GO Internal

Ontology meeting 2017-08-11

GO wiki (new pages) - Thu, 08/10/2017 - 07:27

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = Discussion: *The majority of this meeting will focus on the agenda for the Ontology Editors' Wor..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

Discussion:

*The majority of this meeting will focus on the agenda for the Ontology Editors' Workshop next week.
[http://wiki.geneontology.org/index.php/2017_Berkeley_GO_Editors_Workshop_II logistics page]

*Update on the signaling work. We still have no editor for calcium signaling
**https://github.com/geneontology/go-annotation/projects/4
**https://github.com/geneontology/go-ontology/projects/1


= Minutes =
*On call:


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

GO-CAM August 9th, 2017

GO wiki (new pages) - Tue, 08/08/2017 - 15:35

Vanaukenk: Created page with "= Zoom URL = https://stanford.zoom.us/j/679970729 = Agenda = ==Update on Proposal for a Tabular Editing Interface== https://github.com/geneontology/noctua/issues/461 ==Discu..."

= Zoom URL =
https://stanford.zoom.us/j/679970729

= Agenda =
==Update on Proposal for a Tabular Editing Interface==
https://github.com/geneontology/noctua/issues/461
==Discussion of Models, Inferred Annotations, and GPAD Output==

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

Annotation Conf. Call 2017-08-08

GO wiki (new pages) - Sun, 08/06/2017 - 06:25

David: Created page with "= Meeting URL = *https://stanford.zoom.us/j/976175422 = Agenda = == Ontology Report == *SUMO protease annotations may be too generic https://github.com/geneontology/go-ontol..."

= Meeting URL =
*https://stanford.zoom.us/j/976175422

= Agenda =
== Ontology Report ==
*SUMO protease annotations may be too generic https://github.com/geneontology/go-ontology/issues/13941
*GOC slim ticket https://github.com/geneontology/go-ontology/issues/13996

== Signaling Project ==
*Update on progress to date, github tickets
**Wnt - Giulia, Helen, Kimberly
***[https://docs.google.com/spreadsheets/d/1X1kfjnh_CJbqp7bfCLJuNBlRVyB3PIaLJGLaVfRID78/edit#gid=1354579580 Google spreadsheet with annotation, ontology analysis]
***[https://docs.google.com/document/d/1wrPx0g4FfbV6zObVrCkGWZJvEY2SUumC1CH3soTKuGE/edit Google doc for crystallizing github tickets]
**MAPK - David H. and Sabrina
***Examining gene products annotated to the process with no experimental support for known MFs
***Thinking about how to define the beginning and parts of the pathway
**Ca2+ Signaling
***Fertilization - Penelope
**GPCR - Pascale, Petra
***Some ontology tickets have been addressed
***Needs global annotation review
***Needs GO-CAM model
**Reminder - discussion on specific github tickets, not on project page

= Minutes =
*On call:


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

Ontology meeting 2017-08-04

GO wiki (new pages) - Thu, 08/03/2017 - 10:00

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = Discussion: Update on the signaling work. We still have no editor for calcium signaling https:/..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

Discussion:

Update on the signaling work. We still have no editor for calcium signaling

https://github.com/geneontology/go-annotation/projects/4

https://github.com/geneontology/go-ontology/projects/1

== August Meeting Agenda ==
*Will be added to the [http://wiki.geneontology.org/index.php/2017_Berkeley_GO_Editors_Workshop_II logistics page]


= Minutes =
*On call:


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

Manager Call 2017-08-02

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

Moni: Created page with "= Joining the Call on Zoom = https://stanford.zoom.us/j/754529609 = Agenda = = Notes = Category: GO Managers Meetings"

= Joining the Call on Zoom =
https://stanford.zoom.us/j/754529609

= Agenda =


= Notes =







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

Ontology meeting 2017-07-28

GO wiki (new pages) - Fri, 07/28/2017 - 05:12

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = Discussion: Update on the signaling work. Shall an editor join each group? https://github.com/g..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

Discussion:

Update on the signaling work. Shall an editor join each group?

https://github.com/geneontology/go-annotation/projects/4

https://github.com/geneontology/go-ontology/projects/1

== August Meeting Agenda ==
*Will be added to the [http://wiki.geneontology.org/index.php/2017_Berkeley_GO_Editors_Workshop_II logistics page]


= Minutes =
*On call:



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

GO-CAM July 26th, 2017

GO wiki (new pages) - Tue, 07/25/2017 - 11:48

Vanaukenk: Created page with "= Zoom URL = https://stanford.zoom.us/j/679970729 = Agenda = ==Update on Proposal for a Tabular Editing Interface== https://github.com/geneontology/noctua/issues/461 ==Discu..."

