Annotation Conf. Call 2018-06-12: Difference between revisions
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***Upstream components | ***Upstream components | ||
****Gene products involved in secretion could be annotated to 'Wnt protein secretion' for now; GO-CAM models will also help to capture this information better | ****Gene products involved in secretion could be annotated to 'Wnt protein secretion' for now; GO-CAM models will also help to capture this information better | ||
=== Transcription === | === Transcription === |
Revision as of 15:22, 11 June 2018
Meeting URL
GO Annotation Meetings
- Still will be Tuesdays at 8am PDT
- Proposed meeting schedule:
- 1st Tuesday: Alliance Gene Function
- 2nd Tuesday: GO Consortium
- 3rd Tuesday: Alliance Gene Function/GO-CAM Working Group
- 4th Tuesday: GO-CAM Working Group
- 5th Tuesday: ad hoc, as needed
Annotation Reviews
Signaling Projects
GPCR
- Review annotation to GO:0030816 positive regulation of cAMP metabolic process and GO:0030815 negative
- Review annotations to GO:0030814 regulation of cAMP metabolic process
- 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
- Outstanding reviews: SIB
- Review annotations to GO:0006198 cAMP catabolic process
- Outstanding reviews: dictyBase, MGI, PomBase, and MTBBASE
JAK-STAT
Canonical Wnt Signaling
- Review annotations wrt GO:0090090 'negative regulation of canonical Wnt signaling pathway'
- Outstanding reviews: BHF-UCL, MGI, PARL, UniProt, Zfin
- Review annotations wrt GO:0060070 'canonical Wnt signaling pathway'
- Outstanding reviews: ARUK-UCL, BHF-UCL, DFLAT, MGI, ParkinsonsUK-UCL, UniProt, WB, Zfin
- Annotation questions:
- Wnt ligands can be part of canonical, non-canonical pathways and, as well, as part of one type of Wnt signaling pathway, can regulate another type of Wnt signaling pathway
- Therefore, it's difficult to say definitively which Wnts are part of which types of Wnt signaling pathways; the experiments and context should be the guiding information
- Downstream targets, e.g. Myc and cyclin D, should not be annotated to canonical Wnt signaling
- Information about downstream targets could be captured, for example, as transcriptional targets in AEs, or better yet, in GO-CAM models that can more expressively show how they fit into a specific canonical Wnt signaling pathway
- Upstream components
- Gene products involved in secretion could be annotated to 'Wnt protein secretion' for now; GO-CAM models will also help to capture this information better
- Wnt ligands can be part of canonical, non-canonical pathways and, as well, as part of one type of Wnt signaling pathway, can regulate another type of Wnt signaling pathway
Transcription
Annotation File Pipelines
- Annotation files can now be deposited on a publicly accessible site (SVN submission is no longer needed)
- The source URL for annotation (and gpi) files should be entered in the Source tag of each group's datasets.yaml file
- Reports are available on a daily basis: http://snapshot.geneontology.org/reports/index.html
- QA//QC checks - Eric and Pascale are still working on implementing all of these
- Documentation: http://wiki.geneontology.org/index.php/Release_Pipeline
Minutes
On call: