Web feeds

2017 Corvallis GOC Meeting Agenda

GO wiki (new pages) - Wed, 01/18/2017 - 10:43

Paul Thomas: Created page with "=Day 1= == 9am Welcome, schedule and logistics == * Remote attendees call in via Bluejeans: https://bluejeans.com/993661940 * Schedule * Introductions ==Overview/Plan for U..."

=Day 1=

== 9am Welcome, schedule and logistics ==
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940
* Schedule
* Introductions


==Overview/Plan for Upcoming Year==
*GO PIs presentation

==Introduction to Ontology Editing (David, Chris)==
*How are new terms added?


[[Category: GO Consortium Meetings]] Paul Thomas
Categories: GO Internal

Ontology meeting 2017-01-19

GO wiki (new pages) - Tue, 01/17/2017 - 07:51

MC: Created page with "Attendees: Regrets: Bluejeans: https://bluejeans.com/164681006 ==Tickets for discussion at this meeting:== See https://github.com/geneontology/go-ontology/projects/1, col..."

Attendees:

Regrets:


Bluejeans: https://bluejeans.com/164681006

==Tickets for discussion at this meeting:==

See https://github.com/geneontology/go-ontology/projects/1, column labeled "Ontology Call January 19, 2017" on the right

#[https://github.com/geneontology/go-ontology/issues/12788 Contact for UniProt annotations]
#[https://github.com/geneontology/go-ontology/issues/12341 Bridging ChEBI to Pro]
#[https://github.com/geneontology/go-ontology/issues/12922 Phosphate versus phophate ion]
#[https://github.com/geneontology/go-ontology/issues/12890 relationship between adenylate cyclase and cAMP biosynthetic process]
#[https://github.com/geneontology/go-ontology/issues/12859 Remove all single-step BP classes]


[[Category:Ontology]]
[[Category:Meetings]] MC
Categories: GO Internal

Ontology editor's conference call minutes Jan-June 2017

GO wiki (new pages) - Tue, 01/17/2017 - 07:47

MC: Created page with "*Jan 12 *Jan 19 Category:Meetings Category:Ontology"

*[[Ontology meeting 2017-01-12|Jan 12]]
*[[Ontology meeting 2017-01-19|Jan 19]]



[[Category:Meetings]]
[[Category:Ontology]] MC
Categories: GO Internal

Manager Call 2017-01-18

GO wiki (new pages) - Thu, 01/12/2017 - 08:01

Vanaukenk: /* GO HelpDesk */

= Bluejeans =
*https://bluejeans.com/588333403

= Agenda =
== GO HelpDesk ==
*If we are going to distribute the shifts during the upcoming year, we need a list of people who will be participating.
*We also need to make sure we have a representative from each curation group on the mailing list so when issues come up they can be tagged.
**For example, right now there is no curator from GOA on the GO help desk mailing list.


[[Category: GO Managers Meetings]] Vanaukenk
Categories: GO Internal

Ontology meeting 2017-01-12

GO wiki (new pages) - Wed, 01/11/2017 - 05:03

David: Created page with "Attendees: Regrets: Bluejeans: https://bluejeans.com/164681006 ==Update from Melanie on EBI editors status== ==Tickets for discussion at this meeting:== See https://git..."

Attendees:

Regrets:


Bluejeans: https://bluejeans.com/164681006

==Update from Melanie on EBI editors status==


==Tickets for discussion at this meeting:==

See https://github.com/geneontology/go-ontology/projects/1, column labeled "Ontology Call January 12, 2017" on the right

#[https://github.com/geneontology/go-ontology/issues/12211 Move editors file to this repo on GitHub]
#[https://github.com/geneontology/go-ontology/issues/12788 Contact for UniProt annotations]
#[https://github.com/geneontology/go-ontology/issues/12880 Protege documentation needs updating and ID issue]
#[https://github.com/geneontology/go-ontology/issues/12808 Ghost relations in the OBO file]
#[https://github.com/geneontology/go-ontology/issues/12341 Bridging ChEBI to Pro]
#[https://github.com/geneontology/go-ontology/issues/12811 Merge directly_activates/inhibits relations into directly_positively/negatively_regulates]

[[Category:Ontology]]
[[Category:Meetings]] David
Categories: GO Internal

Ontology editor's conference call minutes July-Dec 2016

GO wiki (new pages) - Tue, 01/10/2017 - 06:31

David: Created page with "*Jul 07 Cancelled *Jul 14 Cancelled *Jul 21 *Ontology meeting 2016-07-28|Jul..."

*[[Ontology meeting 2016-07-07|Jul 07]] Cancelled
*[[Ontology meeting 2016-07-14|Jul 14]] Cancelled
*[[Ontology meeting 2016-07-21|Jul 21]]
*[[Ontology meeting 2016-07-28|Jul 28]]
*[[Ontology meeting 2016-08-04|Aug 4]] Cancelled
*[[Ontology meeting 2016-08-11|Aug 11]] Cancelled
*[[Ontology meeting 2016-08-18|Aug 18]]
*[[Ontology meeting 2016-08-25|Aug 25]]
*[[Ontology meeting 2016-09-01|Sep 1]] Cancelled due to Hinxton LEGO/Noctua workshop
*[[Ontology meeting 2016-09-08|Sep 8]]
*[[Ontology meeting 2016-09-15|Sep 15]]
*[[Ontology meeting 2016-09-22|Sep 22]]
*[[Ontology meeting 2016-09-29|Sep 29]]
*[[Ontology meeting 2016-10-06|Oct 6]]
*[[Ontology meeting 2016-10-13|Oct 13]]
*[[Ontology meeting 2016-10-20|Oct 20]]
*[[Ontology meeting 2016-10-27|Oct 27]]
*[[Ontology meeting 2016-11-03|Nov 3]] Cancelled due to traveling to GOC meeting
*[[Ontology meeting 2016-11-10|Nov 10]]
*[[Ontology meeting 2016-11-17|Nov 17]]
*[[Ontology meeting 2016-11-24|Nov 24]] Thanksgiving
*[[Ontology meeting 2016-12-01|Dec 1]]
*[[Ontology meeting 2016-12-08|Dec 8]]
*[[Ontology meeting 2016-12-15|Dec 15]]
*[[Ontology meeting 2016-12-22|Dec 22]]


[[Category:Meetings]]
[[Category:Ontology]] David
Categories: GO Internal

LEGO Discussion Rota

GO wiki (new pages) - Mon, 01/09/2017 - 11:42

Vanaukenk:

*We would like to reserve the second annotation call of each month for discussion of LEGO models.
*The format will be two 30-minutes presentations.
*Please sign-up here for a time slot.

{| border="1" cellpadding="5" cellspacing="0"
!Date!!Presenter 1!!Link to Model!!Presenter 2!!Link to Model
|-
|January 24 ||||||||
|-
|February 21 ||||||||
|-
|March 28 ||No call - ISB Meeting|| No call - ISB Meeting || No call - ISB Meeting || No call - ISB Meeting
|-
|April 25 ||||||||
|-
|May 23 || || ||||
|-
|}

[[Category:Annotation Working Group]] Vanaukenk
Categories: GO Internal

Annotation Conf. Call 2017-01-10

GO wiki (new pages) - Wed, 01/04/2017 - 11:59

Vanaukenk: Created page with "=Bluejeans= *https://bluejeans.com/993661940 *to join via phone: enter Meeting ID 993661940 after dialing in **from US: +1.408.740.7256 or +1.888.240.2560 **from UK: +44.203.6..."