= Zoom URL =
https://stanford.zoom.us/j/679970729

= Agenda =
==Update on Proposal for a Tabular Editing Interface==
https://github.com/geneontology/noctua/issues/461
==Discussion of Models, Inferred Annotations, and GPAD Output==


= Minutes =
*On call:





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

Annotation Conf. Call 2017-07-25

GO wiki (new pages) - Thu, 07/20/2017 - 07:28

Vanaukenk: Created page with "= Meeting URL - NOTE CHANGE TO ZOOM = *https://stanford.zoom.us/j/976175422 = Agenda = == GO Slims == *AGR is including a GO slim on the gene pages *Launch date for AGR 1.0..."

= Meeting URL - NOTE CHANGE TO ZOOM =
*https://stanford.zoom.us/j/976175422

= Agenda =
== GO Slims ==
*AGR is including a GO slim on the gene pages
*Launch date for AGR 1.0 is October 2017
*Need feedback on GO Slim and ribbon display on gene pages
*Mary Dolan will provide an overview of the methodology used to generate the slim
== Signaling Project ==
*Update on what pathways have been claimed
*Update on progress to date, github tickets


= Minutes =



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

Ontology meeting 2017-07-21

GO wiki (new pages) - Wed, 07/19/2017 - 15:34

David:

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

Discussion:

How will we distribute ontology editing tasks for the signaling work? Shall an editor join each group. Kimberly and DavidH can't do it all.

https://github.com/geneontology/go-ontology/projects/1

== August Meeting Agenda ==
*Will be added to the [http://wiki.geneontology.org/index.php/2017_Berkeley_GO_Editors_Workshop_II logistics page]


= Minutes =
*On call:


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

GO-CAM ectopic meeting July 19th 2017

GO wiki (new pages) - Wed, 07/19/2017 - 09:01

Vanaukenk: /* Minutes */

= Zoom URL =
https://stanford.zoom.us/j/679970729

= Agenda =

Discussion of inference on Wnt signaling LEGO model

http://noctua.berkeleybop.org/editor/graph/gomodel:5966411600000538

===Missing/New inferences: ===

==== contributes_to inference: ====
Added to RO:
part of'(?x, ?y) ^ enables(?y, ?z) ^ molecular_function(?z) -> 'contributes to'(?x, ?z)
e.g. GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z

====Annotation to compound molecular function => annotation to its parts====

enables(?x, ?y) ^ 'has part'(?y, ?z) ^ molecular_function(?y) -> enables(?x, ?z)

e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'

====Inferences from molecular function regulators====

https://github.com/geneontology/go-ontology/issues/13492)

e.g.:

X <— enabled by— protein binding —directly_positively_regulates --> protein kinase activity —enabled_by--> Y

=>

X enables ‘protein binding activity' has_input Y *
X enables 'protein kinase activator activity’ has_input Y *


\* Comes from a new rule:
molecular_function(?x) ^ molecular_function(?y) ^ 'directly regulates'(?x, ?y) ^ enables(?z, ?y) -> 'has input'(?x, ?z)

e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z

=== Wrong inferences that need to be trimmed: ===

regulates o part_of->regulates

https://github.com/geneontology/go-ontology/issues/13926#issuecomment-316054054


=== Strategies for trimming down superfluous inference ===


# enables and other GP/Complex -> MF/BP relations never go in extensions. Inference of the ‘contributes to’ qualifier would make up for this.
# some very high level classes should be blacklisted from extensions (molecular_function, regulation of molecular function. We could perhaps existing no annotation subset flags for these.)
# If we have ‘X regulation’ then the GPAD has only GP involved_in 'regulation of X', not GP involved_in_regulation_of X.
This is hard to implement: simpler alternative would be to just drop this GP-GO term relation and rely on named regulation classes alone

= Minutes =
*On call: David H, David OS, Kimberly, Paul T.

