GO Internal

Manager Call 2017-05-03

GO wiki (new pages) - Fri, 04/28/2017 - 08:14

Vanaukenk: /* Noctua */

= Bluejeans =
https://bluejeans.com/588333403
= Agenda =
==GOC meeting==
* Current state of the Agenda: [http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda]
*Is there time for more ontology editors training in Corvallis or should we try to schedule another workshop over the summer?

== Protege ==
Follow up on idea of doing an advanced Protegé workshop this summer
* Who will participat ?
* Where will it be?
* When will it be?
* Equivalence axioms - editors would like more guidelines on how to construct these
== Noctua ==
*Doodle poll sent around to reinstate the weekly Noctua conference calls
**Responses from: David H, Kimberly, Moni, Pascale, Seth, Suzi
*These calls are needed to keep momentum going for curation, discuss annotation issues, and also to keep everyone informed about software development updates and priorities
*Top time slots right now are: Wednesdays at 10am or 11am EST

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

Annotation Conf. Call 2017-05-09

GO wiki (new pages) - Thu, 04/27/2017 - 08:00

Vanaukenk: Created page with "= Bluejeans URL = https://bluejeans.com/993661940 = Agenda = == Working Groups == === Transcription Decision Tree === *'''AI: Review annotation decision tree which is linked..."

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

= Agenda =
== Working Groups ==
=== Transcription Decision Tree ===
*'''AI: Review annotation decision tree which is linked from the github ticket in go-annotation'''
*[https://github.com/geneontology/go-annotation/issues/1463 github ticket 1463]

= Minutes =






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

Annotation Conf. Call 2017-04-25

GO wiki (new pages) - Mon, 04/24/2017 - 17:36

Vanaukenk: Created page with "= Bluejeans URL = https://bluejeans.com/993661940 = Agenda = == GOC Meeting, Corvallis, Oregon, June 1-3 (plus workshops June 4-5), 2017 == * Logistics: https://sites.google...."

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

= Agenda =
== GOC Meeting, Corvallis, Oregon, June 1-3 (plus workshops June 4-5), 2017 ==
* Logistics: https://sites.google.com/view/goc2017
* [[2017 Corvallis GOC Meeting Agenda]]
** Please check the table at the bottom of the Agenda page and add your name, if not already there. Also please double-check the information associated with your entry.
== Noctua Models ==
*Annotation of activities that change the 'state' of an entity and the processes that depend on that state.
=== Histone acetylation/deacetylation ===
*http://noctua.berkeleybop.org/editor/graph/gomodel:586fc17a00001080
[https://www.ncbi.nlm.nih.gov/pubmed/27864380 Setd5 is essential for mammalian development and the co-transcriptional regulation of histone acetylation.]
=== RNA polyadenylation/deadenylation ===
*http://noctua.berkeleybop.org/editor/graph/gomodel:586fc17a00002035
[https://www.ncbi.nlm.nih.gov/pubmed/26950371 Inhibition of telomerase RNA decay rescues telomerase deficiency caused by dyskerin or PARN defects.]

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

Ontology meeting 2017-04-28

GO wiki (new pages) - Wed, 04/19/2017 - 08:25

Pascale: Created page with "*Bluejeans: https://bluejeans.com/164681006 = Agenda = == Action point from last meeting== == GOC Meeting, Corvallis, Oregon == *GOC Meeting Agenda - Ontology-Related Iss..."

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

= Agenda =

== Action point from last meeting==



== GOC Meeting, Corvallis, Oregon ==
*GOC Meeting Agenda - Ontology-Related Issues
**http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda
**Add discussion point as needed


== Protege ==
Follow up on idea of doing an advanced Protegé workshop this summer. The managers have proposed to do half a day in Corvallis (Reactome day). Is everyone ok with this suggestion?
* Who is the target audience?
* Who would participate ?
* Where will it be?
* When will it be?
* Equivalence axioms - editors would like more guidelines on how to construct these

== Ontology Tickets ==



= Minutes =
*On call:


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

Ontology meeting 2017-04-21

GO wiki (new pages) - Wed, 04/19/2017 - 00:37

Pascale:

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

= Agenda =

== Action point from last meeting==

=== Documentation ===
Moni and Tanya:
**https://github.com/geneontology/go-ontology/pull/13204

*Please check Google document and give feedback
*Organization
**Protege
**github
**Ontology editing
*readthedocs - use this



== GOC Meeting, Corvallis, Oregon ==
*GOC Meeting Agenda - Ontology-Related Issues
**http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda
**What to discuss in Corvallis?


