GO Internal

Ontology meeting 2017-02-23

GO wiki (new pages) - Tue, 02/21/2017 - 07:35

David: 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 February 23rd, 2017" on the right
#[https://github.com/geneontology/go-ontology/issues/13018 Berkeley Protege Workshop]
#[https://github.com/geneontology/go-ontology/issues/12976 regulation by pattern]
#[https://github.com/geneontology/go-ontology/issues/12995 semantic difference between catalytic activity MF and BP]
#[https://github.com/geneontology/go-ontology/issues/12975 response to other organism]
#[https://github.com/geneontology/go-ontology/issues/13012 Is it an MF or BP?]
#[https://github.com/geneontology/molecular_function_refactoring Update on MF refactoring]


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

Manager Call 2017-02-15

GO wiki (new pages) - Tue, 02/14/2017 - 13:29

Vanaukenk: /* Annotation Conference Call */

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

= Agenda =
== GOC Meeting in June ==
*Curators have asked for more information about Reactome workshop in order to make their travel plans
*Who will contact Pankaj and Peter for that and report back to the group?

== Protege Workshop in Berkeley Next Week ==
*What else needs to be done for prep/planning?

== Annotation Conference Call ==
*Some big issues facing the annotation group
*Addition of new qualifiers/relations was thought to be desired and important for several annotation streams - conventional, PAINT, LEGO
*However, the questions of which ones to use and how to apply the ones we do use consistently are still open
*We need a good way to coordinate annotation work to make sure we actually get some useful guidelines
*One suggestion - divide up curators to look at specific areas of biology to generate guidelines for that area
**There's a lot of value in what Val has done for the cell cycle, but would guidelines for cell cycle apply to development, behavior, metabolic processes?
***For example, what is the relation between a transcription factor required for specification of a particular neuron, and the behaviors mediated by that neuron?
**PAINT view of annotations can be very informative here
**LEGO models will help here as well
**Other possibilities - examine genes that are annotated to both a process and regulation of that process
*How much do we need to coordinate this work with ontology development, specifically the molecular function refactoring and design patterns?
*Can we come up with a plan and propose it to the consortium?

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

Ontology meeting 2017-02-16

GO wiki (new pages) - Tue, 02/14/2017 - 08:13

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, co..."

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 February 16th, 2017" on the right
#[https://github.com/geneontology/go-ontology/issues/12948 EC:1.14.12 is being used as an xref in multiple enzyme activities]
#[https://github.com/geneontology/molecular_function_refactoring Update on MF refactoring]
#[https://github.com/geneontology/go-ontology/issues/12976 regulation by pattern]
#[https://github.com/geneontology/go-ontology/issues/12995 semantic difference between catalytic activity MF and BP]
#[https://github.com/geneontology/go-ontology/issues/12975 response to other organism]


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

Protege-OWL Berkeley Training 2017 Agenda

GO wiki (new pages) - Sat, 02/11/2017 - 12:14

Cjm: /* = */

Logistics here: [[Protege-OWL_Berkeley_Training_2017_Logistics]]

Meeting material can be found in [geneontology/protege-tutorial](https://github.com/geneontology/protege-tutorial)

= Pre-meeting preparation =

== Computer setup ==

We assume you will be bringing your normal work laptop. Ideally this will have 8G of memory or more and be a macbook (or PC with linux). Let Chris know if this is *not* the case

1. get a github account and ensure you are in [users.yaml](https://github.com/geneontology/go-site/blob/master/metadata/users.yaml)
2. Install a github client
3. Download Protege from http://protege.stanford.edu (you should have 5.1.0 for this course)
4. Install plugins - [[Protege_setup_for_GO_Eds]] (a bit out of date) and [[Ontology_editor_plugins]]
5. Do some light reading (see below)

== Reading List (optional) ==

* Mungall, C. J., Dietze, H., & Osumi-Sutherland, D. (2014). Use of OWL within the Gene Ontology. In M. Keet & V. Tamma (Eds.), Proceedings of the 11th International Workshop on OWL: Experiences and Directions (OWLED 2014) (pp. 25–36). Riva del Garda, Italy, October 17-18, 2014. http://doi.org/10.1101/010090
* Pizza Tutorial http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ (this is an excellent general purpose intro, some of our material is inspired by this)
* OWL Primer (advanced) https://www.w3.org/TR/owl-primer/

= Agenda =

== Wednesday 2017-02-22 ==

=== am ===

* Git and GitHub
* OWL Concepts

=== pm ===

* Walkthrough and exercises [geneontology/protege-tutorial](https://github.com/geneontology/protege-tutorial)
** Basic Editing Guide
** Using the reasoner

== Thursday 2017-02-23 ==

=== am ===

* external ontologies
* continuous integration: travis, jenkins and automated checks
* advanced ontology debugging
* MF refactor?

