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'
===Annotation Review===
====HTP Annotations====
*[https://github.com/geneontology/go-annotation/issues/1655 Review HTP annotations]
**Forward genetic screens - needs clarification
*[https://github.com/geneontology/go-annotation/issues/1654 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====
*[https://github.com/geneontology/go-annotation/issues/1713 Review annotation to 'receptor ligand activity' (GO:0048018)]
====Ca2+ Signaling - Fertilization====
====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]
====JAK/STAT Signaling Pathway====
====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]


===Requests for Proposals===
==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====
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====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]


===Requests for Guidelines===
====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]
*[https://github.com/geneontology/go-annotation/issues/1517 New qualifiers for biological processes - including how to deal with legacy annotations]
 
==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

Annotation Relations - Cellular Component

Annotation Relations - Biological Process

Cellular Component Annotations for Transmembrane Proteins

https://github.com/geneontology/go-annotation/issues/1621

InterPro2GO Pipeline

Engaging External Experts

Annotation Review

HTP Annotations

Signaling Workshop

In geneontology/go-annotation on github, there is a label 'GO workshop signaling 2017'

General Signaling Issues

Ca2+ Signaling - Fertilization

GPCR-mediated cAMP Signaling

JAK/STAT Signaling Pathway

MAPK Cascade

Canonical Wnt Signaling Pathway

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