Web feeds

GO-CAM June 28th, 2017

GO wiki (new pages) - 16 hours 15 min ago

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) - 22 hours 9 min ago

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

GO-CAM June 14th, 2017

GO wiki (new pages) - Wed, 06/14/2017 - 05:13

David: /* Priority list */

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

= Agenda =
== Recent Software Updates ==

* Editors' preview now available.
* Export GPAD menu option now using reasoner (ie Jim's code; Heiko's is retired)

== 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
** Creating biological process 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

== Review of github Tickets ==
*https://github.com/geneontology/noctua/issues

= Minutes =
*On call:

== Software Updates ==



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

Ontology meeting 2017-06-09

GO wiki (new pages) - Thu, 06/08/2017 - 07:33

David: Created page with "= Conference Line = *Bluejeans: https://bluejeans.com/164681006 = Agenda = For today's meeting we will focus on two things: * We will go over the latest version of the SOP..."

= Conference Line =
*Bluejeans: https://bluejeans.com/164681006

= Agenda =

For today's meeting we will focus on two things:

* We will go over the latest version of the SOP documentation for ontology editing. Pascale will go over the edits that she has made recently. Should we have a crash course in the markdown syntax?

https://github.com/geneontology/go-ontology/blob/master/src/ontology/README-editors.md

* We will go over the agenda for the advanced ontology training in Berkeley in August. Chris has started a page.

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


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

2017 Berkeley GO Editors Workshop II

GO wiki (new pages) - Wed, 06/07/2017 - 20:02

Cjm: Created page with "= Agenda = == Topics == * Equivalence axioms - editors would like more guidelines on how to construct these. * OWL GCIs- Where do they live and how do they work? * Advan..."

= Agenda =

== 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


= Logistics =

== Accommodations ==

* http://www.fourpointssanfranciscobaybridge.com/

Getting there:

* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/MacArthur+BART+Station,+40th+Street,+Oakland,+CA/@37.8346259,-122.2866117,15z/am=t/data=!3m1!5s0x80857e0870dbdd83:0x571df460c4d9d3cb!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857de2a98ae50d:0xc5fce433b2157d9f!2m2!1d-122.267047!2d37.8290643!3e3 shuttle from MacArthur BART]

Taxis also available from either MacArthur or Ashby

== Meeting Location ==

[http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/ Berkeley Lab, Aquatic Park Offices]

Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley
Physical address: 717 Potter Street, Berkeley, CA 94710

=== Travel between hotel and meeting ===

* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8448697,-122.3011831,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e2 Walk, 1.3 miles]
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8450306,-122.3024045,15z/am=t/data=!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e3 Free Hollis Shuttle ]
* Taxi/Lyft/Uber

Aim to be at the lab for 9am

== Participants ==

{| {{Prettytable}}
|-
! Name
! Organization
! Comments
|-
| David Hill
| Jackson Laboratory
|
|
|-
| Kimberly Van Auken
| Caltech
|
|-
| Pascale Gaudet
| SIB Swiss Institute of Bioinformatics
|
|-
| David Osumi-Sutherland
| EBI
|
|-
|}

[[Category:Meetings]]
[[Category:Protege]] Cjm
Categories: GO Internal

Annotation Conf. Call 2017-06-13

GO wiki (new pages) - Wed, 06/07/2017 - 05:56

Vanaukenk: /* Review Corvallis Meeting Action Items */

= Bluejeans URL =
https://bluejeans.com/993661940

= Agenda =
== Review Corvallis Meeting Action Items ==
=== GO github Projects Page ===
https://github.com/orgs/geneontology/projects/1

=== Infrastructure ===
[https://github.com/geneontology/go-site/tree/master/metadata/datasets Use of YAML files for dataset provenance]

=== Noctua and GO-CAM Modeling ===
'''Action Item:''' Provide ways for users to recover and digest CAM units. Ideas include rule-based generations of text statements from model, cytoscape view of network described, etc.

=== Enrichment Analyses ===
[https://github.com/geneontology/go-site/issues/361 Contact Paul Pavlidis about regular reanalysis of genomic automatic annotations]

=== Community Interaction ===
[https://github.com/geneontology/go-site/issues/360 Improve information on citing the GO in analytical publications]

= Minutes =
*On call:




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

GO-CAM May 24th, 2017

GO wiki (new pages) - Tue, 05/23/2017 - 15:53

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