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

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= Meeting URL =
 +
*https://stanford.zoom.us/j/976175422
 +
 
= Agenda =  
 
= Agenda =  
−
== 20th Anniversary GO Meeting, Montreal, Canada ==
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== Annotation Review ==
−
*Dates set for Oct 17-19
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=== 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/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/1978 Review annotations to GO:0009187 cyclic nucleotide metabolic process]
 +
*[https://github.com/geneontology/go-annotation/issues/1977 Review annotations to GO:0006182 cGMP biosynthetic process]
 +
*[https://github.com/geneontology/go-annotation/issues/1974 Review annotations to cAMP catabolic process]
 +
*[https://github.com/geneontology/go-annotation/issues/1971 Review annotations to GO:0030820 regulation of cAMP catabolic process and children]
 +
 
 +
=== Growth ===
 +
*[https://github.com/geneontology/go-annotation/issues/1973 Review annotations to 'growth']
 +
 
 +
=== Canonical Wnt Signaling ===
 +
*[https://github.com/geneontology/go-annotation/issues/1967 Review annotations wrt GO:0090090 'negative regulation of canonical Wnt signaling pathway']
 +
**Refer to first tab in sheet titled, ALL-CHECK
 +
*[https://github.com/geneontology/go-annotation/issues/1966 Review annotations wrt GO:0060070 'canonical Wnt signaling pathway']
 +
**Refer to first tab in sheet title, ALL-CHECK
 +
 
 +
=== MAPK Cascade ===
 +
*[https://github.com/geneontology/go-annotation/issues/1592  MAPK cascade- Signaling Project]
  
−
== Annotation Review ==
+
=== Extracellular Matrix ===
−
=== Cyclic nucleotide metabolic process (and child terms) ===
+
*[https://github.com/geneontology/go-ontology/projects/9 Extracellular matrix revisions]
−
*[https://github.com/geneontology/go-annotation/issues/1979 cyclic nucleotide biosynthetic process]
+
**[https://github.com/geneontology/go-ontology/issues/15294 proposal]
  
−
== GOC Meeting Summary ==
+
== GOC Meeting - NYC ==
 
=== Minutes ===
 
=== Minutes ===
 
*[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
 +
**[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]
−
**If you presented and your slides are not here, please add them.  
+
**If you presented and your slides are not here, please add them.
−
=== Action Items ===
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=== SAB ===
−
=== Curation Decisions ===
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*SAB followed the GOC meeting
 +
*Report to come soon
  
 
== Annotation Survey Results ==
 
== Annotation Survey Results ==
−
*We are conducting a [https://goo.gl/forms/rLovY736aX1gxqHe2 survey] on annotation practices across the GOC
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*We have conducted a [https://goo.gl/forms/rLovY736aX1gxqHe2 survey] on annotation practices across the GOC
 
*Thank you to everyone who responded
 
*Thank you to everyone who responded
−
*Compiling all of the responses
+
*[https://docs.google.com/presentation/d/1iRXy7rrC7x3TjwQyvRhat7Oo6Kc2LZWUV6_kPAeNM-I/edit#slide=id.p1 Presentation on 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.
  
−
== Ontology Development and Annotation Review ==
+
=== Cyclic nucleotide metabolic process and child terms (from GPCR signaling work) ===
−
=== Transcription factor refactoring ===
+
*Proposal is to obsolete these BP terms.
−
*Any updates?
+
*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.
  
−
== Updates on Projects ==
 
 
=== MAPK Cascade ===
 
=== MAPK Cascade ===
−
*[https://github.com/geneontology/go-annotation/issues/1592  MAPK cascade- Signaling Project]
+
*David and Sabrina will double-check if there is any additional work to do here.
 +
 
 
=== Extracellular Matrix ===
 
=== Extracellular Matrix ===
−
*[https://github.com/geneontology/go-ontology/projects/9 Extracellular matrix revisions]
+
*Please review and respond in the ticket if you have questions.
−
**[https://github.com/geneontology/go-ontology/issues/15294 proposal]
+
 
−
=== Canonical Wnt Signaling Pathway ===
 
−
*Have compiled annotations to review
 
−
**[https://github.com/geneontology/go-annotation/issues/1966 Review annotations wrt GO:0060070 'canonical Wnt signaling pathway']
 
−
**[https://github.com/geneontology/go-annotation/issues/1967 Review annotations wrt GO:0090090 'negative regulation of canonical Wnt signaling pathway']
 
−
*Note: each Google spreadsheet has multiple sheets; please be sure to check each sheet
 
−
*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 23rd at 11:00am EDT (see Google calendar)
 
  
−
= Minutes =
 
−
*On call:
 
  
  
  
 
[[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.
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