=Bluejeans=
*https://bluejeans.com/993661940
*to join via phone: enter Meeting ID 993661940 after dialing in
**from US: +1.408.740.7256 or +1.888.240.2560
**from UK: +44.203.608.5256
**from Switzerland: +41.81.588.0256

=Agenda=

=Minutes=


[[Category: Annotation Working Group]] Vanaukenk
Categories: GO Internal

Annotation Call 2017 Minutes

GO wiki (new pages) - Wed, 01/04/2017 - 10:56

Vanaukenk:

* [[Annotation Conf. Call 2017-01-10]]
* [[Annotation Conf. Call 2017-01-24]]
* [[Annotation Conf. Call 2017-02-14]]
* [[Annotation Conf. Call 2017-02-28]]
* [[Annotation Conf. Call 2017-03-14]]
* [[Annotation Conf. Call 2017-03-28]] No Meeting, overlaps with [http://med.stanford.edu/biocuration.html Biocuration 2017]
* [[Annotation Conf. Call 2017-04-11]]
* [[Annotation Conf. Call 2017-04-25]]
* [[Annotation Conf. Call 2017-05-09]]
* [[Annotation Conf. Call 2017-05-23]]
* [[Annotation Conf. Call 2017-06-13]]
* [[Annotation Conf. Call 2017-06-27]]
* [[Annotation Conf. Call 2017-07-11]]
* [[Annotation Conf. Call 2017-07-25]]
* [[Annotation Conf. Call 2017-08-08]]
* [[Annotation Conf. Call 2017-08-22]]
* [[Annotation Conf. Call 2017-09-12]]
* [[Annotation Conf. Call 2017-09-26]]
* [[Annotation Conf. Call 2017-10-10]]
* [[Annotation Conf. Call 2017-10-24]]
* [[Annotation Conf. Call 2017-11-14]]
* [[Annotation Conf. Call 2017-11-28]]
* [[Annotation Conf. Call 2017-12-12]]


[[Category: Annotation Working Group]] Vanaukenk
Categories: GO Internal

Manager Call 2017-01-04

GO wiki (new pages) - Tue, 01/03/2017 - 13:33

Vanaukenk: Created page with "=Bluejeans URL= *https://bluejeans.com/588333403 =Agenda= =Minutes= Category: GO Managers Meetings"

=Bluejeans URL=
*https://bluejeans.com/588333403

=Agenda=

=Minutes=

[[Category: GO Managers Meetings]] Vanaukenk
Categories: GO Internal

Manager Call 2017 Rota

GO wiki (new pages) - Wed, 12/21/2016 - 09:19

David: Created page with "{| border="1" cellpadding="5" cellspacing="0" !Date!!Agenda!!Minutes |- |January 4||Kimberly||Chris |- |January 18||Chr..."

{| border="1" cellpadding="5" cellspacing="0"
!Date!!Agenda!!Minutes
|-
|[[Manager Call 2017-01-04|January 4]]||Kimberly||Chris
|-
|[[Manager Call 2017-01-18|January 18]]||Chris|| Huaiyu
|-
|[[Manager Call 2017-02-01|February 1]]||Huaiyu||Pascale
|-
|[[Manager Call 2017-02-15|February 15]]||Pascale||Moni
|-
|[[Manager Call 2017-03-01|March 1]]||Moni||David
|-
|[[Manager Call 2017-03-15|March 15]]||David||Kimberly
|-
|[[Manager Call 2017-04-05|April 5]]||Kimberly||Chris
|-
|[[Manager Call 2017-04-19|April 19]]||Chris||Huaiyu
|-
|[[Manager Call 2017-05-03|May 3]]||Huaiyu||Pascale
|-
|[[Manager Call 2017-05-17|May 17]]||Pascale||Moni
|-
|[[Manager Call 2017-06-07|June 7]]||Moni||David
|-
|[[Manager Call 2017-06-21|June 21]]||David||Kimberly
|-
|[[Manager Call 2017-07-05|July 5]]||Kimberly||Chris
|-
|[[Manager Call 2017-07-19|July 19]]||Chris||Huaiyu
|-
|[[Manager Call 2017-08-02|August 2]]||Huaiyu||Pascale
|-
|[[Manager Call 2017-08-16|August 16]]||Pascale||Moni
|-
|[[Manager Call 2017-09-06|September 6]]||Moni||David
|-
|[[Manager Call 2017-09-20|September 20]]||David||Kimberly
|-
|[[Manager Call 2017-10-04|October 4]]||Kimberly||Chris
|-
|[[Manager Call 2017-10-18|October 18]]||Chris||Huaiyu
|-
|[[Manager Call 2017-11-01|November 1]]||Huaiyu||Pascale
|-
|[[Manager Call 2017-11-15|November 15]]||Pascale||Moni
|-
|[[Manager Call 2017-12-06|December 6]]||Moni||David
|-
|[[Manager Call 2017-12-20|December 20]]||David||Kimberly

[[Category:GO Managers Meetings]] David
Categories: GO Internal

Ontology meeting 2016-12-22

GO wiki (new pages) - Wed, 12/21/2016 - 04:27

David:

Attendees:

Regrets: Paola, Melanie


Bluejeans: https://bluejeans.com/164681006


==Tickets for discussion at this meeting:==

See https://github.com/geneontology/go-ontology/projects/1, column labeled "Ontology Call December 22, 2016" on the right

#[https://github.com/geneontology/go-ontology/issues/12880 Protege documentation needs updating and ID issue]
#[https://github.com/geneontology/go-ontology/issues/12811 Merge directly_activates/inhibits relations into directly_positively/negatively_regulates.]
#[https://github.com/geneontology/go-ontology/issues/12341 Bridging ChEBI to Pro]
#[https://github.com/geneontology/go-ontology/issues/12808 Ghost relations in the obo-file]


[[Category:Ontology]]
[[Category:Meetings]] David
Categories: GO Internal

SGD December 2016

GO wiki (new pages) - Mon, 12/19/2016 - 12:54

Hdrabkin: GO Consortium

= Overview: =
= 1. Staff: =
PI: Mike Cherry

Biocurators: Rob Nash (0.5 FTE), Edith Wong (0.15 FTE), Stacia Engel (0.25 FTE)

Developers: Shuai Weng (0.25 FTE), Kalpana Karra (0.1 FTE)

Systems Administrators: Stuart Miyasato (0.5 FTE), Matt Simison (0.25 FTE)


Total 2 FTE funded by GOC NIHGRI grant


= 2. Annotation Progress =

{| style="border-spacing:0;"
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"|
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total annotations by end of 2015
| style="border:0.0069in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Annotations added 2016

|-
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Genes with manual annotations
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 20641
| style="border:0.0069in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 677

|-
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Papers with manual annotations
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 14509
| style="border:0.0069in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 342

|-
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Manual annotations
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 44460
| style="border:0.0069in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 1146

|-
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Genes with HTP annotations
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 5091
| style="border:0.0069in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 1229

|-
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Papers with HTP annotations
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 121
| style="border:0.0069in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 1

|-
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| HTP annotations
| style="border-top:0.0069in solid #000000;border-bottom:0.0069in solid #000000;border-left:0.0069in solid #000000;border-right:none;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 5797
| style="border:0.0069in solid #000000;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 1400

|}
'''3. Methods and strategies for annotation'''

''(please note % effort on literature curation vs. computational annotation methods)''


# ''Literature curation: 95%''

Literature curation continues to be the major focus of our annotation efforts.


