Annotation Conf. Call 2018-01-09: Difference between revisions
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==Review of Cambridge meeting action items and milestones for 2018-05 GOC meeting in NYC== | ==Review of Cambridge meeting action items and milestones for 2018-05 GOC meeting in NYC== | ||
In geneontology/go-annotation on github, there is a Milestone '2018-05 GOC meeting' | In geneontology/go-annotation on github, there is a Milestone '2018-05 GOC meeting' | ||
==Requests for Proposals== | |||
====Protein Complexes Working Group==== | |||
*[https://github.com/geneontology/go-annotation/issues/1662 Inferring MF annotations for complex members] | |||
*[https://github.com/geneontology/go-annotation/issues/1650 Proposal for guidelines for using contributes_to] | |||
*[https://github.com/geneontology/go-annotation/issues/1500 should we really use "colocalizes_with" with cc complex terms] | |||
*[https://github.com/geneontology/go-annotation/issues/1661 Protein complex representation in Noctua] | |||
*[https://github.com/geneontology/go-ontology/issues/14375 Do we have to hard-code CC complex terms to MF and BP relationships in the ontology?] | |||
**Working group established, one meeting in late November | |||
**Next meeting? | |||
====Annotation Relations - Cellular Component==== | |||
*[https://github.com/geneontology/go-annotation/issues/1500 should we really use "colocalizes_with" with cc complex terms] | |||
*[https://github.com/geneontology/go-annotation/issues/1639 Relations to describe gene product - component annotation] | |||
*Draft proposal (Kimberly) - need input from Chris on RO | |||
**Relations between gene products and organelles/locations | |||
**Relations between gene products and macromolecular complexes | |||
====InterPro2GO Pipeline==== | |||
*[https://github.com/geneontology/go-annotation/issues/1653 InterPro2GO pipeline] | |||
**Need to establish a working group here | |||
====Engaging External Experts==== | |||
*[https://github.com/geneontology/go-annotation/issues/1652 Recommendations and guidelines for next time we engage an external group of experts] | |||
**Need to have a working group or responsible persons here, too | |||
==Annotation Review== | ==Annotation Review== | ||
====HTP Annotations==== | ====HTP Annotations==== | ||
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*https://github.com/geneontology/go-ontology/issues/14275 NTR: “receptor ligand agonist activity” and “receptor ligand antagonist activity”] | *https://github.com/geneontology/go-ontology/issues/14275 NTR: “receptor ligand agonist activity” and “receptor ligand antagonist activity”] | ||
==Requests for Guidelines== | ==Requests for Guidelines== | ||
====GO-CAM and Noctua==== | ====GO-CAM and Noctua==== | ||
*Wednesday calls ongoing | |||
*[https://github.com/geneontology/go-annotation/issues/1651 QC for Noctua models] | *[https://github.com/geneontology/go-annotation/issues/1651 QC for Noctua models] | ||
*[https://github.com/geneontology/go-annotation/issues/1517 New qualifiers for biological processes - including how to deal with legacy annotations] | *[https://github.com/geneontology/go-annotation/issues/1517 New qualifiers for biological processes - including how to deal with legacy annotations] |
Revision as of 11:56, 8 January 2018
Meeting URL
Agenda
Review of Cambridge meeting action items and milestones for 2018-05 GOC meeting in NYC
In geneontology/go-annotation on github, there is a Milestone '2018-05 GOC meeting'
Requests for Proposals
Protein Complexes Working Group
- Inferring MF annotations for complex members
- Proposal for guidelines for using contributes_to
- should we really use "colocalizes_with" with cc complex terms
- Protein complex representation in Noctua
- Do we have to hard-code CC complex terms to MF and BP relationships in the ontology?
- Working group established, one meeting in late November
- Next meeting?
Annotation Relations - Cellular Component
- should we really use "colocalizes_with" with cc complex terms
- Relations to describe gene product - component annotation
- Draft proposal (Kimberly) - need input from Chris on RO
- Relations between gene products and organelles/locations
- Relations between gene products and macromolecular complexes
InterPro2GO Pipeline
- InterPro2GO pipeline
- Need to establish a working group here
Engaging External Experts
- Recommendations and guidelines for next time we engage an external group of experts
- Need to have a working group or responsible persons here, too
Annotation Review
HTP Annotations
- Review HTP annotations
- HTP_Guidelines_condensed_version
- Forward genetic screens - may need further clarification and examples of what is/is not high throughput
- HTP_Guidelines_condensed_version
- HTP-types will not be allowed as evidence for ISS+ISO
Signaling Workshop
In geneontology/go-annotation on github, there is a label 'GO workshop signaling 2017'
General Signaling Issues
- Review annotation to 'receptor ligand activity' (GO:0048018)
- MP cell surface receptor signaling pathway
Ca2+ Signaling - Fertilization
GPCR-mediated cAMP Signaling
- Review annotations to 'cAMP biosynthetic process'
- Review annotation for GPCR
- NTR: regulation terms for adenylate cyclase-activating adrenergic receptor signaling pathway
- cAMP biosynthetic process - merges & obsoletion
- GO:0007189 adenylate cyclase-activating G-protein coupled receptor signaling pathway... missing parent
JAK/STAT Signaling Pathway
MAPK Cascade
Canonical Wnt Signaling Pathway
- PAINT:PTN000226268 Wnt signaling pathway to positive regulation of...
- Review annotations to beta catenin
- PANTHER:PTN000139394: remove wnt binding annotation to smoothened receptors
- https://github.com/geneontology/go-ontology/issues/14275 NTR: “receptor ligand agonist activity” and “receptor ligand antagonist activity”]
Requests for Guidelines
GO-CAM and Noctua
- Wednesday calls ongoing
- QC for Noctua models
- New qualifiers for biological processes - including how to deal with legacy annotations
Minutes
- On call: