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==== | ====Protein Complexes Working Group==== | ||
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**Working group established, one meeting in late November | **Working group established, one meeting in late November | ||
**Next meeting? | **Next meeting? | ||
*Updates from Birgit: | |||
**Latest: I have to design a user survey to answer some of the open questions from our call. It's on my to-do list for this month. | |||
**Other discussion points rely on us finishing the complex IDs. Our developers were rather stretched this autumn so it's taking a little longer than expected but they are back on it and it's really close! | |||
====Annotation Relations - Cellular Component==== | ====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/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] | *[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 | |||
====Annotation Relations - Biological Process==== | |||
*[https://github.com/geneontology/go-annotation/issues/1517 New qualifiers for biological processes - including how to deal with legacy annotations] | |||
====Cellular Component Annotations for Transmembrane Proteins==== | |||
[https://github.com/geneontology/go-annotation/issues/1621 https://github.com/geneontology/go-annotation/issues/1621] | |||
====InterPro2GO Pipeline==== | ====InterPro2GO Pipeline==== | ||
Line 43: | Line 39: | ||
====Engaging External Experts==== | ====Engaging External Experts==== | ||
*[https://github.com/geneontology/go-annotation/issues/1652 Recommendations and guidelines for next time we engage an external group of 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== | |||
====HTP Annotations==== | |||
*[https://github.com/geneontology/go-annotation/issues/1655 Review HTP annotations] | |||
**[https://drive.google.com/drive/u/0/folders/0BwxQUKMmvm0kRTlSNmNmZV9aTHc HTP_Guidelines_condensed_version] | |||
***Forward genetic screens - may need further clarification and examples of what is/is not high throughput | |||
*[https://github.com/geneontology/go-annotation/issues/1654 HTP-types will not be allowed as evidence for ISS+ISO] | |||
**Set date for meeting to discuss ISS/ISO transfer from HTP to be discussed in Feb. | |||
====Signaling Workshop==== | |||
In geneontology/go-annotation on github, there is a label 'GO workshop signaling 2017' | |||
====General Signaling Issues==== | |||
*[https://github.com/geneontology/go-annotation/issues/1713 Review annotation to 'receptor ligand activity' (GO:0048018)] | |||
*[https://github.com/geneontology/go-ontology/issues/13912 MP cell surface receptor signaling pathway] | |||
=== | ====Ca2+ Signaling - Fertilization==== | ||
====GO-CAM and Noctua== | *[https://github.com/geneontology/go-ontology/issues/13980 Revision of relationship of GO:0060468 (prevention of polyspermy) and GO:0060471 ( cortical granule exocytosis)] | ||
====GPCR-mediated cAMP Signaling==== | |||
*[https://github.com/geneontology/go-annotation/issues/1712 Review annotations to 'cAMP biosynthetic process'] | |||
*[https://github.com/geneontology/go-annotation/issues/1691 Review annotation for GPCR] | |||
*[https://github.com/geneontology/go-ontology/issues/14733 NTR: regulation terms for adenylate cyclase-activating adrenergic receptor signaling pathway] | |||
*[https://github.com/geneontology/go-ontology/issues/14718 cAMP biosynthetic process - merges & obsoletion] | |||
*[https://github.com/geneontology/go-ontology/issues/13903 GO:0007189 adenylate cyclase-activating G-protein coupled receptor signaling pathway... missing parent] | |||
====JAK/STAT Signaling Pathway==== | |||
====MAPK Cascade==== | |||
*[https://github.com/geneontology/go-ontology/issues/14676 How to name specific MAPK pathways] | |||
====Canonical Wnt Signaling Pathway==== | |||
*[https://github.com/geneontology/go-annotation/issues/1736 PAINT:PTN000226268 Wnt signaling pathway to positive regulation of... ] | |||
*[https://github.com/geneontology/go-annotation/issues/1714 Review annotations to beta catenin] | |||
*[https://github.com/geneontology/go-annotation/issues/1696 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”] | |||
==GO-CAM and Noctua== | |||
*No call tomorrow | |||
*Software team has been working on the priority issues for Noctua 1.0 release | |||
*[https://github.com/geneontology/go-annotation/issues/1651 QC for Noctua models] | *[https://github.com/geneontology/go-annotation/issues/1651 QC for Noctua models] | ||
* | |||
==Protein2GO Reports== | |||
*Protein2GO users please remember to check the monthly reports and work on updating/fixing flagged annotations | |||
==Two Working Meetings== | |||
*January 22nd - 26th: Docathon at Berkeley | |||
*February 12 - 16th: Ontology GitHub jamboree in Denver | |||
= Minutes = | = Minutes = | ||
*On call: | *On call: David H, Eric, George, Giulia, Harold, Helen, Karen, Kimberly, Li, Liz, Pascale, Paul T., Petra, Rachael, Rob, Sabrina, Sage, Sandra, Stacia, Stan, Suzi, Tanya, Tom, Val | ||
Latest revision as of 14:11, 9 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?
- Updates from Birgit:
- Latest: I have to design a user survey to answer some of the open questions from our call. It's on my to-do list for this month.
- Other discussion points rely on us finishing the complex IDs. Our developers were rather stretched this autumn so it's taking a little longer than expected but they are back on it and it's really close!
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
Annotation Relations - Biological Process
Cellular Component Annotations for Transmembrane Proteins
https://github.com/geneontology/go-annotation/issues/1621
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
- Set date for meeting to discuss ISS/ISO transfer from HTP to be discussed in Feb.
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”]
GO-CAM and Noctua
- No call tomorrow
- Software team has been working on the priority issues for Noctua 1.0 release
- QC for Noctua models
Protein2GO Reports
- Protein2GO users please remember to check the monthly reports and work on updating/fixing flagged annotations
Two Working Meetings
- January 22nd - 26th: Docathon at Berkeley
- February 12 - 16th: Ontology GitHub jamboree in Denver
Minutes
- On call: David H, Eric, George, Giulia, Harold, Helen, Karen, Kimberly, Li, Liz, Pascale, Paul T., Petra, Rachael, Rob, Sabrina, Sage, Sandra, Stacia, Stan, Suzi, Tanya, Tom, Val