=== pm ===

* Design Patterns: what are they are how they can help you
* How TermGenie works; limitations and why we're switching
* Editing parts of the ontology as tables

== Friday 2017-02-24 ==

* Exercises
* Real-world ontology editing
* Discussion

[[Category:Meetings]]
[[Category:Protege]] Cjm
Categories: GO Internal

TAIR December 2016

GO wiki (new pages) - Fri, 02/10/2017 - 10:08

TanyaB: /* 4. Presentations and publications */

'''<span style="color:#FF0000">IN PROGRESS</span>'''

== TAIR, The Arabidopsis Information Resource, December 2016 ==

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

Tanya Berardini (0.35 FTE), Donghui Li (0.3 FTE), Leonore Reiser (0.5 FTE)

The total number of FTE working on GOC tasks is 1.15.

=== 2. Annotation progress ===

Dates are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.

'''Table 1: Number of Annotations to Various GO Aspects'''

{| border="1"
|-
! Annotations
! BP (12/15)
! BP (12/16)
! change
! MF (12/15)
! MF (12/16)
! change
! CC (12/15)
! CC (12/16)
! change
|-
| non-IEA/non-ND|| 22786 || ||- ||14584 || ||+ || 56339 || || + ||
|-
| IEA || 5689 || || - ||9236 || || - || 1354 || || - ||
|-
| ND ||8106 || || - || 4861|| || - || 4065|| || - ||

|}


'''Table 2: Number of Genes Annotated to Various GO Aspects'''

{| border="1"
|-
! Genes
! BP (12/15)
! BP (12/16)
! change
! MF (12/15)
! MF (12/16)
! change
! CC (12/15)
! CC (12/16)
! change
|-
| non-IEA/non-ND|| 9730 || || - || 8020 || || + ||23782 || || + ||
|-
| IEA || 4593 || || - || 6574 || || - || 1224 || || - ||
|-
| ND ||8106 || || - || 4861|| || - || 4065|| || - ||

|}

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

a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.

b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:

1. Literature-based annotations made by TAIR curators
2. Community annotations made via TAIR's TOAST annotation tool (see below)
3. GOA annotations for Arabidopsis with experimental evidence codes
4. PAINT-based Arabidopsis annotations from RefGenome group
5. Function-Process link-based annotations from GOC
6. INTERPRO2GO-based IEA annotations from UniProtKB
7. TIGR's annotations from Arabidopsis functional annotation project

c. Priorities for annotation:

1. literature describing the characterization of previously undescribed ('novel') genes,
2. genes that do not have any GO annotations at all (none of the three aspects),
3. recent literature from high impact factor journals
4. user requested annotation requests

d. Review of user-submitted annotations (see TOAST section below)
Donghui, Leonore, and Tanya review the annotations submitted via TOAST,
making sure that terms were mapped correctly and that the proper
evidence_with information is entered, if necessary. Sometimes,
follow-up with the submitter via email is necessary.

=== 4. Presentations and publications ===
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2016 GO 2016 Publications, Talks, Posters]


<span style="color:#FF0000">UPDATE NEEDED - please add to linked page as necessary</span>

'''Publications - GO-related but not primarily about GO'''

<span style="color:#FF0000">UPDATE NEEDED</span>


'''Talks - GO-related but not primarily about GO'''

<span style="color:#FF0000">UPDATE NEEDED </span>

=== 5. Other Highlights ===

'''A. Ontology Development Contributions'''
* '''GO terms contributed by TAIR'''

<span style="color:#FF0000">UPDATE NEEDED - redo counts in Dec. 2016</span>

Tanya Berardini and Donghui Li have created 108 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', 'created_by: dhl', 'created_by: donghui', date range: 12/5/13 - 12/9/14).

* '''Other ontology development work'''

Tanya Berardini:
*participates in the rota for GitHub (formerly Sourceforge) requests (4 total people in rota, one week at a time, biweekly conference call)
*participates in the rota for the gatekeeper for the TermGenie requests (4 total people in rota, one week at a time)
*attends weekly GO editors conference call
*attends biweekly GO annotation conference calls


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

* '''PAINT annotation'''

<span style="color:#FF0000">UPDATE NEEDED</span>

Donghui Li does PAINT-based annotation.
*attends regular PAINT annotation conference calls
*curated 43 families.

* '''TOAST (TAIR Online Annotation Submission Tool)'''

TAIR continues to collect controlled vocabulary annotations via its online tool.
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]

TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.

* '''GO help'''

Tanya Berardini and Donghui Li participate in manning the GO helpdesk. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time.

'''C. Other highlights'''


[[Category:Reports]]
[[Category:TAIR]] TanyaB
Categories: GO Internal

Ontology meeting 2017-02-09

GO wiki (new pages) - Tue, 02/07/2017 - 08:53

Paola: 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 February 9, 2017" on the right

#[https://github.com/geneontology/molecular_function_refactoring Update on MF refactoring]
#[https://github.com/geneontology/go-ontology/issues/12948 EC:1.14.12 is being used as an xref in multiple enzyme activities]
#[https://github.com/geneontology/go-ontology/issues/12786 Discussion of 'positive regulation' and 'maintenance']
#[https://github.com/geneontology/go-ontology/issues/12976 regulation by pattern]
#[https://github.com/geneontology/go-ontology/issues/12995 semantic difference between catalytic activity MF and BP]
#[https://github.com/geneontology/go-ontology/issues/12975 response to other organism]



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

Annotation Conf. Call 2017-02-14

GO wiki (new pages) - Fri, 02/03/2017 - 09:52

Vanaukenk: /* New Qualifiers for Biological Process */

= Bluejeans URL =
*https://bluejeans.com/993661940

= Agenda =
== Meeting Reminder ==
*Next Consortium Meeting: June 1-3, 2017 in Corvallis, Oregon
*Noctua Workshop on June 4th
*Reactome Workshop on June 5th
== New Qualifiers for Biological Process ==
[https://github.com/geneontology/go-annotation/issues/1517 Link to github Discussion]

== Jenkins Jobs ==
== Working Groups ==
== February 28th Call ==
*Discussion of LEGO Models

= Minutes =

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

Logistics

GO wiki (new pages) - Thu, 02/02/2017 - 06:18

Hdrabkin:

Meeting Location
Berkeley: Chris has rooms

Accommodations
Chris looking into appropriate hotel for all participants
Need Uber to meeting site.

Travel

Participants: Hdrabkin
Categories: GO Internal

Ontology meeting 2017-02-02

GO wiki (new pages) - Wed, 02/01/2017 - 00:02

Paola: /* Tickets for discussion at this meeting: */

Attendees:

Regrets: 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 February 2, 2017" on the right

#[https://github.com/geneontology/go-ontology/issues/12902 Add dc:title to ontology file]
#[https://github.com/geneontology/go-ontology/issues/12948 EC:1.14.12 is being used as an xref in multiple enzyme activities]
#[https://github.com/geneontology/go-ontology/issues/12786 Discussion of 'positive regulation' and 'maintenance']
#[https://github.com/geneontology/go-ontology/issues/12849 cellular processes in GO]


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

Manager Call 2017-02-01

GO wiki (new pages) - Mon, 01/30/2017 - 10:36

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

[[Category: GO Managers Meetings]]

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

=Agenda= Mi
Categories: GO Internal

Ontology meeting 2017-01-26

GO wiki (new pages) - Tue, 01/24/2017 - 23:37

Paola: 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 26, 2017" on the right

#[https://github.com/geneontology/go-ontology/issues/12948 EC:1.14.12 is being used as an xref in multiple enzyme activities]
#[https://github.com/geneontology/go-ontology/issues/12859 Remove all single-step BP classes]


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

Annotation Conf. Call 2017-01-24

GO wiki (new pages) - Mon, 01/23/2017 - 14:10

Vanaukenk: Created page with "= Bluejeans URL = https://bluejeans.com/993661940 = Agenda = == GO Meeting Reminder == *Corvallis, Oregon - June 1-3rd, Noctua Workshop - June 4th, Reactome Workshop - June..."

= Bluejeans URL =
https://bluejeans.com/993661940

= Agenda =
== GO Meeting Reminder ==
*Corvallis, Oregon - June 1-3rd, Noctua Workshop - June 4th, Reactome Workshop - June 5th
== github Tickets ==
*[https://github.com/geneontology/go-annotation/issues/1517 - New qualifiers for biological process]
**Will be discussed on the February 14th annotation call, but please look at the ticket and comment there, if needed
== LEGO Models ==
=== MGI - David and Karen ===

=== WB - Kimberly ===

= Minutes =

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

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