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Ontology meeting 2017-03-24

Wed, 03/22/2017 - 10:24

Vanaukenk: Created page with "*Bluejeans: https://bluejeans.com/164681006 = Agenda = *Format for documentation on github **Separate files for specific tasks, e.g. obsoleting a term **One larger file for e..."

*Bluejeans: https://bluejeans.com/164681006

= Agenda =
*Format for documentation on github
**Separate files for specific tasks, e.g. obsoleting a term
**One larger file for everything


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

Ontology meeting 2017-03-16

Tue, 03/14/2017 - 05:44

David: Created page with "Bluejeans: https://bluejeans.com/164681006 Is there a better time for this meeting? Updates on editing using GitHub and the new rota. *Any reports on how editing in Github..."

Bluejeans: https://bluejeans.com/164681006

Is there a better time for this meeting?


Updates on editing using GitHub and the new rota.
*Any reports on how editing in Github is going? Any new issues?
*Strange behavior of Protege- 'macromolecular complex' displays as having two identical labels. Has anyone else seen this?


==Tickets for discussion at this meeting:==

See https://github.com/geneontology/go-ontology/projects/1, column labeled "Ontology Call March 9th, 2017" on the right
#[https://github.com/geneontology/go-ontology/issues/12329 lipid transferases]
#[https://github.com/geneontology/go-ontology/issues/13143 more binding terms]
#[https://github.com/geneontology/go-ontology/issues/12976 regulation by pattern]
#[https://github.com/geneontology/go-ontology/issues/12975 response to other organism]
#[https://github.com/geneontology/go-ontology/issues/13021 chaperones again]


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

Annotation Conf. Call 2017-03-14

Fri, 03/10/2017 - 05:50

Vanaukenk: /* Software, Infrastructure */

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

= Agenda =
== GO Meeting Reminder ==
*Corvallis, Oregon - June 1-3rd, Noctua Workshop - June 4th, Reactome Workshop - June 5th
*[https://sites.google.com/view/goc2017 Meeting Registration Site]
*[http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda Meeting Agenda]

== Software, Infrastructure ==
*GO-Help, Ontology migration to github, Jenkins pipeline - Chris, Seth
*Migration of annotation files to github at some point in the future?

== Annotation Review ==
*Review of IMP annotations for possible use of new qualifiers - What is the scope of the problem?
**[https://docs.google.com/spreadsheets/d/1HbvdyKmRI7Zhj6qPqVEsvyN6cMwahsf4aLa54fiROvs BP_Annotation_Qualifiers_Spreadsheet]
*Single-step biological processes - review annotations to help assess impact if such terms are obsoleted
**[https://github.com/geneontology/go-ontology/issues/12859 Github ticket 'Remove all single-step BP classes']

== Working Groups ==
*Transcription factor decision tree
*Annotating high throughput experiments




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

Manager Call 2017-03-15

Thu, 03/09/2017 - 12:08

Vanaukenk:

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

= Agenda =

== GO and AGR ==
*What should GO be doing wrt AGR?
*Working group? What would the goals of that working group be?

= Minutes =

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

Ontology meeting 2017-03-09

Tue, 03/07/2017 - 09:46

David: Created page with "Attendees: Regrets: Bluejeans: https://bluejeans.com/164681006 Is there a better time for this meeting? * Kimberly - I would like to be able to attend all of the ontology..."

Attendees:

Regrets:


Bluejeans: https://bluejeans.com/164681006

Is there a better time for this meeting?
* Kimberly - I would like to be able to attend all of the ontology calls, but our site-wide WB call conflicts with this time slot on the first and third Thursdays of each month. If we could find a new slot for the ontology calls, that'd be great.

Updates on editing using GitHub and the new rota.
Strange behavior of Protege- 'macromolecular complex' displays as having two identical labels. Has anyone else seen this?

What is the etiquette of reviewing pull requests? Does the reviewer commit if everything looks ok?


==Tickets for discussion at this meeting:==

See https://github.com/geneontology/go-ontology/projects/1, column labeled "Ontology Call March 9th, 2017" on the right
#[https://github.com/geneontology/go-ontology/issues/12976 regulation by pattern]
#[https://github.com/geneontology/go-ontology/issues/12975 response to other organism]
#[https://github.com/geneontology/go-ontology/issues/13021 chaperones again]

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

Ontology meeting 2017-03-01

Wed, 03/01/2017 - 05:10

David:

Attendees:

Regrets:


Bluejeans: https://bluejeans.com/164681006

Is there a better time for this meeting?

==Tickets for discussion at this meeting:==

See https://github.com/geneontology/go-ontology/projects/1, column labeled "Ontology Call March 2nd, 2017" on the right
#[https://github.com/geneontology/go-ontology/issues/13018 Berkeley Protege Workshop]
#[https://github.com/geneontology/go-ontology/issues/13013 Slim Needed for AGR]
#[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?]


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

Annotation Conf. Call 2017-02-28

Sun, 02/26/2017 - 10:41

Vanaukenk:

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

= Agenda =
== GO Meeting Reminder ==
*Corvallis, Oregon - June 1-3rd, Noctua Workshop - June 4th, Reactome Workshop - June 5th
*[https://sites.google.com/view/goc2017 Meeting Registration Site]
*[http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda Meeting Agenda]

== Noctua Modeling Discussion ==
=== Sabrina Toro, Zfin ===
*[http://noctua.berkeleybop.org/editor/graph/gomodel:583f430000000041 ZDB-PUB-160610-16 myb, cebp1 and neutrophil maturation]
*[https://www.ncbi.nlm.nih.gov/pubmed/27268086 c-Myb acts in parallel and cooperatively with Cebp1 to regulate neutrophil maturation in zebrafish.]
=== Midori Harris, PomBase ===
*[http://noctua.berkeleybop.org/editor/graph/gomodel:586fc17a00000338 myo2_rlc1_PMID19570908]
*[https://www.ncbi.nlm.nih.gov/pubmed/19570908 Regulation of fission yeast myosin-II function and contractile ring dynamics by regulatory light-chain and heavy-chain phosphorylation.]
=== April Discussion ===
*April 25th
*Sign up: [http://wiki.geneontology.org/index.php/LEGO_Discussion_Rota LEGO Discussion Rota]

= Minutes =
*On call:

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

Manager Call 2017-03-01

Fri, 02/24/2017 - 10:08

Vanaukenk:

= Bluejeans URL =
*https://bluejeans.com/588333403
*Regrets: Kimberly (traveling back to NJ)

= Agenda =
*Documentation Jamboree
**Discussed as a possible working group meeting at Berkeley Ontology/Protege workshop
**Agree that we need a uniform system for documentation that integrates well with github, the GO web site
**Can we schedule a working group meeting? When? Where? Who?


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

Ontology meeting 2017-02-23

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

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

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

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

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

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

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

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

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

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