== Protein Complex Annotations ==
*New rule will allow for individual members of the complex to inherit the MF annotation with a contributes_to qualifier
*For BP annotations, if the MF is performed by a protein complex, and the MF is part_of the BP, then each member of the complex is involved_in the BP


[[Category:Annotation Working Group]] David os
Categories: GO Internal

2017 Cambridge GOC Meeting Agenda

GO wiki (new pages) - Tue, 07/18/2017 - 01:31

Hla28: Created page with "=GOC Meeting, Cambridge , October 2-4, 2017= ==Agenda== ===Monday 2nd October=== *Evening: Poster session ===Tuesday 3rd October=== ===Wednesday 4th October=== ====Hands-on/W..."

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

==Agenda==
===Monday 2nd October===
*Evening: Poster session
===Tuesday 3rd October===
===Wednesday 4th October===
====Hands-on/Workshop Suggestions====

* Creating a good slim,

* Displaying annotations on gene pages,

* Good annotation practice: phenotype vs process,

* Representing biologists’ view of biology: author intent & protein domains,

* IDA v IC v New evidence code

[[Category: GO Consortium Meetings]] Hla28
Categories: GO Internal

Ontology meeting 2017-07-14

GO wiki (new pages) - Thu, 07/13/2017 - 11:20

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = DavidH will present a quick workaround for making logical definitions and subclasses using terms..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

DavidH will present a quick workaround for making logical definitions and subclasses using terms with single quotes.

Other discussion:
https://github.com/geneontology/go-ontology/projects/1

== August Meeting Agenda ==
*Will be added to the [http://wiki.geneontology.org/index.php/2017_Berkeley_GO_Editors_Workshop_II logistics page]


= Minutes =
*On call:






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

GO-CAM July 12th, 2017

GO wiki (new pages) - Tue, 07/11/2017 - 09:46

David: Created page with "= Zoom URL = https://stanford.zoom.us/j/679970729 = Agenda = ==Update on Proposal for a Tabular Editing Interface== == Priority list == *Handling evidence properly ** Com..."

= Zoom URL =
https://stanford.zoom.us/j/679970729

= Agenda =

==Update on Proposal for a Tabular Editing Interface==

== Priority list ==

*Handling evidence properly
** Complex model resolution to specify gene products along with evidence.
***http://noctua.berkeleybop.org/editor/graph/gomodel:586fc17a00001081
***http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001750
*** Karen's concerns regarding evidence usage and mapping
* Handling groups as output in the GPAD file.
* Creating biological processes to generate regulation annotations.
**http://noctua.berkeleybop.org/editor/graph/gomodel:586fc17a00000366
*Generating a tabular interface
*Filtering GPAD annotations
** Regulation annotations when a named class exists
***http://noctua.berkeleybop.org/editor/graph/gomodel:586fc17a00000366
** Causal annotations to molecular functions
***http://noctua.berkeleybop.org/editor/graph/gomodel:55c3ef4c00000001
*Curators should evaluate their workflow for areas where we can improve efficiency - high priority
*Import existing CC and BP annotations
*Documentation


= Minutes =
*On call:

== Software Updates ==



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

Manager Call 2017-07-19

GO wiki (new pages) - Mon, 07/10/2017 - 08:51

Pascale: Created page with "= Joining the Call on Zoom = https://stanford.zoom.us/j/754529609 = Agenda = == From June 21st Call == === Annotation Qualifiers === *What are the next steps? **Add guidelin..."

= Joining the Call on Zoom =
https://stanford.zoom.us/j/754529609

= Agenda =
== From June 21st Call ==

=== Annotation Qualifiers ===
*What are the next steps?
**Add guidelines to github documentation with examples for use of each BP qualifier (include positive and negative directionality)
**Propose a half-day online working group meeting for this
***acts_upstream_of_or_within
***acts_upstream_of
***involved_in
***regulates
**Decide on SOP for legacy annotations
***This may be different for different annotation groups.
***What would be involved in providing computational approaches to help curators?



===Working groups management on GitHub===
Pascale has created new ‘Projects’ from the action items that proposed working groups at the GOC meeting, see
https://github.com/orgs/geneontology/projects
It would be nice to have a project lead on each of these, and add any relevant ticket.

We need to prioritize and probably add additional working groups.