# ''Computational annotation strategies:'' ''5%''

1. Yeast genes manually curated by other groups are brought in electronically from GOA with their associated evidence codes and the originating group acknowledged in the source.


2. Electronic annotations for yeast genes based on GO mapping to InterPro, Enzyme Commission and Swiss-Prot keywords, are brought in electronically with IEA evidence code from GOA. Annotations from GOA for all categories are updated weekly.


# ''Priorities for annotation: ''Annotation priorities are currently set via our ‘Fast Track/Author Response’ system in which we first triage papers for potential GO information, then contact authors of those papers to ask them specific questions about relevant genes and results.

'''4. Presentations and Publications'''


a.'' Papers with substantial GO content:''


''N/A''


b. ''Presentations including Talks and Tutorials and Teaching''


''1. ''SGD Webinar: ''SGD: A Catalyst for Biological Research [https://www.youtube.com/watch?v=57VPZYdttzY https://www.youtube.com/watch?v=57VPZYdttzY]


''2. SGD Webinar: Predicting Chemotherapy Targets in YeastMine''

[https://www.youtube.com/watch?v=-Qefg1gm7ho https://www.youtube.com/watch?v=-Qefg1gm7ho]


''3. SGD Webinar: Exploring Expression Datasets & Coexpressed Genes w/SPELL''

[https://www.youtube.com/watch?v=NAUOx1BxmJ8 https://www.youtube.com/watch?v=NAUOx1BxmJ8]


''4. SGD Webinar: Homology and Disease Data at SGD [https://www.youtube.com/watch?v=PI-nuN8uLdI https://www.youtube.com/watch?v=PI-nuN8uLdI]


''5. SGD Help video: YeastMine Scenario - Finding Uncharacterized Subunits of the Mitochondrial Ribosome''

[https://www.youtube.com/watch?v=AoVfmaZmTK4 https://www.youtube.com/watch?v=AoVfmaZmTK4]


''6. SGD Help video: Uploading Gene Lists to JBrowse''

[https://www.youtube.com/watch?v=HUI-of9IYXo https://www.youtube.com/watch?v=HUI-of9IYXo]


''7. SGD Help video: Exploring Expression Datasets with SPELL''

[https://www.youtube.com/watch?v=PnYD1D2ZjWU https://www.youtube.com/watch?v=PnYD1D2ZjWU]


''8. SGD Help video: Introduction to SGD's Faceted Search''

[https://www.youtube.com/watch?v=hw4LZJJSHMw&t=10s https://www.youtube.com/watch?v=hw4LZJJSHMw]


''9. SGD Help video: Finding Human Homology & Disease Information''

[https://www.youtube.com/watch?v=hzBHJZILkIE https://www.youtube.com/watch?v=hzBHJZILkIE]


''10. Senior Biocuration Scientist Rob Nash presented a tutorial at the [http://meetings.cshl.edu/courses.aspx?course=c-yeas&year=16 Yeast Genetics and Genomics] course at CSHL in late July. He demonstrated the use of YeastMine and how to navigate through SGD's website, including the use of GO annotations provided by SGD.''


c.'' Poster presentations''


''N/A''


'''5. Other Highlights:'''


'''A. Ontology Development Contributions:'''


SGD curators requested new terms and participated in ontology-related discussions periodically throughout the past year on an as-needed basis.


=== B. Annotation Outreach and User Advocacy Efforts: ===
Both Edith Wong and Rob Nash continue to serve on the GO-help rota.


= C. Other Highlights: =
Stacia Engel served as a beta tester for the Noctua annotation tool, and participated in weekly development calls.


Edith Wong and Stacia Engel attended the Noctua workshop at USC on November 7, 2016. Hdrabkin
Categories: GO Internal

WormBase December 2016

GO wiki (new pages) - Mon, 12/19/2016 - 11:39

Vanaukenk: /* Annotation Progress */

'''The data is currently for 2015. Report is in progress.'''

Overview:

= Staff =

Person, Group [Effort, Funding]

Paul Sternberg, PI, WormBase, GO [8%; 0% funded by GOC]

Juancarlos Chan, Developer, WormBase [25%; 25% funded by GOC]

Sibyl Gao, Developer, WormBase [5%; 0% funded by GOC]

Kevin Howe, Project Lead, WormBase - EBI [5%; 0% funded by GOC]

Raymond Lee, Curator, WormBase [10%; 0% funded by GOC]

Yuling Li, Developer, Textpresso [30%; 25% funded by GOC]

Jane Lomax, Curator, WormBase ParaSite [10%; 0% funded by GOC]

Hans Michael Mueller, Project Lead, Textpresso [75%; 50% funded by GOC]

Daniela Raciti, Curator [10%; 0% funded by GOC]

Kimberly Van Auken, Curator, Co-Manager, Annotation Working Group [100%; 75% funded by GOC]

= Annotation Progress =

'''WormBase GO Annotation Statistics as of December 20, 2016'''

Manual annotation statistics are summarized in Tables 1 - 3.

Total number of unique manual annotations: 39290 (+43.3% from 2014)

Total number of genes with manual annotations: 6762 (+44.2% from 2014)

'''Table 1: Summary of ''C. elegans'' Manual Biological Process Annotations'''

'''Numbers refer to total number of annotations; annotations in parentheses represent annotations with extensions.'''
{| class="wikitable" style="text-align:center"
{| border="1" cellpading="2"
|-
! Annotation Group !! IMP !! IGI !! IDA !! ISS !! TAS !! IEP !! IPI !! IC !! NAS !! ISM !! ND !! IBA
|-
! WormBase
| 7649 (367) || 3104 (78) || 1105 (23) || 324 (1) || 111 || 285 (58) || 51 || 51 (10) || 32 || 2 || 3 || 0
|-
!UniProt
| 801 (229) || 155 (94) || 126 (9) || 190 || 25 (2) || 14 || 2 (2) || 5 || 104 || 0 || 65 || 0
|-
!CACAO
| 18 || 1 || 3 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
!GOC
| 59 || 14 || 261 || 122 || 17 || 0 || 4 || 2 || 10 || 0 || 0 || 379
|-
!BHF-UCL
| 11 || 0 || 0 || 0 || 0 || 4 || 0 || 0 || 0 || 0 || 0 || 0
|-
!MGI
| 5 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
!HGNC
| 0 || 0 || 0 || 4 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
!GO_Central
| 2 || 0 || 0 || 4 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 8119
|-
!ParkinsonsUK-UCL
| 10 (4) || 5 (2) || 9 || 2 (1) || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
!Totals
| 8555 (600) || 3279 (174) || 1504 (32) || 646 (2) || 153 (2) || 303 (58) || 57 (2) || 58 (10) || 146 || 2 || 68 || 8498
|}



'''Table 2: Summary of ''C. elegans'' Molecular Function Annotations'''

