GO Internal

GO-CAM May 24th, 2017

GO wiki (new pages) - 5 hours 18 min ago

Vanaukenk: Created page with "= Bluejeans URL = https://bluejeans.com/969313231 = Agenda = == Recent Software Updates == == Review of github Tickets == *https://github.com/geneontology/noctua/issues C..."

= Bluejeans URL =
https://bluejeans.com/969313231

= Agenda =
== Recent Software Updates ==
== Review of github Tickets ==
*https://github.com/geneontology/noctua/issues

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

Annotation Conf. Call 2017-05-23

GO wiki (new pages) - Mon, 05/22/2017 - 07:20

Vanaukenk:

= 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 - especially the column about attending the GO dinner.

== Noctua Models ==
*Presenter: Petra Fey (dictyBase)
* [https://www.ncbi.nlm.nih.gov/pubmed/22323285 Rab8a regulates the exocyst-mediated kiss-and-run discharge of the Dictyostelium contractile vacuole]


= Minutes =
*On call:



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

Ontology meeting 2017-05-26

GO wiki (new pages) - Fri, 05/19/2017 - 06:54

Pascale:



Discussion points (Pascale):
# NTR RO: 'transports' https://github.com/oborel/obo-relations/issues/161
# Keeping old stanzas as synonyms for merged terms: Could this rule be relaxed? Sometimes the other name is not appropriate.
# Otherwise- is it possible to move secondary IDs ? For example "GO:0019060 intracellular transport of viral protein in host cell " (https://github.com/geneontology/go-ontology/issues/13478) has synonyms
#* viral capsid transport in host cell nucleus,
#* intracellular viral protein transport,
#* intracellular viral capsid transport and
#* viral capsid transport in host cell cytoplasm

Presumably the merge was done to the wrong term, these seem like synonyms for 'GO:0075733 intracellular transport of virus'



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

Ontology meeting 2017-05-19

GO wiki (new pages) - Thu, 05/18/2017 - 09:18

David: Created page with "*Bluejeans: https://bluejeans.com/164681006 = Agenda = == GOC Meeting, Corvallis, Oregon == *GOC Meeting Agenda - Ontology-Related Issues **http://wiki.geneontology.org/inde..."

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

= Agenda =

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

==Annotation Documentation==
Add the 'curator note' property to selected classes: improving curator documentation centered around particular terms in the ontology, by embedding it directly in the ontology. See GitHub issue at
https://github.com/geneontology/go-ontology/issues/13384

==Ontology Editing (Protege/GitHub) Documentation==
* What's up with this? Final version somewhere?
* Where to find the documentation for obsoleting terms?

==Inference e-mails are Back ==
https://github.com/geneontology/go-ontology/issues/13396

David has checked the file and has noted the strange ones in the ticket.
*The response ones are pretty easy. They don't have necessary and sufficient logical defs.
*The dentin transport one is a weird result of the reasoning.
*The protein ones are technically correct but misleading. I am pretty sure it is due to the equivalence between PRO and ChEBI. I suspect Pascale might have these in her sights for clean up.

== Ontology Developer Training ==
Follow up on idea of doing an advanced Ontology Developer Training workshop this summer
* Who will participate ?
** People who are currently active in editing the ontology.
* Where will it be?
**The Bay area.
* When will it be?
**The week of August 14th is best, but we won't have Seth.
* Potential Topics
**Equivalence axioms - editors would like more guidelines on how to construct these.
**OWL GCIs- Where do they live and how do they work?
**Advanced Querying?
**Pipelines and how they run. Starting jobs with ROBOT.
**Build failures
***Document the various fail messages and how to correct the issues.
**Problematic GitHub tickets/mini Projects

== Github Ticket Discussion==
https://github.com/geneontology/go-ontology/projects/1

= Minutes =



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

Manager Call 2017-05-17

GO wiki (new pages) - Wed, 05/17/2017 - 08:03

Moni: /* GOC meeting */

= Bluejeans =
https://bluejeans.com/588333403
= Agenda =
==GOC meeting==
* Times for discussions will be 2 full days on Thursday and Friday and half a day on Saturday.
* Add an item for GO help report. This will be brief. There isn’t a Help desk rotation anymore, and the number of questions and requests is lower than in the past, with users submitting more refined and detail questions and requests.
* Criteria for proposed discussion items (by to S. Lewis):
** whether it is a status report
** whether it is a specific proposal to address a particular issue
* Adding items to the agenda:
** Dealing with applying qualifiers to legacy annotations.
*** Do we change GAF 2.0 to allow additional qualifiers?
*** The easiest and most consistent application would be to use ''involved_in'' or ''causally_upstream_of''. The longer we wait, the longer it will take us to change.
*** We should issue an announcement along the lines of “We are creating a relationship term, everything is getting the parent qualifier term and we believe it is accurate. All annotations have a relationship between the entity and the GO and the default one is *this* and we are applying it to everything. Some suggestions to applying a more specific one are “x, y, and z”. Here are some examples when using experiments of “a” kind and here when annotating experiments of “b” kind”.
*** Concern about having some guidelines for approach on how we are making other annotations more precise. Explain clearly what ''causally_upstream_of'' means. ''involved_in'' is very precise, and should not be the default relation.
*** Let’s make the annotation guidelines Noctua-centric, with the expectation that people will be primarily using Noctua to add these qualifiers.
* Suzi: if you have specific questions you want the PIs to ask regarding immediate future plans and overall goals of the current GOC efforts, please send them to us.
** David: it would be good to have concrete goals for the end of the year. e.g. all groups should be using Noctua by the end of the year.

