAURANT PEZ VELA 3 Km from venue<br />
http://www.eltenedor.es/restaurante/pez-vela/11409 <br />
<br />
* BAR CASA TOMAS (best "dobles mixtas" = French fries with a 'ali oli' sauce and red spicy sauce) <br />
Major de Sarria 49<br />
<br />
* LA PARADETA (restaurant serving fish and sea food)<br />
C/Riego 27 (Sants neighborhood)<br />
<br />
* PLA DE LA GARSA (restaurant serving local cheese and cured meat)<br />
Assaonadors 13<br />
<br />
* LA VINATERIA DEL CALL <br />
Sant Domünec del Call 9 (In Gothic neighborhood)<br />
<br />
* MADRID-BARCELONA (typical dishes; near Plaza Catalunya)<br />
Arago 282<br />
<br />
* BOADAS (mythic cocktail near Plaza Catalunya)<br />
c/Tallers 1<br />
<br />
* CAELUM (desserts moade in Spanish monasteries for coffee/tea time)<br />
c/De la Palla 8<br />
<br />
<br />
=== Weather ===<br />
Average high in October: 23 C / 72 F<br />
Average low: 15 C / 60 F<br />
<br />
=== Things to do ===<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_Dec_5-March_09&diff=48654ZFIN Dec 5-March 092014-03-12T21:59:48Z<p>Dhowe: Created new page for this report as it didn't seem possible to edit the name of the original report, which included the string "in progress"..this is final.</p>
<hr />
<div>[[Category:Reports]]<br />
<br />
= Zebrafish Model Organism Database Summary, December 5, 2013 -March 10, 2014 =<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |7 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.7 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |4 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |3 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GO.<br />
<br />
= Annotation Progress =<br />
==Annotation Statistics==<br />
[[File:GOStats GOCannualreport 20140309.jpg]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of literature focusing first on new mutants, phenotypes, expression, and Human disease models from the current literature. We also generate literature sets for seminal papers from heavily published genes. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers. <br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature generally, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We also curate papers from a list of the seminal publications associated with heavily published genes. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development. Varsha K Khodiyar, Doug Howe, Philippa J Talmud, Ross Breckenridge, Ruth C Lovering [http://f1000research.com/articles/2-242/v2 F1000]<br />
<br />
= Ontology Development Contributions =<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =</div>Dhowehttps://wiki.geneontology.org/index.php?title=Progress_reports_1rst_quarter_January-March&diff=48648Progress reports 1rst quarter January-March2014-03-12T21:47:07Z<p>Dhowe: ZFIN report complete</p>
<hr />
<div>==Working Groups==<br />
<br />
*[[Annotation Advocacy]]<br />
*[[Common Annotation Framework]]<br />
*[[Ontology Group Progress Report Q1 2014]]<br />
<br />
<br />
<br />
<br />
<br />
[[Category:Reports]]<br />
<br />
==MODS and Annotation Groups==<br />
<br />
[http://wiki.geneontology.org/images/3/39/MODProgressReportTemplate_2008.doc MOD template]<br />
<br />
[[MGI Dec 5-March 3]]<br />
<br />
[[RGD Dec 5-March 3]]<br />
<br />
<br />
[[TAIR Dec 2013-March 2014]]<br />
<br />
[[UniProt-GOA Dec 5-March 3]]<br />
<br />
[[dictyBase Dec 5-March 3]]<br />
<br />
[[WormBase Dec 5-March 3 - in progress]]<br />
<br />
[[UCL-annotation team Dec 5-March 10]]<br />
<br />
[[ZFIN Dec 5-March 09]]</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_Dec_5-March_11_-_in_progress&diff=48647ZFIN Dec 5-March 11 - in progress2014-03-12T21:45:45Z<p>Dhowe: /* Annotation Statistics */ added table of annotation stats</p>
<hr />
<div>[[Category:Reports]]<br />
<br />
= Zebrafish Model Organism Database Summary, December 5, 2013 -March 10, 2014 =<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |7 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.7 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |4 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |3 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GO.<br />
<br />
= Annotation Progress =<br />
==Annotation Statistics==<br />
[[File:GOStats GOCannualreport 20140309.jpg]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of literature focusing first on new mutants, phenotypes, expression, and Human disease models from the current literature. We also generate literature sets for seminal papers from heavily published genes. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers. <br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature generally, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We also curate papers from a list of the seminal publications associated with heavily published genes. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development. Varsha K Khodiyar, Doug Howe, Philippa J Talmud, Ross Breckenridge, Ruth C Lovering [http://f1000research.com/articles/2-242/v2 F1000]<br />
<br />
= Ontology Development Contributions =<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =</div>Dhowehttps://wiki.geneontology.org/index.php?title=File:GOStats_GOCannualreport_20140309.jpg&diff=48646File:GOStats GOCannualreport 20140309.jpg2014-03-12T21:37:50Z<p>Dhowe: ZFIN GO annotation stats, March 9, 2014</p>
<hr />
<div>ZFIN GO annotation stats, March 9, 2014</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_Dec_5-March_11_-_in_progress&diff=48596ZFIN Dec 5-March 11 - in progress2014-03-11T16:45:54Z<p>Dhowe: </p>
<hr />
<div>[[Category:Reports]]<br />
<br />
= Zebrafish Model Organism Database Summary, December 5, 2013 -March 10, 2014 =<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |7 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.7 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |4 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |3 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GO.<br />
<br />
= Annotation Progress =<br />
==Annotation Statistics==<br />
--DATA COMING SOON--<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of literature focusing first on new mutants, phenotypes, expression, and Human disease models from the current literature. We also generate literature sets for seminal papers from heavily published genes. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers. <br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature generally, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We also curate papers from a list of the seminal publications associated with heavily published genes. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development. Varsha K Khodiyar, Doug Howe, Philippa J Talmud, Ross Breckenridge, Ruth C Lovering [http://f1000research.com/articles/2-242/v2 F1000]<br />
