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GO wiki (new pages) - Fri, 05/11/2018 - 08:01

Vanaukenk: Created page with "Category: GO-CAM Relations"

[[Category: GO-CAM Relations]] Vanaukenk
Categories: GO Internal

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GO wiki (new pages) - Thu, 05/10/2018 - 17:06

Vanaukenk: Created page with "Category: Gene Product to Term Relations"

[[Category: Gene Product to Term Relations]] Vanaukenk
Categories: GO Internal

Part of (GP2Term)

GO wiki (new pages) - Thu, 05/10/2018 - 17:06

Vanaukenk: Created page with "Category: Gene Product to Term Relations"

[[Category: Gene Product to Term Relations]] Vanaukenk
Categories: GO Internal

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GO wiki (new pages) - Thu, 05/10/2018 - 17:01

Vanaukenk: Created page with " Category: Gene Product to Term Relations"



[[Category: Gene Product to Term Relations]] Vanaukenk
Categories: GO Internal

Procedure for unmaintained annotations

GO wiki (new pages) - Wed, 05/09/2018 - 01:20

Pascale:

=Procedure to deal with unmaintained annotations=
* GOC becomes responsible for maintaining annotations for groups no longer maintaining their annotations. This means that:
# GOC/EBI runs QC checks
# GOC becomes an editor of the annotations
# Annotations will be rolled into the main GAF file

=Procedure done by EBI to clean up annotations=

==Unmapped identifiers==
* Annotations are removed
* We need to be able to map to a UniProt accession (or RNAcentral or ComplexPortal ID) in order to be able to import annotations.

==Annotations to obsolete GO terms for which no replacement is available==
* Annotations are removed

==Annotations to GO terms that are flagged as do_not_(manually_)annotate==
* Annotations are removed

==Annotations with an invalid combination of evidence code and with/from==
* Annotations are removed
As governed by the rules in https://github.com/geneontology/go-site/blob/master/metadata/eco-usage-constraints.yaml

==ISA/ISS Pfam/TIGRFAM==
Should be subjected to the 1-year expiration date rule.
We probably want to remove old 'ISA-like' annotation: TIGR_TIGRFAMS identifier in their with/from. The type of the entities supplied by these two databases is not compatible - according to the rules in eco-usage-constraints.yaml - with the ISS evidence code (strictly, not compatible with ECO:0000250); however, it is compatible with ECO:0000247 (ISA)

=Special cases=

==For bacterial species==
Replace:
* GO:0001539 cilium or flagellum-dependent cell motility -> GO:0071973 bacterial-type flagellum-dependent cell motility for all bacterial annotations
* GO:0000910 cytokinesis -> GO:0043093 FtsZ-dependent cytokinesis




[[Category: Annotation]] Pascale
Categories: GO Internal

GO-CAM Noctua Call 2018-05-09

GO wiki (new pages) - Tue, 05/08/2018 - 17:47

Vanaukenk:

= Meeting URL =
*https://stanford.zoom.us/j/679970729

= Agenda =
== Progress Towards Noctua 1.0 Release ==
*[https://github.com/orgs/geneontology/projects/6 Review of github tickets for Noctua 1.0]

== Review Schedule of Talks for GOC Meeting ==

== Simple Annoton Editor ==
*Review tickets on [https://github.com/geneontology/simple-annoton-editor/issues github tracker]
*Planning to integrate code with Noctua later this week
*Karen and Kimberly have tested many features
*A few small things left to address for 1.0
*Other issues to discuss for the next release
**Editing
**Model searching
**Protein complexes
**TPC integration
**More real-time error checks

== Derived GPAD Output ==
*[https://github.com/geneontology/minerva/issues/109 Causal relations in GPAD output]
*Annotation extensions to include
*Results of syntax check from Tony S. at UniProt
**Qualifier list
**Annotation extensions white list
**Obsolete GO IDs
**IPI annotations: With/From vs has_input AE
**Evidence codes that don't map to three-letter GO codes
**Do not annotate or Do not manually annotate subsets

== Annotation SOPs ==
*https://github.com/geneontology/noctua/issues/552

== Annotation Templates ==
*We need to give curators templates of common biological processes so we can get consistent annotation
*Examples:
**Transcription
*Do we need a separate working group for this?