'''Numbers refer to total number of annotations; annotations in parentheses represent annotations with extensions.'''
{| class="wikitable" style="text-align:center"
{| border="1" cellpading="2"
|-
! Annotation Group !! IMP !! IGI !! IDA !! ISS !! TAS !! IPI !! IC !! NAS !! ISM !! ND !! IBA !! ISO
|-
! WormBase
| 152 (6) || 33 || 1658 (188) || 650 (1) || 47 || 1298 (2) || 15 || 5 || 4 || 63 || 0 || 2
|-
!IntAct
| 0 || 0 || 0 || 0 || 0 || 1989 (52) || 0 || 0 || 0 || 0 || 0 || 0
|-
!UniProt
| 37 (1) || 2 || 119 (2) || 181 || 21 || 272 (3) || 4 || 51 || 0 || 126 || 0 || 0
|-
!CACAO
| 1 || 0 || 7 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
!GO_Central
| 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 5531 || 0
|-
!HGNC
| 0 || 0 || 0 || 2 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
!ParkinsonsUK-UCL
| 0 || 0 || 4 || 0 || 0 || 2 (2) || 0 || 0 || 0 || 0 || 0 || 0
|-
!Totals
| 190 (7) || 35 || 1784 (190) || 833 (1) || 68 || 3561 (59) || 19 || 56 || 4 || 189 || 5531 || 2
|}


'''Table 3: Summary of ''C. elegans'' Cellular Component Annotations'''

'''Numbers refer to total number of annotations; annotations in parentheses represent annotations with extensions.'''
{| class="wikitable" style="text-align:center"
{| border="1" cellpading="2"
|-
! Annotation Group !! IMP !! IGI !! IDA !! ISS !! TAS !! IPI !! IC !! NAS !! ISM !! ND !! IBA
|-
! WormBase
| 9 (3) || 0 || 5818 (738) || 345 || 26 || 140 || 46 || 6 || 4 || 8 || 0
|-
!GO_Central
| 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 4927
|-
!UniProt
| 24 (9) || 1 || 246 (31) || 196 || 16 || 0 || 19 || 50 || 0 || 118 || 0
|-
!GOC
| 36 || 11 || 22 || 6 || 0 || 0 || 3 || 0 || 0 || 0 || 47
|-
!MGI
| 0 || 0 || 14 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
!HGNC
| 0 || 0 || 0 || 8 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
! BHF-UCL
| 0 || 0 || 7 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
! Reactome
| 0 || 0 || 0 || 0 || 5 || 0 || 0 || 0 || 0 || 0 || 0
|-
!CACAO
| 0 || 0 || 3 || 0 || 0 || 0 || 0 || 0 || 0 || 0 || 0
|-
!Totals
| 69 (12) || 12 || 6110 (769) || 555 || 47 || 140 || 68 || 56 || 4 || 126 || 4974
|}


'''Table 4: Summary of ''C. elegans'' Computational Annotations'''

Based on WormBase Release WS250

Total number of genes with Phenotype2GO-based Annotation: 5,628

Total number of genes with IEA-based Annotation: 11,342

Total number of genes with only IEA-based Annotation: 6,075

Total number of genes with only non-IEA-based Annotation: 1,182

{| class="wikitable" style="text-align:center"
{| border="1" cellpading="2"
|-
! Type of Annotation !! IEA
|-
!Phenotype2GO Mappings - WormBase
| 36,708
|-
!IEA/InterPro2GO - WormBase
| 25,011
|-
|}


[[Category:Reports]]

= Methods and strategies for annotation =

==Curation methods==

===Literature curation===

Curation of the primary literature continues to be the major focus of our manual annotation efforts.

Over the past year, WormBase has begun a topic-based approach to curation in which curators focus curation efforts on one or more biological topics, or processes, for each release cycle. Topics over the past year have included the endoplasmic reticulum and mitochondrial unfolded protein responses, innate immunity and defense response, and Wnt signaling pathways (see below).

===Semi-automated curation using the Textpresso information retrieval system===

We also employ the Textpresso information retrieval system for semi-automated curation of GO Cellular Component and Molecular Function annotations.

===Computational annotation strategies===

Our computational annotation strategies include mapping genes to GO terms using InterPro domains performed as part of the WormBase build cycle, as well as computational predictions made via the UniProtKB pipeline, including keyword mappings and UniRule mapping.
Also as part of the WormBase build cycle, we map genes to Biological Process terms based upon mappings between terms in the Worm Phenotype Ontology (WPO). Beginning with the WS246 WormBase release, these Phenotype2GO-based annotations include phenotypes based upon genetic variations as well as RNAi experiments. Results from automated methods are generated anew with each WormBase database build to reflect any changes in the underlying reference genome sequence and/or gene models.

==Curation strategies==

===Priorities for annotation===

Selection of genes for annotation is guided by several criteria:

*Annotation of gene sets involved in specific biological processes as part of the LEGO working group and WormBase's coordinated topic-based approach to curation
**Topics annotated to date:
***Unfolded Protein Response (ER and mitochondrial)
***innate immune response
***defense response to pathogen (fungal as well as Gram-negative and Gram-positive bacteria)
***Wnt signaling
***RNAi-mediated behavioral response to odor
***anchor cell invasion (in progress)
*Genes identified in Textpresso-based curation pipelines
*Re-annotation of genes affected by changes to the ontology, e.g. cilia biology, ubiquitination, enzyme regulator activities
*Publication of newly characterized genes

= Presentations and Publications =
==Papers with substantial GO content==
*Gene Ontology Consortium: going forward. Gene Ontology Consortium. Nucleic Acids Research 2015 Jan;43(Database issue):D1049-56. doi: 10.1093/nar/gku1179, PMID:25428369

== Presentations including Talks and Tutorials and Teaching ==
*Kimberly van Auken: Gene Ontology (GO): Finding GO annotations and performing enrichment analysis. 2015 International C. elegans Meeting, UCLA, Los Angeles, CA, June 25 and 27, 2015.

== Poster presentations ==
*Textpresso Central: A System for Integratng Full Text Literature Curation with Diverse Curation Platforms. Kimberly Van Auken, Yuling Li, Hans-Michael Muller, and Paul Sternberg. BioCreative Workshop V, September 9-11, 2015. cicCartuja Research Center, Seville, Spain.

=Other Highlights=

== Ontology Development Contributions ==
*Ontology Contributions and Discussions in 2015:
**amino acid transport and transporter terms
**ascaroside binding
**chitin-based cuticle extracellular matrix
**hemidesmosome
**modulation of age-related behavioral decline
**posttranscriptional regulation of synapse organization
**numerous TermGenie requests

== Annotation Outreach and User Advocacy Efforts ==
* Kimberly Van Auken continues to serve on the GO-help rota.
* Kimberly Van Auken and Dmitry Snitnikov (MGI) are working with a group at Peking University to incorproate human lncRNA annotations into the GOC.

== Annotation Advocacy ==
* Kimberly Van Auken participated in the LEGO working group as an alpha tester of the Noctua software and participated in the Geneva LEGO workshop, December 8-10, 2015.
* Starting in October, 2015, Kimberly Van Auken and David Hill (MGI) are now Annotation Advocacy Co-Managers.

== Other Highlights ==
=== WormBase Data Models and Software ===
*WormBase GO Annotation Model - Starting with WS248, we have incorporated a new GO annotation model into WormBase. The model allows for full incorporation of annotation extension data into WormBase, as well as additional annotation details and new IEA annotations from the UniProt-GOA group.
*WormBase GO Annotation Display - To support the new GO annotation model, we revised the GO annotation web display on WB gene pages. The web display now has two views that users can select: Summary and View. The summary view allows users to see the GO ID, GO term, and annotation extension. The full view additionally provides the evidence code, reference, contributor, and supporting evidence in the With/From column of the gene association file.