== Ontology Tickets ==




= Minutes =
*On call:





== GOC Meeting - Corvallis, Oregon ==
*Ontology issues
*Single-step biological processes - can/should be deleted or removed?
*Modified protein binding proposal


**Workshop this summer? Bar Harbor?
**Equivalence axioms - editors would like more guidelines on how to construct these


== Ontology Tickets ==
*Import pipeline: how do we import a term, for example a new Taxon?
see [https://github.com/geneontology/go-ontology/issues/13341]


== Modified Protein Binding Proposal ==
*Reviewed Pascale and Sylvain's proposal
**Suggestions:
***Include the term 'dependent' in the term name to try to make it as clear as possible what the term really means, i.e. the binding is dependent upon the specified modification
***Plan is to add a subset of protein modifications; others as needed
***PRO could be used to help make clear what protein form is actually bound
***What grouping terms are useful here?
**Will then need to review annotations to make sure term usage is correct







== Editors Rota ==
*David H away 4/14 - 4/23
*Kimberly away 4/17 - 4/22




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

2017 Cambridge GOC Meeting Logistics

GO wiki (new pages) - Tue, 04/18/2017 - 03:42

Valwood: /* Arriving */

=GOC Meeting, Cambridge , October 2-4, 2017=

* Location:
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]


==Registration==
* Please register at:

==Consortium dinner ==

To be added

==Planned Schedule==

* '''Monday October 2nd''':
:* Meeting will run from 9am to 5pm.

*'''Tuesday November 3rd''':
:* Meeting will run from 9am to 5pm.

*'''Wednesday November 4th''':
:* Meeting will run from 9am to 1pm.
:* Optional break out groups may follow.

==Meeting Venue and Directions==
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]

===Arriving===
* International Flights and travel to Cambridge (to be added)

===Meeting Dinner===
* Dinner will be on Monday or Tuesday evening

==Attendees==
Please add your name to the table if you intend to attend the meeting, the dinner, so we can get a headcount estimate.
{| {{Prettytable}} class='sortable'
|-
! Name
! Organization
! Are you planning to attend the GOC meeting
! Are you planning to attend the GOC dinner

|-
| Valerie Wood
| Cambridge University
| Yes
| Yes
|-

|}

NOT attending:

==Accommodations==


== Local activities ==


[[Category: GO Consortium Meetings]] Valwood
Categories: GO Internal

Manager Call 2017-04-19

GO wiki (new pages) - Fri, 04/14/2017 - 06:46

Pascale: Created page with "= Bluejeans = https://bluejeans.com/588333403 = Agenda = == Noctua== Define a list of blocking issues for wider deployment Develop a 'simple' version to do smaller scale ann..."

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


== Noctua==
Define a list of blocking issues for wider deployment
Develop a 'simple' version to do smaller scale annotation ('à la' protein2GO)?

== Protege ==
Follow up on idea of doing an advanced Protegé workshop this summer
Who will participate ?
Where will it be ?


== Documentation ==
Pascale
* It is not realistic to expect the documentation to be up to date.
I propose that manageable units of the documentation be reviewed and the last update date be stated for the documentation. I think we all wonder what is stale and what is current.

A few 'basic' point about the scope of GO annotation I would like to review with managers (and then at an annotation call):
* We only annotate the normal function/process and localization of a protein. Hence:
* '''Localization'''
** secreted proteins are not annotated to the secretory pathway (Golgi, vesicle, etc)
** Should internalized receptors be annotated to endocytic vesicle, and other downstream localizations?
** Should extracellular hormones be annotated to plasma membrane/extrinsic to the external side of plasma membrane when they are bound to their receptor ?

