Difference between revisions of "Annotation Conf. Call 2018-05-22"

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== Annotation Review ==
 
== Annotation Review ==
 
=== Cyclic nucleotide metabolic process and child terms (from GPCR signaling work) ===
 
=== Cyclic nucleotide metabolic process and child terms (from GPCR signaling work) ===
 +
==== New Today ====
 
*[https://github.com/geneontology/go-annotation/issues/1986 Review annotations to GO:0030814 regulation of cAMP metabolic process]
 
*[https://github.com/geneontology/go-annotation/issues/1986 Review annotations to GO:0030814 regulation of cAMP metabolic process]
 +
*[https://github.com/geneontology/go-annotation/issues/1985 Review annotations to 'regulation of cGMP metabolic/catabolic/biosynthetic process', and + and - children]
 +
*[https://github.com/geneontology/go-annotation/issues/1984 Review annotations to GO:0052653 3',5'-cyclic diguanylic acid metabolic process]
 +
*[https://github.com/geneontology/go-annotation/issues/1983 Review annotations to GO:0030803 negative regulation of cyclic nucleotide biosynthetic process]
 +
*[https://github.com/geneontology/go-annotation/issues/1982 Review annotations to GO:0030802 regulation of cyclic nucleotide biosynthetic process]
 +
==== Existing ====
 
*[https://github.com/geneontology/go-annotation/issues/1979 Review annotations to GO:0009190 cyclic nucleotide biosynthetic process]
 
*[https://github.com/geneontology/go-annotation/issues/1979 Review annotations to GO:0009190 cyclic nucleotide biosynthetic process]
 
*[https://github.com/geneontology/go-annotation/issues/1978 Review annotations to GO:0009187 cyclic nucleotide metabolic process]
 
*[https://github.com/geneontology/go-annotation/issues/1978 Review annotations to GO:0009187 cyclic nucleotide metabolic process]
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*[https://docs.google.com/document/d/1Px8AgghIABKaGP174Av2XYXQ8NfUrkMRT1yJ8kwCgx4/edit Agenda and Minutes]
 
*[https://docs.google.com/document/d/1Px8AgghIABKaGP174Av2XYXQ8NfUrkMRT1yJ8kwCgx4/edit Agenda and Minutes]
 
*GO managers will review action items and prioritize for the coming months
 
*GO managers will review action items and prioritize for the coming months
 +
**[https://docs.google.com/presentation/d/1Q-KVvjQBnNIDfZ4R8crphnMDrMQk0Dca9XYn9BecV4I/edit#slide=id.g3960910e46_0_0 GO Consortium Dataflow]
 +
**[https://docs.google.com/presentation/d/1agvvMwb_DE32zFZyBJji2sNswYpCZmRhyWVS7x-KRBw/edit#slide=id.p1 Gene Product-to-Term Relationships]
 
=== Presentations/Slides ===
 
=== Presentations/Slides ===
 
*Presentations and slides are available in the GO's [https://drive.google.com/drive/folders/1wxi52dercOofm6cCg1jr6eCvU2py6wtI Google drive]
 
*Presentations and slides are available in the GO's [https://drive.google.com/drive/folders/1wxi52dercOofm6cCg1jr6eCvU2py6wtI Google drive]
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= Minutes =  
 
= Minutes =  
*On call:  
+
*On call: Barbara, Giulia, Harold, Karen, Kimberly, Li, Liz, Michele, Pascale, Petra, Ruth, Sabrina, Shur-Jen, Stan, Suzi L, Tanya, Val
 +
 
 +
== Annotation Review ==
 +
*'''AI:''' Add links to ontology tickets, and more rationale, to annotation review tickets.
 +
*We should include ISS annotations in our annotation review pipeline.
 +
*Protein2GO checks that the gene product referenced in the With/From for an ISS annotation still has a valid annotation.
 +
*We still have older ISS annotations with nothing in the With/From column; these should be reviewed and removed, or updated, as appropriate.
 +
 
 +
=== Cyclic nucleotide metabolic process and child terms (from GPCR signaling work) ===
 +
*Proposal is to obsolete these BP terms.
 +
*One issue:
 +
**Papers that describe a mutant phenotype that results in less cAMP; there is no in vitro assay for the enzymatic activity.
 +
**Is this sufficient evidence to make an IMP annotation to the MF, adenylate cyclase activity, if the gene product has similarity to known adenylate cyclases?
 +
**Have the cyclic nucleotide metabolic process terms been used in the With/From for IC annotations?
 +
**Papers may show the effects on level of cyclic nucleotides, but no effect on a specific signaling pathway.
 +
**GO-CAM models will allow for multiple pieces of evidence; combinatorial code for conventional annotations?
 +
 
 +
=== Growth ===
 +
*Made 'do not annotate'
 +
*PAINT annotations will get flagged if they need to be reviewed
 +
 
 +
=== Canonical Wnt Signaling ===
 +
*Please review and respond in the ticket if you have questions.
 +
 
 +
=== MAPK Cascade ===
 +
*David and Sabrina will double-check if there is any additional work to do here.
 +
 
 +
=== Extracellular Matrix ===
 +
*Please review and respond in the ticket if you have questions.
 +
 
 +
 
 +
 
  
  
  
 
[[Category:Annotation Working Group]]
 
[[Category:Annotation Working Group]]

Latest revision as of 07:50, 22 May 2018

Meeting URL

Agenda

Annotation Review

Cyclic nucleotide metabolic process and child terms (from GPCR signaling work)

New Today

Existing

Growth

Canonical Wnt Signaling

MAPK Cascade

Extracellular Matrix

GOC Meeting - NYC

Minutes

Presentations/Slides

  • Presentations and slides are available in the GO's Google drive
    • If you presented and your slides are not here, please add them.

SAB

  • SAB followed the GOC meeting
  • Report to come soon

Annotation Survey Results

GO-CAM/Noctua

  • Next call tomorrow, Wednesday, May 23rd at 11:00am EDT (see Google calendar)

Minutes

  • On call: Barbara, Giulia, Harold, Karen, Kimberly, Li, Liz, Michele, Pascale, Petra, Ruth, Sabrina, Shur-Jen, Stan, Suzi L, Tanya, Val

Annotation Review

  • AI: Add links to ontology tickets, and more rationale, to annotation review tickets.
  • We should include ISS annotations in our annotation review pipeline.
  • Protein2GO checks that the gene product referenced in the With/From for an ISS annotation still has a valid annotation.
  • We still have older ISS annotations with nothing in the With/From column; these should be reviewed and removed, or updated, as appropriate.

Cyclic nucleotide metabolic process and child terms (from GPCR signaling work)

  • Proposal is to obsolete these BP terms.
  • One issue:
    • Papers that describe a mutant phenotype that results in less cAMP; there is no in vitro assay for the enzymatic activity.
    • Is this sufficient evidence to make an IMP annotation to the MF, adenylate cyclase activity, if the gene product has similarity to known adenylate cyclases?
    • Have the cyclic nucleotide metabolic process terms been used in the With/From for IC annotations?
    • Papers may show the effects on level of cyclic nucleotides, but no effect on a specific signaling pathway.
    • GO-CAM models will allow for multiple pieces of evidence; combinatorial code for conventional annotations?

Growth

  • Made 'do not annotate'
  • PAINT annotations will get flagged if they need to be reviewed

Canonical Wnt Signaling

  • Please review and respond in the ticket if you have questions.

MAPK Cascade

  • David and Sabrina will double-check if there is any additional work to do here.

Extracellular Matrix

  • Please review and respond in the ticket if you have questions.