===Text Mining and Textpresso Central===
*Monica McAndrews (MGI), Kimberly Van Auken, and Yuling Li are collaborating on a document classification pipeline to help MGI identify papers suitable for curation. Using training and testing papers supplied by MGI, we have developed an SVM classifier to distinguish mouse from non-mouse papers. We are beginning steps to put this pipeline into production.
*Hans-Michael Muller, Yuling Li, and Kimberly Van Auken have developed the Textpresso Central that enables curators to perform full text literature searches and then view the search results in the context of the paper, annotate text, and send those annotations to the Protein2GO tool hosted by the UniProt group at the EBI. The system is designed with the intent to empower the user to perform as many operations on a literature corpus or a particular paper as possible. It uses state-of-the-art software packages and frameworks such as the Unstructured Information Management Architecture (http://uima.apache.org), Lucene (http://lucene.apache.org), and Wt (http://www.webtoolkit.eu/wt). The corpus of papers can be build from fulltextarticles that are available in PDF format (http://en.wikipedia.org/wiki/Portable\_Document\_Format) or NXML (http://dtd.nlm.nih.gov/). An extension for articles published in HTML (http://en.wikipedia.org/wiki/HTML) is planned.

Back to http://wiki.geneontology.org/index.php/Progress_Reports

[[Category: Reports]] Vanaukenk
Categories: GO Internal

DictyBase December 2016

GO wiki (new pages) - Mon, 12/19/2016 - 09:32

Hdrabkin: GO Consortium

= Mod NamedictyBaseDecember , 2016 =
= Overview: =
= 1. Staff: =
PI: Rex Chisholm

Annotators: Petra Fey*, Robert Dodson

Developer: Siddhartha Basu


<nowiki>* funded</nowiki>

All dictyBase staff contribute to GO activities. This is currently a total of 3 FTE positions. Of these we receive sufficient funding from the GO grant to support 0.45 FTEs.


= 2. Annotation Progress =
The total and non-IEA annotation numbers include annotations that are not from dictyBase, with most of these from the PAINT project and a few from INTACT and SwissProt. At this point we cannot easily query them by source; however, the experimental annotations are nearly all from dictyBase and the indicated annotation extensions have been exclusively annotated by dictyBase curators (Table 3).


'''Table 1: Number of Annotations'''


{| style="border-spacing:0;"
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"|
| style="border-top:0.0139in solid #6d6d6d;border-bottom:0.0139in solid #6d6d6d;border-left:none;border-right:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Dec2015'''
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Dec2016'''
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''

|-
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Total number of annotations'''
| style="border-top:0.0139in solid #6d6d6d;border-bottom:0.0139in solid #6d6d6d;border-left:none;border-right:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 69130
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 68587
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| - 0.8%

|-
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Function
| style="border-top:0.0139in solid #6d6d6d;border-bottom:0.0139in solid #6d6d6d;border-left:none;border-right:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 22915
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 23971
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| + 4.6%

|-
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Process
| style="border-top:0.0139in solid #6d6d6d;border-bottom:0.0139in solid #6d6d6d;border-left:none;border-right:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 24209
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 21283
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| - 12% *

|-
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Component
| style="border-top:0.0139in solid #6d6d6d;border-bottom:0.0139in solid #6d6d6d;border-left:none;border-right:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 22006
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 23333
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| + 6%

|}
'''Table 2: Number of non-IEA Annotations'''


{| style="border-spacing:0;"
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"|
| style="border-top:0.0139in solid #6d6d6d;border-bottom:0.0139in solid #6d6d6d;border-left:none;border-right:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Dec2015'''
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Dec2016'''
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''

|-
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Total number of annotations'''
| style="border-top:0.0139in solid #6d6d6d;border-bottom:0.0139in solid #6d6d6d;border-left:none;border-right:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 29547
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 31081
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| + 5.2%

|-
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Function
| style="border-top:0.0139in solid #6d6d6d;border-bottom:0.0139in solid #6d6d6d;border-left:none;border-right:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 7572
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 8777
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| + 15.9%

|-
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Process
| style="border-top:0.0139in solid #6d6d6d;border-bottom:0.0139in solid #6d6d6d;border-left:none;border-right:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 13267
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 12068
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| - 9% *

|-
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Component
| style="border-top:0.0139in solid #6d6d6d;border-bottom:0.0139in solid #6d6d6d;border-left:none;border-right:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 8708
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 10236
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| + 17.5%

|}
'''Table 3: Additional Numbers'''


{| style="border-spacing:0;"
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"|
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Dec2015'''
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''Dec2016'''
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| '''% Change'''

|-
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Total EXP annotations
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 7049
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 7428
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| + 5.4%

|-
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| Annotation extensions
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 367
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| 928
| style="border:0.0139in solid #6d6d6d;padding-top:0in;padding-bottom:0in;padding-left:0.075in;padding-right:0.075in;"| + 153% **

|}
<nowiki>* Nearly 3,000 process annotations from a single paper using the RCA evidence code have been deleted, prompted by researcher request and new internal giudelines for high throuput annotations; improving annotation quality</nowiki>.


<nowiki>** Not yet available in the current dictyBase, will be release in 2017.</nowiki>


'''3. Methods and strategies for annotation'''

''(please note % effort on literature curation vs. computational annotation methods)''


# ''Literature curation: ''Gene Ontology annotation is integral to the curation process at dictyBase. Annotation of gene products to GO terms is done concurrently with curation of literature, strains, phenotypes, and general nomenclature. Both curators work to annotate gene products of the ''Dictyostelium'' genom''e''. 95% is currently dedicated to manual annotations from the literature.

We use the Protein2GO tool from the EBI to annotate GO for ''Dictyostelium''. We re-import annotations monthly from GOA back into dictyBase, including electronic annotations. We currently still append our GO annotations to RNAs and send the GAF file to the GO consortium. Protein2GO allows curators to add annotation extensions, which will be imported into an upgraded dictyBase within the next year.


# ''Computational annotation strategies:'' Importing annotations monthly from GOA into dictyBase, including electronic annotations.

# ''Priorities for annotation:'' Highest priority is literture curation. GO annotations are added during ''Dictyostelium'' literature curation, along with strain, phenotype, nomenclature and gene product information. We focus on new papers but go back to older papers when cited and containing important functional data for GO annotation.

'''4. Presentations and Publications'''


a. Basu S, Fey P, Jimenez-Morales D, Dodson RJ, Chisholm RL.dictyBase 2015: Expanding data and annotations in a new software environment. Genesis. 2015 Aug;53(8):523-34.


b. Poster at the International Biocurator Meeting in Geneva, April, 2016. The Future of Curation at dictyBase, P. Fey, S. Basu, R. Dodson, R. Chisholm; A large part showed annotation extension representation in the new dictyBase environment.


'''5, Other Highlights:'''


'''A. Ontology Development Contributions:'''

Both dictyBase curators work to improve the GO with GO editors and other curators in the field, and contribute to discussions in the bi-weekly annotation calls and on GitHub. When necessary, they use TermGenie or GitHub to create new GO terms or improve exiting terms and GO structure.