= Minutes =

*On call:



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

Annotation Conf. Call 2017-07-11

GO wiki (new pages) - Mon, 07/10/2017 - 04:55

Vanaukenk: /* Annotation of Signaling Pathways in GO */

= Meeting URL - NOTE CHANGE TO ZOOM =
*https://stanford.zoom.us/j/976175422

= Agenda =
== Annotation of Signaling Pathways in GO ==
*[https://github.com/geneontology/go-annotation/projects Github Projects Page for GO-Annotation]
*[http://www.cellsignallingbiology.org/csb/002/002.pdf Cell Signaling Pathways Review Article]
*[http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Signalling_Workshop October Cambridge Meeting Agenda]
*Suggested pathways from curators:
**Apoptosis
**GPCR
***Gastrin
**Jak/STAT
**MAPK
***Erk
***Jnk
***p38
**Nodal
**Notch
**Sonic Hedgehog
**TOR
**VEGF
**Wnt

= Minutes =
*On call:


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

Ontology meeting 2017-07-07

GO wiki (new pages) - Thu, 07/06/2017 - 08:53

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = This week we will have Pascale go over the work she is doing on targeting. Other discussion: htt..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

This week we will have Pascale go over the work she is doing on targeting.

Other discussion:
https://github.com/geneontology/go-ontology/projects/1


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

Ontology editor's conference call minutes July-Dec 2017

GO wiki (new pages) - Thu, 07/06/2017 - 08:50

David:

*[[Ontology meeting 2017-07-07|July 7]]







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

Manager Call 2017-07-05

GO wiki (new pages) - Wed, 07/05/2017 - 06:02

Vanaukenk: /* New Issues */

= Joining the Call on Zoom =
https://stanford.zoom.us/j/754529609

= Agenda =
== From June 21st Call ==
=== Licensing ===
*The DO has recently gone to a CC0 license. http://disease-ontology.org/
=== Attributes in Noctua Annotations ===
*https://github.com/geneontology/go-ontology/issues/13511

== New Issues ==
=== Signaling Project and Cambridge Meeting ===
*Project strategy
*Cambridge meeting, Sunday, October 1st
**Any funding available for non GO-funded groups?
=== GO AGR Slim ===
*[https://github.com/geneontology/go-ontology/issues/13791 Modification to AGR slim]
=== Annotation Qualifiers ===
*What are the next steps?
**Add guidelines to github documentation with examples for use of each BP qualifier (include positive and negative directionality)
***acts_upstream_of_or_within
***acts_upstream_of
***involved_in
***regulates
**Decide on SOP for legacy annotations
***This may be different for different annotation groups.
***What would be involved in providing computational approaches to help curators?

= Minutes =

*On call:



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

Ontology meeting 2017-06-30

GO wiki (new pages) - Thu, 06/29/2017 - 05:12

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = This week we will have Eric give us an overview of the GO-Rules, so we all understand where they..."

= Conference Line =

*Zoom: https://stanford.zoom.us/j/828418143

= Agenda =

This week we will have Eric give us an overview of the GO-Rules, so we all understand where they live and how they work.

* https://github.com/geneontology/go-ontology/tree/master/src/sparql - go-ontology SPARQL rules (Chris)
* https://github.com/geneontology/go-site/blob/master/metadata/rules/ - annotation rules + SPARTA (Eric)

Other discussion:

https://github.com/geneontology/go-ontology/projects/1


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

GO-CAM June 28th, 2017

GO wiki (new pages) - Wed, 06/28/2017 - 07:43

David: Created page with "= Zoom URL = https://stanford.zoom.us/j/679970729 = Agenda = == Priority list == *Handling evidence properly ** Complex model resolution to specify gene products along wit..."

= Zoom URL =
https://stanford.zoom.us/j/679970729

= Agenda =

== Priority list ==

*Handling evidence properly
** Complex model resolution to specify gene products along with evidence.
***http://noctua.berkeleybop.org/editor/graph/gomodel:586fc17a00001081
***http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001750
*** Karen's concerns regarding evidence usage and mapping
* Handling groups as output in the GPAD file.
* Creating biological processes to generate regulation annotations.
**http://noctua.berkeleybop.org/editor/graph/gomodel:586fc17a00000366
*Generating a tabular interface
*Filtering GPAD annotations
** Regulation annotations when a named class exists
***http://noctua.berkeleybop.org/editor/graph/gomodel:586fc17a00000366
** Causal annotations to molecular functions
***http://noctua.berkeleybop.org/editor/graph/gomodel:55c3ef4c00000001
*Curators should evaluate their workflow for areas where we can improve efficiency - high priority
*Import existing CC and BP annotations
*Documentation


= Minutes =
*On call:

== Software Updates ==



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