<br />
= Ontology Development Contributions =<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_Dec_5-March_11_-_in_progress&diff=48595ZFIN Dec 5-March 11 - in progress2014-03-11T16:43:13Z<p>Dhowe: removed overview section</p>
<hr />
<div>[[Category:Reports]]<br />
<br />
= Zebrafish Model Organism Database Summary, December 5, 2013 -March 10, 2014 =<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |7 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.7 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |4 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |3 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GO.<br />
<br />
= Annotation Progress =<br />
--DATA COMING SOON--<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of literature focusing first on new mutants, phenotypes, expression, and Human disease models from the current literature. We also generate literature sets for seminal papers from heavily published genes. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers. <br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature generally, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We also curate papers from a list of the seminal publications associated with heavily published genes. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development. Varsha K Khodiyar, Doug Howe, Philippa J Talmud, Ross Breckenridge, Ruth C Lovering [http://f1000research.com/articles/2-242/v2 F1000]<br />
<br />
= Ontology Development Contributions =<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_Dec_5-March_11_-_in_progress&diff=48594ZFIN Dec 5-March 11 - in progress2014-03-11T16:40:30Z<p>Dhowe: added publication</p>
<hr />
<div>[[Category:Reports]]<br />
<br />
= Zebrafish Model Organism Database Summary, December 5, 2013 -March 10, 2014 =<br />
= Overview =<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |7 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.7 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |4 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |3 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GO.<br />
<br />
= Annotation Progress =<br />
--DATA COMING SOON--<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of literature focusing first on new mutants, phenotypes, expression, and Human disease models from the current literature. We also generate literature sets for seminal papers from heavily published genes. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers. <br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature generally, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We also curate papers from a list of the seminal publications associated with heavily published genes. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development. Varsha K Khodiyar, Doug Howe, Philippa J Talmud, Ross Breckenridge, Ruth C Lovering [http://f1000research.com/articles/2-242/v2 F1000]<br />
<br />
= Ontology Development Contributions =<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =</div>Dhowehttps://wiki.geneontology.org/index.php?title=ZFIN_Dec_5-March_11_-_in_progress&diff=48593ZFIN Dec 5-March 11 - in progress2014-03-11T16:38:19Z<p>Dhowe: copy of last report..content in progress</p>
<hr />
<div>[[Category:Reports]]<br />
<br />
= Zebrafish Model Organism Database Summary, December 5, 2013 -March 10, 2014 =<br />
= Overview =<br />
= Staff: =<br />
{| cellspacing="0" cellpadding="4" align="left"<br />
! style="background:lightgray; width:100px;" | Name<br />
! style="background:lightgray; width:170px;" | Position Type<br />
! style="background:lightgray; width:150px;" | FTE for GO<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe<br />
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN<br />
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |7 Curators<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial<br />
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.7 in aggregate<br />
|-<br />
|style="border-bottom:1px solid lightgray;" valign="top" |4 Technical <br />
|style="border-bottom:1px solid lightgray;" valign="top" |3 Developers, 1 DBA<br />
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate<br />
|}<br />
<br />
<br style="clear:both;"><br />
<br />
No direct funding from GO.<br />
<br />
= Annotation Progress =<br />
[[File:GOStats_GOCannualreport2013.png]]<br />
<br />
== Methods and strategies for annotation ==<br />
ZFIN does not have curators dedicated exclusively to GO curation. Our curators work on a prioritized set of literature focusing first on new mutants, phenotypes, expression, and Human disease models from the current literature. We also generate literature sets for seminal papers from heavily published genes. Any GO that is found in those papers gets added to ZFIN in the course of curating those papers. <br />
<br />
'''''Literature curation:'''''<br />
<br />
We curate many data types, including GO, as a routine part of our curation effort focused on the most current publications. The only real exception to that is when we participate in a focused annotation effort spearheaded by members of the GO consortium. During those efforts, we curate GO from any papers associated with genes in the set of genes being focused on for the project.<br />
<br />
<br />
'''''Computational annotation strategies:'''''<br />
<br />
We continue to align our gene records with UniProt protein records on an approximately monthly basis. At that time, we also apply current versions of the GO translation tables interpro2go, UniProtKW2go, and ec2go to generate electronic annotations in our system. On a monthly basis we also load GO annotations from GOA, PAINT, and computationally inferred GO annotations provided by the GOC. In some cases the resulting new annotations in ZFIN are electronic in origin, particularly from GOA (sub cellular location for example).<br />
<br />
<br />
'''''Priorities for annotation:'''''<br />
<br />
Our curation priority remains focused on keeping up with the current zebrafish literature generally, focusing first on papers with new mutants, phenotypes, expression, and Human disease models. We also curate papers from a list of the seminal publications associated with heavily published genes. We consider this to be "paper-centric" curation. Though many of these papers do contain GO annotations, we do not currently prioritize our curation on the basis of their potential GO content. When GOC members ask us to participate in a focused annotation effort we do make an effort to participate as fully as possible in the required "gene-centric" GO curation.<br />
<br />
= Presentations and Publications =<br />
<br />
<br />
= Ontology Development Contributions =<br />
<br />
= Annotation Outreach and User Advocacy Efforts =<br />
<br />
= Other Highlights =</div>Dhowe