In the past year, we added '''10 new GO terms'''. Some of these new terms involved renaming and/or '''updating 5 existing terms''', and one resulted from '''restructuring''' the graph for ‘fruiting body development‘. One additional issue involves taxon restrictions to ‘social behavior’, which is still under discussion. All dictyBase issues can be viewed here:

https://github.com/geneontology/go-ontology/issues?q=is%3Aclosed+label%3AdictyBase

=== B. Annotation Outreach and User Advocacy Efforts: ===
: Petra contributes to the GO Help Desk and provides all GO help to dictyBase users as needed.

= C. Other Highlights: =
: Petra attended 2 LEGO workshops at recent GO meetings and modeled Dicty annotations with David, Kimberly and Paul in fall 2016. Curators will now regularly add LEGO models for Dicty data. With the emergence of LEGO annotations in OWL format we have therefore started exploring options for storing our GO annotations in a graph database in the near future. As documented here https://github.com/geneontology/noctua-models#availability , first we will convert our GAF to owl format and then store those owl files in a suitable graph database. Hdrabkin
Categories: GO Internal

Manager Call 2016-12-21

GO wiki (new pages) - Mon, 12/19/2016 - 03:53

Paola: Created page with "=Bluejeans URL= *https://bluejeans.com/588333403 '''Agenda:''' Paola Roncaglia '''Minutes:''' David Hill '''Present:''' '''Regrets:''' Melanie Category:GO Managers Me..."

=Bluejeans URL=
*https://bluejeans.com/588333403

'''Agenda:''' Paola Roncaglia

'''Minutes:''' David Hill

'''Present:'''

'''Regrets:''' Melanie


[[Category:GO Managers Meetings]] Paola
Categories: GO Internal

FlyBase December 2016

GO wiki (new pages) - Mon, 12/19/2016 - 02:23

Hla28: /* 1. Staff working on GOC tasks */

=== 1. Staff working on GOC tasks ===

Helen Attrill (GO curator/literature curator) 0.3 FTE

Giulia Antonazzo (GO curator/literature curator) 0.1 FTE

Alix Rey (GO curator/literature curator) 0.2 FTE

Steven Marygold (Literature curator) 0.1 FTE

Gillian Millburn (Literature curator) 0.2 FTE

Kathleen Falls (Developer)

Josh Goodman (Web Developer)

=== 2. Annotation progress ===

==== Table showing progress in annotating Drosophila localized genes Nov 2014 - Nov 2015 (FB2014_06 - FB2015_05) ====

{| border="1"
|-
!
! Nov 14
! Nov 15
! % change
! % of total genes
|-
| Total number of localized genes (excluding pseudogenes) || 17382 || 17406 || +0.14% ||
|-
| Localized genes with no GO annotation || 4692 || 4449 || -5.0% || 25.6%
|-
| Localized genes with any GO annotation || 12690 || 12947 || +2.0% || 74.4%
|-
| Localized genes with 1 or more term based on experimental evidence || 6095 || 9727 || +59.6% || 55.9%
|-
| Localized genes with other non-IEA, non-ND evidence || 3746 || 3830 || +2.2% || 22.0%
|-
| Localized genes with only IEA evidence || 1074 || 991 || -7.7% || 5.7%
|-
| Localized genes with only ND evidence || 1775 || 1840 || +3.7% || 10.6%
|-
|}

==== Table showing total annotation progress for localized genes Nov 2014 - Nov 2015 (FB2014_06 - FB2015_05)====

{| border="1"
|-
!
! November 2014
! November 2015
! % change
|-
| GO Biological Process (BP) annotations || 46245 (9471 genes) || 48093 (8360 genes) || +4.0% (+2.6%)
|-
| GO Molecular Function (MF) annotations || 27872 (9037 genes) || 28273 (9121 genes) || +1.4% (+0.9%)
|-
| GO Cellular Component (CC) annotations || 22911 (7959 genes) || 24219 (8360 genes) || +5.7% (+5.0%)
|-
| Total annotations for localized genes || 97028 || 100585 || +3.7%
|-
|} Hla28
Categories: GO Internal

GOA December 2016

GO wiki (new pages) - Thu, 12/15/2016 - 08:15

Penelope: Created page with "'''UniProt Gene Ontology Annotation (GOA) Project Summary 2016''' '''Overview''' EMBL-EBI has been a member of the GO Consortium since 2001. One of the major activities is t..."

'''UniProt Gene Ontology Annotation (GOA) Project Summary 2016'''

'''Overview'''

EMBL-EBI has been a member of the GO Consortium since 2001. One of the major activities is the UniProt Gene Ontology Annotation project which is delivered by staff from the Protein Function Content and Development teams. The core UniProt-GOA project staff are primarily responsible for supplying the GO Consortium with manual and electronic GO annotations to the human proteome. UniProt-GOA staff not only create manual annotations, but coordinate and check the integration of GO annotations from other curation efforts at the EMBL-EBI (including from InterPro, IntAct and Reactome). The UniProt-GOA dataset is supplemented with manual annotations from 35 annotating groups, including all members of the GO Consortium, as well as a number of external groups which produce relevant functional data. Nine electronic annotation pipelines are incorporated into the UniProt-GOA dataset, which provide the vast majority of annotations for non-model organism species. UniProt-GOA is therefore able to consolidate multiple sources of specialised knowledge, ensuring the UniProt-GOA resource remains a key up-to-date reference for a large number of research communities.

In addition, all UniProt Knowledgebase (UniProtKB) curators in the Protein Function Content team at EMBL-EBI, SIB Swiss Institute of Bioinformatics (SIB) and Protein Information Resource (PIR) are actively involved in curating UniProtKB entries with Gene Ontology terms during the UniProt literature curation process, providing both high-quality manual GO annotations in addition to their contributions to electronic GO annotation pipelines. The multi-species nature of UniProtKB means that the GO Annotation project is able to assist in the GO curation of proteins from around 675,000 taxonomic groups.

'''Staff from the Protein Function Content and Development teams at EMBL-EBI who deliver the GOA project:'''

Claire O'Donovan, Protein Function Content Team Leader (Consortium PI)

Maria J. Martin Protein Function Development Team Leader (Senior Personnel)

Michele Magrane Annotation Coordinator (with responsibility for GOA since September 2016)

Melanie Courtot, GO/GOA Project Leader (until September 2016)

George Georghiou GOA curator

Penelope Garmiri GOA curator

Tony Sawford* GOA programmer

Aleksandra Shypitsyna* GOA curator

Tony Wardell GOA programmer

* Funded partially by GOC.

UniProt contributors (EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, UK; SIB, Geneva, Switzerland; and PIR, Washington DC): Ioannis Xenarios, Lydie Bougueleret, Ghislaine Argoud-Puy, Andrea Auchinchloss, Kristian Axelsen, Marie-Claude Blatter, Emmanuel Boutet, Lionel Breuza, Alan Bridge, Elizabeth Coudert, Isabelle Cusin, Paula Duek Roggli, Anne Estreicher, Livia Famiglietti, Marc Feuermann, Arnaud Gos, Nadine Gruaz-Gumowski, Ursula Hinz, Chantal Hulo, Florence Jungo, Guillaume Keller, Kati Laiho, Philippe Lemercier, Damien Lieberherr, Michele Magrane, Patrick Masson, Ivo Pedruzzi, Klemens Pichler, Diego Poggioli, Sylvain Poux, Catherine Rivoire, Bernd Roechert, Michel Schneider, Elena Speretta, Hema Bye-A-Jee, Rossana Zaru, Andre Stutz, Shyamala Sundaram, Michael Tognolli

'''Annotation Progress'''

12 sets of UniProt-GOA release files were produced by the GOA project between January 2016 and November 2016. These included non-redundant sets of GO annotations to 13 specific proteomes as well as data releases for annotations of all proteins in UniProtKB.

