GO Internal

Causally upstream of or within, positive effect

GO wiki (new pages) - Fri, 05/11/2018 - 13:58

Vanaukenk: /* Examples of Usage */

== Overview ==
The 'causally upstream of or within, positive effect' relation is used to relate two GO Biological Processes.
=== Definition ===


=== Child Terms ===

== Examples of Usage ==
Exemplar:http://noctua.berkeleybop.org/editor/graph/gomodel:57c82fad00000847

== Quality Control Checks ==

== Relations Ontology ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0004047 causally upstream of or within, positive effect]

== Review Status ==

Last reviewed: May 11, 2018

[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]

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

Directly positively regulates

GO wiki (new pages) - Fri, 05/11/2018 - 12:30

Vanaukenk: /* Examples of Usage */

== Overview ==
The 'directly positively regulates' relation is used to relate two GO Molecular Functions whenever two Molecular Functions succeed one another directly, and the first provides regulates the activity of the second via a direct physical interactions. The 'directly positively regulates' relation is used to describe a relation, for example, between a ligand and the receptor that it activates.
=== Definition ===
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.

=== Child Terms ===

== Examples of Usage ==
*In GO-CAM models, the 'directly positively regulates' relation is used for associations between two Molecular Functions.

*In canonical Wnt signaling, a Wnt ligand 'directly positively regulates' the activity of a Frizzled receptor.
* Examplar: http://noctua.berkeleybop.org/editor/graph/gomodel:56d1143000003025

== Quality Control Checks ==

== Relations Ontology ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002413 directly provides input for]

== Review Status ==

Last reviewed: May 11, 2018

[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]

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

Directly provides input for

GO wiki (new pages) - Fri, 05/11/2018 - 11:30

Vanaukenk: /* Examples of Usage */

== Overview ==
The 'directly provides input for' relation is used to relate two GO Molecular Functions whenever two Molecular Functions succeed one another directly, and the first provides an input for the Molecular Function of the second. The 'directly provides input for' relation is used to describe a relations, for example, between the Molecular Functions that are part of metabolic pathways.

=== Definition ===
P1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c

=== Child Terms ===

== Examples of Usage ==
*In GO-CAM models, the 'directly provides input' relation is used for associations between two Molecular Functions.

*In glycolysis, triose phosphate isomerase activity 'directly provides input for' glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity.
* Examplar: http://noctua.berkeleybop.org/editor/graph/gomodel:55c3ef4c00000001
** Inferred GPAD: http://noctua.berkeleybop.org/workbench/annpreview/?model_id=gomodel:5323da1800000002

== Quality Control Checks ==

== Relations Ontology ==
[http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0002413 directly provides input for]

== Review Status ==

Last reviewed: May 11, 2018

[http://wiki.geneontology.org/index.php/Annotation_Relations Back to: Annotation Relations]

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

Enabled by

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

Is active in

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

Contributes to

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