Annotation Conf. Call 2018-05-22: Difference between revisions
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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 11:50, 22 May 2018
Meeting URL
Agenda
Annotation Review
Cyclic nucleotide metabolic process and child terms (from GPCR signaling work)
New Today
- Review annotations to GO:0030814 regulation of cAMP metabolic process
- Review annotations to 'regulation of cGMP metabolic/catabolic/biosynthetic process', and + and - children
- Review annotations to GO:0052653 3',5'-cyclic diguanylic acid metabolic process
- Review annotations to GO:0030803 negative regulation of cyclic nucleotide biosynthetic process
- Review annotations to GO:0030802 regulation of cyclic nucleotide biosynthetic process
Existing
- Review annotations to GO:0009190 cyclic nucleotide biosynthetic process
- Review annotations to GO:0009187 cyclic nucleotide metabolic process
- Review annotations to GO:0006182 cGMP biosynthetic process
- Review annotations to cAMP catabolic process
- Review annotations to GO:0030820 regulation of cAMP catabolic process and children
Growth
Canonical Wnt Signaling
- Review annotations wrt GO:0090090 'negative regulation of canonical Wnt signaling pathway'
- Refer to first tab in sheet titled, ALL-CHECK
- Review annotations wrt GO:0060070 'canonical Wnt signaling pathway'
- Refer to first tab in sheet title, ALL-CHECK
MAPK Cascade
Extracellular Matrix
GOC Meeting - NYC
Minutes
- Agenda and Minutes
- GO managers will review action items and prioritize for the coming months
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
- We have conducted a survey on annotation practices across the GOC
- Thank you to everyone who responded
- 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.
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.