The UniProt-GOA project currently provides GO annotations for 65% of UniProtKB entries. Altogether, UniProt-GOA now provides almost 321 million GO annotations for more than 49 million proteins in over 675,000 different taxonomic groups. UniProt-GOA provides 403,251 annotations for the 61,394 proteins in the human reference proteome.

'''UniProt-GOA UniProt gene association file release stats (comparison of January 2016 and November 2016 releases)'''

[[File:Report2016.png]]

* The difference in the numbers is due to a change in the pipeline for predicting orthologs

** The difference the numbers is due to a change in the GOC rules

'''Methods and strategies for annotation'''

'''''Expert curation priorities:'''''

1. Human proteins

2. Disordered proteins

2. Moonlighting proteins

3. Requests from user community

4. Proteins annotated during UniProt curation duties

5. Annotation corrections based on quality control reports

'''''Computational annotation:'''''

UniProt-GOA provides IEA annotations from the following methods:

# UniProt Keyword 2GO (SPKW2GO)<sup>1,2</sup>
# UniProt Subcellular Locations2GO (SPSL2GO)<sup>1,2</sup>
# UniPathway2GO<sup>1,2</sup>
# HAMAP2GO<sup>1,2</sup>
# Unirule2GO<sup>1,2</sup>
# InterPro2GO
# Ensembl Compara (vertebrates)
# Ensembl Genomes Compara (plants, fungi)

'''Key'''

'''<sup>1</sup>''': mapping tables created and maintained by UniProt

'''<sup>2</sup>''': electronic annotations generated by UniProt

UniProtKB curators add information to entries that is subsequently used in electronic GO annotation pipelines such as UniProtKB keywords2GO, UniProtKB subcellular location2GO, UniRule2GO and HAMAP2GO. Altogether, automatic annotation pipelines provide 318 million annotations to almost 49 million proteins.

'''Presentations and Publications'''

''a. Publications''

'''An expanded evaluation of protein function prediction methods shows an improvement in accuracy'''. Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

'''Extending gene ontology in the context of extracellular RNA and vesicle communication.''' Cheung KH, Keerthikumar S, Roncaglia P, Subramanian SL, Roth ME, Samuel M, Anand S, Gangoda L, Gould S, Alexander R, Galas D, Gerstein MB, Hill AF, Kitchen RR, Lötvall J, Patel T, Procaccini DC, Quesenberry P, Rozowsky J, Raffai RL, Shypitsyna A, Su AI, Théry C, Vickers K, Wauben MH, Mathivanan S, Milosavljevic A, Laurent LC. J Biomed Semantics. 2016 Apr 12;7:19. doi: 10.1186/s13326-016-0061-5.

''b. Presentations including Talks, Tutorials and Teaching''

Talk “The Gene Ontology and Its Annotation Sets”. Plant and Animal Genome Conference XXIV. Claire O’Donovan, San Diego, CA, January, 2016.

Training “The Gene Ontology (GO) &amp; GOA”. Industry workshop. Melanie Courtot, March 2016.

Training “Ontologies for life sciences: examples from the Gene Ontology.” Earlham Institute summer school on bioinformatics. Melanie Courtot, May 2016.

Training “Describing your data – standards and ontologies.” Bioinformatics for PI course. Melanie Courtot, June 2016.

Webinar “QuickGO - Gene ontology annotation.” Aleksandra Shypitsyna, July 2016.

Talk “Annotation project: community curation standards and best practices.” Melanie Courtot, ''Aleksandra Shypitsyna,'' Elena Speretta, Alexander Holmes, Tony Sawford, Tony Wardell, Maria Martin and Claire O'Donovan. Biocuration, Geneva, Switzerland, April 2016.

''c. Posters''

“QuickGO: a web-based tool for Gene Ontology browsing, interpretation and analysis.” ''Aleksandra Shypitsyna'', Melanie Courtot, Elena Speretta, Alexander Holmes, Tony Sawford, Tony Wardell, Sangya Pundir, Xavier Watkins, Maria Martin and Claire O'Donovan. Biocuration, Geneva, Switzerland, April 2016

“Ten simple rules for biomedical ontology development.” International Conference on Biological Ontology &amp; BioCreative. ''Melanie Courtot'' , James Malone , Chris Mungall. August 2016

'''Ontology Development Contributions'''

* All curators continue to request new GO terms or updates to the ontology where necessary, using either Term Genie or the GitHub tracker.

'''Annotation Outreach and User Advocacy Efforts'''

* Aleksandra Shypitsyna and Penelope Garmiri trained 3 new curators in GO annotation.
* Melanie Courtot is on the rota for the GO Consortium helpdesk.
* Melanie Courtot and Aleksandra Shypitsyna are on the rota for UniProt-GOA project helpdesk.
* The Protein Function teams support external annotation groups, such as AgBase, BHF-UCL, DFLAT at Tuft's University, SIB and PIR by providing use of the Protein2GO curation tool, including WormBase and SGD this year.
* The Protein Function teams assist GO Consortium groups with migration of their annotations into the GOA files and UniProtKB, as well as providing access and training for the UniProt curation tool Protein2GO.
* Access and training for the Protein2GO curation tool has been given to recently joined curators from several groups, such as UCL, HGNC and NTNU.

'''Other Highlights'''

''i. Improvements to the QuickGO user interface''

Work to improve the QuickGO user interface has continued throughout 2016. This work also involves extending the range of features currently provided by QuickGO, as well as extensive testing for the new version of QuickGO and contributions to the user interface design.

''ii. Improvements to the Protein2GO curation tool''

As more GO Consortium curation groups migrate their annotations into the UniProt database and move to using Protein2GO as their sole curation tool for protein GO annotation, we continue to add more functionality to the tool.

* support for new with_string format, plus all of the ECO-code-specific usage constraints

At the 2015 GOC meeting in Washington and 2016 GOC meeting in Geneva a change to the format of the with/from annotation column (&quot;with_string&quot;) was agreed, which allows components of the with_string to be separated by both pipes and commas. In addition, a new set of rules was agreed that govern the usage, and acceptable format, of with/from with the GO evidence codes. Protein2GO now fully supports this enhanced format and the usage rules.

* Annotation provenance and other newly implemented features

A number of usability enhancements have been made to Protein2GO this year, but one of the most useful is the ability to trace the provenance of the annotations. It allows to easily identify the original annotations and acknowledges all the parties which were participating in the annotation process. For example, if the user selects an annotation created by the inference based on sequence or structure similarity, he/she is able to find immediately the original manual annotation and the group that created the annotation; this makes the task of checking the validity of annotations, for example, much easier. Apart from that, as Textpresso Literature Search Function and Lookup function for UniProtKB identifiers with priority listing (SWISS/TrEMBL entries) have been implemented this year as a result of GOC community requests. In terms of number of users, we currently have 125 active users, with 23 different affiliations. We continue to provide group-specific reports with the statistical data of curation and quality checks which require curator input. In addition, Protein2GO technical support is provided via GitHub website: https://github.com/geneontology/go-ontology/issues. Penelope
Categories: GO Internal

ZFIN December 2016

GO wiki (new pages) - Wed, 12/14/2016 - 13:54

Dhowe: Adding first draft of ZFIN 2016 report...not yet complete.

