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Ontology meeting 2017-09-15

GO wiki (new pages) - Thu, 09/14/2017 - 08:14

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = Update on the GH rota. ==GH project link== https://github.com/geneontology/go-ontology/projects..."

= Conference Line =

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

= Agenda =

Update on the GH rota.

==GH project link==

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

==David OS update on latest projects==

==Discussion==
*On call:



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

GO-CAM Sept 13, 2017

GO wiki (new pages) - Wed, 09/13/2017 - 07:54

David:

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

= Agenda =

== Table Editor Workbench ==
*Feedback from anyone using it?

== Annotation Provenance ==
*Review of how attribution is assigned for Noctua annotations
**de novo annotations
**imported annotations using function and component companions

== Annotating with any UniProtID ==
*Use add individual functionality

== On the Call ==
HJD, Edith, Karen, Sage, DavidH, Rob, TJackson

==Table Editor==

Karen has put in a few tickets. Moving the with field next to the evidence code. Make the with field a list of relevant identifiers.
If you leave the molecular function blank, it makes and annotation to a generic molecular function and gives an ND evidence code. But there is no reference, so nothing propagates.It would be better to put no evidence and have the curator add the evidence on the canvas.

Harold put in a ticket about going back and forth between the table and the canvas and seeing spurious gene product boxes on the canvas. This seems to have been fixed. Karen didn't see this. The presence of the boxes didn't seem to hurt anything.

== Provenance/Attribution ==

No one on the call has tested the provenance. It would be good to see that in the annotation preview. It would be nice to see as much information that we can that will end up in the GPAD in the preview.

== UniProtKB identifiers ==

If someone tries to use a suffixed UniProtKB identifier, there is no entity in NEO. There is also and issue putting UniProtKB identifiers in the 'with' field. In some cases is resolves to the gene and in some cases it doesn't. It never resolves with an MGI identifier. It might work with human.








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

Annotation Conf. Call 2017-09-12

GO wiki (new pages) - Fri, 09/08/2017 - 07:21

Vanaukenk: /* Update on Signaling Projects */

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

= Agenda =

== Update on Signaling Projects ==

[https://github.com/geneontology/go-annotation/projects/4 github/go-annotation Signaling Projects page]

* JAK/STAT
* GPCR
* MAPK - David, Sabrina
* Wnt - Helen (Kimberly away)
* Ca2+ (Penelope away)

== Cambridge GO Meeting ==
*Review [http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Meeting_Agenda Meeting Agenda]

= Minutes =
*On call:





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

Ontology meeting 2017-09-08

GO wiki (new pages) - Fri, 09/01/2017 - 09:56

Pascale: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = ==David OS update on latest projects== ==Discussion== Category: Ontology Category: Me..."

= Conference Line =

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

= Agenda =


==David OS update on latest projects==

==Discussion==




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

Ontology meeting 2017-09-01

GO wiki (new pages) - Wed, 08/30/2017 - 10:27

Pascale:

= Conference Line =

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

= Agenda =

==Discussion==

===Ontology developers Documentation===
* Are we OK to keep our documentation on the wiki?
** So far readthedocs has not been conclusive- barrier of entry is pretty high, so even fewer people can edit the documentation
** Creating a new doc repo (as demo'ed by Moni) is not trivial
** Having all documents in a single place makes it easier to search


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

Ontology meeting 2017-08-25

GO wiki (new pages) - Fri, 08/25/2017 - 08:17

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = Discussion: *Review of the Berkeley Workshop. What's next? [http://wiki.geneontology.org/index.p..."

= Conference Line =

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

= Agenda =

Discussion:

*Review of the Berkeley Workshop. What's next?
[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

Ontology meeting 2017-08-18

GO wiki (new pages) - Fri, 08/25/2017 - 08:12

David: Created page with "No meeting due to travel from ontology developers' workshop. Category: Ontology Category: Meetings"

No meeting due to travel from ontology developers' workshop.


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

GO-CAM August 23, 2017

GO wiki (new pages) - Wed, 08/23/2017 - 06:27

Vanaukenk: /* Agenda */

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

= Agenda =

== Table Editor Workbench ==
*Chris and Seth will demo the new 'Simple annoton editor' workbench now available in Noctua
*The table editor allows curators to add, and edit, simple annotons in a table format
*Annotations entered in the table are automatically added to the Noctua graph editor

== Annotation Provenance ==
*Review of how attribution is assigned for Noctua annotations
**de novo annotations
**imported annotations using function and component companions

== Annotating with any UniProtID ==
*Use add individual functionality

= Minutes =
*On call:


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

Annotation Conf. Call 2017-08-22

GO wiki (new pages) - Thu, 08/17/2017 - 21:04

Vanaukenk:

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

= Agenda =

== Cambridge Meeting, October, 2017 ==
* [[2017 Cambridge GOC Meeting Logistics]]
**Regsitration
* [[2017 Cambridge GOC Meeting Agenda]]
**Wednesday afternoon hands-on/workshop session. Suggestions:
***Creating a biologically useful slim (complete coverage by aspect, biologically useful terms i.e sufficient granularity, avoiding single step process terms (i.e functions), different slims for different purposes.
***Displaying GO annotations (non redundantly, in MODs, in AmiGO, in AGR), general data presentation.
****Conventional annotation display as well as GO-CAM model display
***Good annotation practice: phenotype vs process,
***Representing biologists’ view of biology: author intent & protein domains; IDA v IC v New evidence code
* [[2017 Cambridge GOC Signalling Workshop]]

== 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]] Vanaukenk
Categories: 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