GO Internal

Annotation Conf. Call 2017-10-24

GO wiki (new pages) - Fri, 10/20/2017 - 06:48

Vanaukenk: Created page with "= Meeting URL = *https://stanford.zoom.us/j/976175422 = Agenda = = Minutes = *On call: Category: Annotation Working Group"

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

= Agenda =

= Minutes =
*On call:



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

Ontology meeting 2017-10-20

GO wiki (new pages) - Thu, 10/19/2017 - 11:13

David:

= Conference Line =

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

= Agenda =

== Review of the GOC meeting paying particular attention to ontology tasks ==

== Should we pick a different time for this meeting? ==

==GH project link==

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

David H will be away next week and for several weeks in November. We need a volunteer to host these meetings.


==Discussion==
*On call:



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

Ontology meeting 2017-10-13

GO wiki (new pages) - Thu, 10/19/2017 - 11:10

David: Created page with "No meeting due to PRO meeting travel. Category: Ontology Category: Meetings"

No meeting due to PRO meeting travel.


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

Ontology meeting 2017-10-06

GO wiki (new pages) - Thu, 10/19/2017 - 11:10

David: Created page with "No meeting due to GOC meeting Category: Ontology Category: Meetings"

No meeting due to GOC meeting


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

Ontology meeting 2017-09-29

GO wiki (new pages) - Thu, 10/19/2017 - 11:09

David: Created page with "No meeting due to GOC meeting Category: Ontology Category: Meetings"

No meeting due to GOC meeting


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

Manager Call 2017-10-18

GO wiki (new pages) - Thu, 10/05/2017 - 23:26

Pascale: Created page with "* GOC meeting action item review * GOC mailing lists clean up: ** Remove/merge some lists ** Remove some people for eg from Managers list ? Category: GO Managers Meetin..."

* GOC meeting action item review
* GOC mailing lists clean up:
** Remove/merge some lists
** Remove some people for eg from Managers list ?




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

GO-CAM Sept 27, 2017

GO wiki (new pages) - Wed, 09/27/2017 - 07:08

Vanaukenk: /* GPAD Outputs */

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

= Agenda =
== GPAD Outputs ==
[https://github.com/geneontology/noctua/issues/500 GPAD missing annotations via 'causally upstream of'?]

[http://noctua.berkeleybop.org/editor/graph/gomodel:59bee34700000110 TEST: causally upstream of - KRC]

== Attribution ==
[https://github.com/geneontology/noctua/issues/458 Attribution with GO-CAM exports to GOC annotation files]

== Simple Annoton Editor ==

[https://github.com/geneontology/noctua/issues/492 dealing with blank MF in the simple annoton editor]

[https://github.com/geneontology/simple-annoton-editor/issues/12 Extend form to include standard GO-CAM model fields]

[https://github.com/geneontology/simple-annoton-editor/issues/10 Bare MF annotation should generate part-of triples]

= Minutes =
*On call:




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

Annotation Conf. Call 2017-09-26

GO wiki (new pages) - Sun, 09/24/2017 - 10:19

Vanaukenk: /* Update on Signaling Project */

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

= Agenda =
== Review Cambridge Consortium Meeting Logistics and Agenda ==

== Update on Signaling Project ==
*[http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Signalling_Workshop Workshop, Sunday, October 1st]
**Please update the [http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Signalling_Workshop#Attendees Attendees table]
*[http://wiki.geneontology.org/index.php/Signalling_Workshop_Agenda Agenda Page]
**Need volunteers for minutes - one topic/person
*Presenters - please add all relevant docs, spreadsheets, slides to [https://drive.google.com/drive/u/0/folders/0B7bEr6HANSlGQmlCYm5VRHNMNW8 Signaling Project folder] on GO's Google Drive

= Minutes =
*On call:



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

Ontology meeting 2017-09-22

GO wiki (new pages) - Thu, 09/21/2017 - 09:43

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = ==GH project link== https://github.com/geneontology/go-ontology/projects/1 ==Orverview of the G..."

= Conference Line =

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

= Agenda =

==GH project link==

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

==Orverview of the GOC meeting Agenda==

http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Meeting_Agenda

http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Signalling_Workshop

==Discussion==
*On call:



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

Manager Call 2017-09-20

GO wiki (new pages) - Tue, 09/19/2017 - 13:01

David: Created page with "= Joining the Call on Zoom = https://stanford.zoom.us/j/754529609 = Agenda = ==GOC meeting agenda== Since this is the last meeting before the GOC Meeting in Cambridge, we sh..."

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

= Agenda =

==GOC meeting agenda==
Since this is the last meeting before the GOC Meeting in Cambridge, we should go over the agenda.

http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Meeting_Agenda


* At annotation call, some people requested the workshops to be moved earlier in the meeting (Tuesday AM 3rd October?)

= Minutes =



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

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