[[Category:ZFIN]] [[Category:Reports]]
= Zebrafish Model Organism Database Summary, December 14, 2016 =
=DRAFT - NOT YET COMPLETED=

= Overview =
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.

= Staff: =
{| cellspacing="0" cellpadding="4" align="left"
! style="background:lightgray; width:100px;" | Name
! style="background:lightgray; width:170px;" | Position Type
! style="background:lightgray; width:150px;" | FTE for GO
|-
|style="border-bottom:1px solid lightgray;" valign="top" | Doug Howe
|style="border-bottom:1px solid lightgray;" valign="top" | Data Curation Manager <br/>Principle GO contact at ZFIN
|style="border-bottom:1px solid lightgray;" valign="top" | 0.2
|-
|style="border-bottom:1px solid lightgray;" valign="top" |9 Curators
|style="border-bottom:1px solid lightgray;" valign="top" |Curatorial
|style="border-bottom:1px solid lightgray;" valign="top" |~0.1 each; 0.9 in aggregate
|-
|style="border-bottom:1px solid lightgray;" valign="top" |6 Technical
|style="border-bottom:1px solid lightgray;" valign="top" |5 Developers, 1 DBA
|style="border-bottom:1px solid lightgray;" valign="top" |Variable; ~0.1 in aggregate
|}

<br style="clear:both;">

No direct funding from GOC NHGRI grant.

= Annotation Progress =
[[File:|ZFIN curation stats from X, 2015 to Y, 2016]]

DATA TO BE ADDED FOR 2016

== Methods and strategies for annotation ==
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.

'''''Literature curation:'''''

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.

'''''Computational annotation strategies:'''''

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).


'''''Priorities for annotation:'''''

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.

= Presentations and Publications =


= Ontology Development Contributions =



= Annotation Outreach and User Advocacy Efforts =

= Other Highlights =
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 Dhowe
Categories: GO Internal

RGD December 2016

GO wiki (new pages) - Wed, 12/14/2016 - 13:10

Slaulederkind: Created page with "== RGD, The Rat Genome Database, December 2016 == === 1. Staff working on GOC tasks === RGD Admin: Mary Shimoyama GO Curators: Stan Laulederkind, Tom Hayman, Shur-Jen Wang,..."

== RGD, The Rat Genome Database, December 2016 ==

=== 1. Staff working on GOC tasks ===

RGD Admin: Mary Shimoyama

GO Curators: Stan Laulederkind, Tom Hayman, Shur-Jen Wang, Victoria Petri
(~1.5 fte, 0 funded by NHGRI GOC grant)

IT staff associated with GO related projects such as the development of the online curation tool and of pipelines, the updates/loads of GO ontologies in the database and the generation and submission of RGD Gene Association files:
Omid Ghiasvand, Marek Tutaj, Jeff DePons (1 fte, 0 fte funded by NHGRI GOC grant)

=== 2. Annotation progress ===

{| border="1" cellspacing="0" cellpadding="5" align="center"
! Gene Products
! Annotations 2014
! Annotations 2015
! % Change
|-
| 39,206
| 547,064 (314,567 non-IEA)
| 599,250 (323,853 non-IEA)
| +9.5%
|-
|}


The table above is based on a review of the GOC gene_association.rgd files from December 2015 to December 2016. The number of manual annotations from RGD has increased from 44,967 to 49,791 (+ 4,824 annotations, +11%) and the number of genes with manual annotations has increased from 5,625 to 5,998 (+373, +7%).

=== 3. Methods and strategies for annotation ===

Because the pipelines for GO annotations are automated and updated weekly, all of the curators’ efforts are involved in manual annotation. Although RGD curators also annotate to other ontologies, approximately 25% of their curation efforts have been related to GO annotations in the past year.

a. Literature curation: RGD targets gene sets for manual curation and all rat papers published about those genes are curated. In 2015, there have been 2 major types of gene datasets curated:

# disease related: sensory organ disease genes and age-related disease genes
# genes involved in targeted metabolic, signaling, regulatory, and disease pathways.

b. Computational annotation strategies:

# Rat genes manually curated by other groups are brought in electronically from GOA with their associated evidence codes and the originating group acknowledged in the source.
# ISO - RGD is not currently doing manual annotation with ISO. ISO annotations are created through our automated pipelines that map GO annotations from mouse genes over to their Rat orthologs. For each mouse gene that has a confirmed rat ortholog, if the GO annotation to the Mouse gene is of evidence type IDA, IMP, IPI, IGI or IEP then the annotation is loaded onto the rat ortholog as an ISO annotation.
# IEA - rat annotations based on GO mapping to InterPro, Enzyme Commission and Swiss-Prot keywords, are brought in electronically with IEA evidence code from GOA. Annotations from GOA for all categories are updated weekly.

c. Priorities for annotation: There are several ways in which RGD assigns priorities for the annotation of genes to GO ontology terms. These include: genes associated with targeted disease categories, genes involved in particular biological pathways, and genes associated with specific QTLs.

=== 4. Presentations and publications ===


a. Papers with substantial GO content

# Liu W, Laulederkind SJ, Hayman GT, Wang SJ, Nigam R, Smith JR, De Pons J, Dwinell MR, Shimoyama M. OntoMate: a text-mining tool aiding curation at the Rat Genome Database. Database (Oxford). 2015 Jan 25;2015. pii: bau129. doi: 10.1093/database/bau129. Print 2015.
# Shimoyama M, De Pons J, Hayman GT, Laulederkind SJ, Liu W, Nigam R, Petri V, Smith JR, Tutaj M, Wang SJ, Worthey E, Dwinell M, Jacob H. The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease. Nucleic Acids Res. 2015 Jan;43(Database issue):D743-50. doi: 10.1093/nar/gku1026.

b. Presentations including Talks and Tutorials and Teaching

# Eighth International Biocuration Conference, April 23-26, 2015, Friendship Hotel, Beijing, China: "Gene Curation Software at the Rat Genome Database: Update 2015", Stanley J. F. Laulederkind - lightning talk based on poster mentioned below, included information on curating GO data

c. Poster presentations with GO content

# Eighth International Biocuration Conference, April 23-26, 2015, Friendship Hotel, Beijing, China: "Gene Curation Software at the Rat Genome Database: Update 2015", Stanley J. F. Laulederkind, Weisong Liu, Marek Tutaj, G. Thomas Hayman, Rajni Nigam, Victoria Petri, J. R. Smith, Shur-Jen Wang, Jeff De Pons, M. R. Dwinell, Mary Shimoyama - included information on curating GO data

=== 5. Other Highlights ===

'''A. GO terms and related contributions by RGD'''

RGD has contributed 400 - 450 new terms, new synonyms, or definition/synonym/spelling corrections to GO from December 2014 to December 2015.

'''B. Annotation outreach and user advocacy efforts'''


'''C. Other highlights'''

Education Video tutorials, available on YouTube, Vimeo.com, and rgd.mcw.edu.

* OLGA (Object List Generator tool) Tutorial- including information on using curated GO data
* Gene Annotator Tutorial- including information on using curated GO data Slaulederkind
Categories: GO Internal