= Minutes =
*On call: Chris, Dustin, Edith, Harold, Jim, Kevin, Kimberly, Laurent-Philipe, Rob, Sage, Seth, Stacia, Suzi A., Suzi L., Tremayne

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

Annotation Conf. Call 2018-05-08

GO wiki (new pages) - Mon, 05/07/2018 - 14:30

Vanaukenk: Created page with "= Agenda = == GOC Meeting, NYU, New York, NY, May 12-14th == *Review Agenda *[http://wiki.geneontology.org/index.php/2018_NYU_GOC_Meeting_Logistics Logistics] *[http://wiki.g..."

= Agenda =
== GOC Meeting, NYU, New York, NY, May 12-14th ==
*Review Agenda
*[http://wiki.geneontology.org/index.php/2018_NYU_GOC_Meeting_Logistics Logistics]
*[http://wiki.geneontology.org/index.php/2018_NYU_GOC_Meeting_Agenda Agenda]

== 20th Anniversary GO Meeting, Montreal, Canada ==
*Dates set for Oct 17-19

== Annotation Survey ==
*We are conducting a [https://goo.gl/forms/rLovY736aX1gxqHe2 survey] on annotation practices across the GOC
*Thank you to everyone who responded
*Compiling all of the responses

== Ontology Development and Annotation Review ==
=== Transcription factor refactoring ===
*Any updates?

== Updates on Projects ==
=== MAPK Cascade ===
*[https://github.com/geneontology/go-annotation/issues/1592 MAPK cascade- Signaling Project]
=== Extracellular Matrix ===
*[https://github.com/geneontology/go-ontology/projects/9 Extracellular matrix revisions]
**[https://github.com/geneontology/go-ontology/issues/15294 proposal]
=== Canonical Wnt Signaling Pathway ===
*Have compiled annotations to review
*Main issues:
**Distinguishing gene products that are involved in canonical Wnt signaling vs +/- regulation of canonical Wnt signaling
**Annotating to more granular child of Wnt signaling pathway when appropriate
**Annotation of downstream targets to the canonical Wnt signaling pathway

== GO-CAM/Noctua ==
*Next call tomorrow, Wednesday, May 9th at 11:00am EDT (see Google calendar)

= Minutes =
*On call:



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

Ontology meeting 2018-05-07

GO wiki (new pages) - Mon, 05/07/2018 - 06:20

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 == Editors Discussio..."

= Conference Line =

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

= Agenda =


==GH project link==
https://github.com/geneontology/go-ontology/projects/1

== Editors Discussion ==
=== Outstanding Pull Requests ===



= Minutes =
*On call:


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

Manager Call 2018-05-03

GO wiki (new pages) - Wed, 05/02/2018 - 04:22

Vanaukenk:

[[Category:GO Managers Meetings]]

= Call in info=
https://stanford.zoom.us/j/754529609

== New Annotation File Submissions ==
*GeneDB would like to submit new files
*SVN or pick up from their website?

=Pipeline=
Review of the GO release pipeline.

= Agenda =
== NYC Meeting Agenda ==
*Start working on the agenda in more details
**https://github.com/geneontology/go-ontology/milestone/5
**https://github.com/geneontology/go-annotation/milestone/2

===SAB agenda, plans===
'''ACTION POINT'''
Please everyone make slides for the SAB meeting for your part by '''Friday April 27'''
Slides should be added here: https://drive.google.com/drive/u/0/folders/1iOGHjKc9FN_ShrlNEW0CvOmJANzXqep-
*Looks like this was done. Shall we have a look at the materials? David
Categories: GO Internal

Ontology meeting 2018-04-30

GO wiki (new pages) - Mon, 04/30/2018 - 05:05

Pascale: Created page with "= Conference Line = *Zoom: https://stanford.zoom.us/j/828418143 = Agenda = ==GH project link== https://github.com/geneontology/go-ontology/projects/1 == Editors Discussio..."

= Conference Line =

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

= Agenda =


==GH project link==
https://github.com/geneontology/go-ontology/projects/1

== Editors Discussion ==
Discussion of slim maintenance:
(Pascale)
https://docs.google.com/document/d/1KMASaUdOJSwB1EClRQ69RK77Wqc7AdbWa8EcENidLjM/edit




= Minutes =
*On call:



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