* '''Multi-organism processes'''
** Should host proteins that are hacked by viruses be annotated? For example in transcription, translation, internalization ? A possibility suggested by the Swiss-Prot viral group is to limit these annotations to terms that contain 'host'

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

Ontology meeting 2017-04-14

GO wiki (new pages) - Thu, 04/13/2017 - 06:46

Vanaukenk: /* Ontology Tickets */

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

= Agenda =
== Documentation ==
*Format for documentation on github: Kimberly and David have been working on the SOP Google document.
*Need to test this on a new user and transition to github md format
== GOC Meeting, Corvallis, Oregon ==
*GOC Meeting Agenda - Ontology-Related Issues
**http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda
**What to discuss in Corvallis?
**Is there time for more ontology editors training in Corvallis or should we try to schedule another workshop over the summer?
== Ontology Tickets ==
*Import pipeline
**[https://github.com/geneontology/go-ontology/pull/13345 Fixing import generation]
**[https://github.com/geneontology/go-ontology/issues/13338 Ontology imports into Protege cause undesirable side effects]
**[https://github.com/geneontology/go-ontology/issues/13269 taxon imports incomplete?]
**[https://github.com/geneontology/go-ontology/issues/13286 Load of go-plus.owl fails while importing uberon_import.owl]
**[https://github.com/geneontology/go-ontology/issues/13205 Automate generation of import modules]
**[https://github.com/geneontology/go-ontology/issues/13343 Taxon constraint for GO:0001944]
*[https://github.com/geneontology/go-ontology/issues/12787 Modified protein binding proposal]
*[https://github.com/geneontology/go-ontology/issues/12859 What do we need to do for the single step BP?]





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

Annotation Conf. Call 2017-04-11

GO wiki (new pages) - Fri, 04/07/2017 - 06:08

Vanaukenk:

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

= Agenda =


= Minutes =


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

Ontology meeting 2017-04-07

GO wiki (new pages) - Thu, 04/06/2017 - 06:16

David:

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

= Agenda =
*Format for documentation on github: Kimberly and David have been working on the SOP Google document. How are we going to transition that to GH as an indexed document for ontology editor reference?
*Github transition
** Ticket assignment and how it works.
* Other issues GOC Meeting discussion
**[[https://github.com/geneontology/go-ontology/projects/1 Ontology tickets]]
** Inconsistent term creating: protein complex binding [[https://github.com/geneontology/go-ontology/issues/13136]], etc.
** What do we need to do for the single step BP? [[https://github.com/geneontology/go-ontology/issues/12859]]
* Please begin assembling any other agenda items for the GOC meeting.



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

Manager Call 2017-04-05

GO wiki (new pages) - Mon, 04/03/2017 - 09:15

Vanaukenk: Created page with "= Bluejeans = https://bluejeans.com/588333403 = Agenda = == Protein2GO == *Discuss current and future status of Protein2GO as a curation tool == Noctua and Conventional Annota..."

= Bluejeans =
https://bluejeans.com/588333403
= Agenda =
== Protein2GO ==
*Discuss current and future status of Protein2GO as a curation tool
== Noctua and Conventional Annotation Pipelines ==
*Trying to achieve consistency between Noctua and conventional annotations
**For example, Annotation extensions vs With/From
***Binding annotations use annotation extensions and has_input in Noctua but With/From in conventional annotations
***Can we switch to just using annotation extensions?
== June Consortium Meeting ==
*Agenda

= Minutes =

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

Ontology meeting 2017-03-31

GO wiki (new pages) - Thu, 03/30/2017 - 10:43

David: Created page with "*Bluejeans: https://bluejeans.com/164681006 = Agenda = *Format for documentation on github: Kimberly and David have been working on the SOP Google document. How are we going..."

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

= Agenda =
*Format for documentation on github: Kimberly and David have been working on the SOP Google document. How are we going to transition that to GH as an indexed document for ontology editor reference?
*Github transition
** Travis checks don't catch everything. Should they? If so, we need to open tickets to add.
*** Circular references
*** Missing synonyms in merged terms. The term name of the merged term should always appear as a synonym after a merge.
* Other issues if time permits
**[[https://github.com/geneontology/go-ontology/projects/1 Ontology tickets]]
** Inconsistent term creating: protein complex binding [[https://github.com/geneontology/go-ontology/issues/13136]], etc.
** What do we need to do for the single step BP? [[https://github.com/geneontology/go-ontology/issues/12859]]
* Please begin assembling agenda items for the GOC meeting.



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

Ontology meeting 2017-03-24

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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

GO wiki (new pages) - 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