== Ontology Developer Training ==


Follow up on idea of doing an advanced Ontology Developer Training workshop this summer
* Who will participate David H, Kimberly, David OS, Moni, Chris, Pascale, Karen, Huaiyu, Barbara, Paul T, ....
* Where will it be: Berkeley
* When will it be: Tues Aug 15- Friday Aug 19

* *Potential Topics*
**Equivalence axioms - editors would like more guidelines on how to construct these.
**OWL GCIs- Where do they live and how do they work?
**Advanced Querying?
**Pipelines and how they run. Starting jobs with ROBOT.
**Build failures
***Document the various fail messages and how to correct the issues.
**Problematic GitHub tickets



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

Manager Call 2017-12-06

GO wiki (new pages) - Wed, 05/17/2017 - 02:54

Moni: Created page with "= Joining the Call on Bluejeans = https://bluejeans.com/588333403 = Agenda = = Minutes = Category: GO Managers Meetings"

= Joining the Call on Bluejeans =
https://bluejeans.com/588333403


= Agenda =



= Minutes =



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

Manager Call 2017-09-06

GO wiki (new pages) - Wed, 05/17/2017 - 02:54

Moni: Created page with "= Joining the Call on Bluejeans = https://bluejeans.com/588333403 = Agenda = = Minutes = Category: GO Managers Meetings"

= Joining the Call on Bluejeans =
https://bluejeans.com/588333403


= Agenda =



= Minutes =



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

Ontology meeting 2017-05-12

GO wiki (new pages) - Thu, 05/11/2017 - 09:44

David: /* Agenda */

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

= Agenda =

Kimberly will chair the call.

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

==Annotation Documentation==
https://github.com/geneontology/go-ontology/issues/13384

==Inference e-mails are Back ==
https://github.com/geneontology/go-ontology/issues/13396

David has checked the file and has noted the strange ones in the ticket.
*The response ones are pretty easy. They don't have necessary and sufficient logical defs.
*The dentin transport one is a weird result of the reasoning.
*The protein ones are technically correct but misleading. I am pretty sure it is due to the equivalence between PRO and ChEBI. I suspect Pascale might have these in her sights for clean up.

== Ontology Developer Training ==
Follow up on idea of doing an advanced Ontology Developer Training workshop this summer
* Who will participate ?
** People who are currently active in editing the ontology.
* Where will it be?
**The Bay area.
* When will it be?
**Second week of August is best, but we won't have Seth.
* Potential Topics
**Equivalence axioms - editors would like more guidelines on how to construct these.
**OWL GCIs- Where do they live and how do they work?
**Advanced Querying?
**Pipelines and how they run. Starting jobs with ROBOT.
**Build failures
***Document the various fail messages and how to correct the issues.
**Problematic GitHub tickets/mini Projects

== Github Ticket Discussion==
https://github.com/geneontology/go-ontology/projects/1

= Minutes =
*On call:


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

GO-CAM May 10th, 2016

GO wiki (new pages) - Tue, 05/09/2017 - 12:18

Vanaukenk: /* Review of github Tickets */

= Bluejeans URL =
https://bluejeans.com/969313231

= Agenda =
== Recent Software Updates ==
== Review of github Tickets ==
*https://github.com/geneontology/noctua/issues

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

Ontology meeting 2017-05-05

GO wiki (new pages) - Thu, 05/04/2017 - 10:36

David: /* Ontology Developer Training */

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

= Agenda =

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

==Annotation Documentation==
https://github.com/geneontology/go-ontology/issues/13384

== Ontology Developer Training ==
Follow up on idea of doing an advanced Ontology Developer Training workshop this summer
* Who will participate ?
* Where will it be?
** Kimberly will be in CA for the worm meeting (UCLA) from ~June 20-25th, but no flights yet, so trip could be extended in either direction
** It makes most sense logistically to have the meeting in CA.
** David cannot make it either before the 20th or after the 25th.
* When will it be?
** Doodle poll?
* Potential Topics
**Equivalence axioms - editors would like more guidelines on how to construct these.
**OWL GCIs- Where do they live and how do they work?
**Advanced Querying?
**Pipelines and how they run. Starting jobs with ROBOT.
**Build failures
***Document the various fail messages and how to correct the issues.
**Problematic GitHub tickets/mini Projects

== Github Ticket Discussion==
https://github.com/geneontology/go-ontology/projects/1

= Minutes =
*On call:


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

Manager Call 2017-06-07

GO wiki (new pages) - Wed, 05/03/2017 - 07:51

Moni:

= Joining the Call on Bluejeans =
https://bluejeans.com/588333403


= Agenda =

This date is shortly after GO Meeting in Corvallis.

= Minutes =



[[Category: GO Managers Meetings]] Moni
Categories: 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