Web feeds

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

Signalling Workshop Agenda

GO wiki (new pages) - Wed, 06/28/2017 - 01:49

Ruth.lovering:

[[http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Signalling_Workshop Back to Signalling Workshop page]]


{| {{Prettytable}} class='sortable'
|-
! Time
! Item

|-
| 9am to 11am
|
|-
| 11am to 11:30 am
| Break
|-
| 11:30am to 1pm
|
|-
| 1pm to 2pm
| Lunch
|-
| 2pm to 3:30pm
|
|-
| 3:30pm to 3:30pm
| Break
|-
| 3:30pm to 5:00pm
|
|}


==Proposed topics for discussion==

==Additional Notes==




[[Category: GO Consortium Meetings]]
[[Category: Working Groups]] Ruth.lovering
Categories: GO Internal

2017 Cambridge GOC Signalling Workshop

GO wiki (new pages) - Tue, 06/27/2017 - 04:25

Valwood: Signalling Workshop

placeholder Valwood
Categories: GO Internal

Ontology meeting 2017-06-23

GO wiki (new pages) - Thu, 06/22/2017 - 11:09

Cjm:

= Conference Line =

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

= Agenda =

There are several people traveling or at meetings, so we will leave the agenda of this meeting in a bit of flux.
The current proposal is to have Eric give us an overview of the GO-Rules, so we all understand where they live and how they work.
But, if we don't have enough editors on the call, we will postpone that.

* 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

Annotation Conf. Call 2017-06-27

GO wiki (new pages) - Mon, 06/19/2017 - 15:17

Vanaukenk: /* Minutes */

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

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

Manager Call 2017-06-21

GO wiki (new pages) - Mon, 06/19/2017 - 10:00

David: Created page with "= Joining the Call on Zoom = https://bluejeans.com/588333403 = Agenda = Licensing- The DO has recently gone to a CC0 license. http://disease-ontology.org/ = Minutes =..."

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


= Agenda =

Licensing- The DO has recently gone to a CC0 license. http://disease-ontology.org/


= Minutes =



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

Ontology meeting 2017-06-16

GO wiki (new pages) - Fri, 06/16/2017 - 05:28

David: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = Update on Barbara coming on board as an ontology editor. She will be trained after the October GO..."

= Conference Line =

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

= Agenda =

Update on Barbara coming on board as an ontology editor. She will be trained after the October GO meeting.

Please make your hotel reservations for the August Ontology developers' Meeting in CA. See Chris' email.

For today's meeting we will focus on the GitHub Projects page:

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


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