Annotation Conf. Call 2017-11-28
Meeting URL
Agenda
Infrastructure
users.yaml file
- users.yaml file is used to store curator metadata and will also be used for proper annotation attribution (i.s. Assigned by) in the GPAD outputs from Noctua
- ACTION: One curator from each curation site should review entries in users.yaml file to fill in information for:
- groups
- orcid (uri)
- ACTION: Berkeley will be providing a report that indicates where users have edit permission in Noctua but don't have an orcid or group associated with them
Annotation Review
Signaling Project
adenylate cyclase-activating G-protein coupled receptor signaling pathway
- Review of cAMP-related signaling and biosynthesis terms and annotations
- Questions about existing annotations that could not be immediately re-housed:
- Zebrafish
- C. elegans
- GO:0007194 negative regulation of adenylate cyclase activity
- We've annotated a phospholipase C to this term and it is believed to reduce adenylate cyclase activity via competitive binding of an adenylate cyclase activator, Ha-Ras.
- Drosophila
- Gprk2 seems to be required for maintaining cellular cAMP levels and for Hh signaling, but does not act via Smoothened or G-proteins. Could be regulating AC directly or indirectly.
- Mouse
- Questions about existing annotations that could not be immediately re-housed:
Wnt signaling pathway
- beta-catenin annotations to review
- DNA binding
- Upgrade to canonical Wnt signaling
- annotations to receptor ligand activity
- Wild-type function vs disease state
- Annotation extensions to capture where receptor ligand activity occurs
- has_start_location, has_end_location
- More work may be done on the receptor ligand activity branch of the MF
- We will also be examining the MF term 'signal transducer activity' to see if it is really needed
Ontology Development
Synaptic vesicle endocytosis
Protein import into the nucleus
HTP Evidence Codes
- New HTP paper google spreadsheet for potential HTP papers annotated using the GO:Sheet laballed:"Over_40_per_evidencecode"
- https://github.com/geneontology/go-annotation/issues/1655
- Generated by splitting out the experimental evidence codes and collating the papers with >40 lines of annotation per paper/per evidence code.
- For most contributors, I have been able to do this directly from the GAF they submit to the GOC so that any DB-specific refs are included and any other sources that are incorporated into the anointed set.
- For a few others, indicated on the sheet, had to download them from QuickGO.
- Note: As they have been separated on evidence code, same paper may feature on separate lines.
- Note: Only equivalent evidence codes to HTPs looked at (EXP, IDA, IEP, IGI, IMP).
- Summary of lines in "Over_40_per_evidencecode"
Source | Publications | Done? | Summary of Action |
---|---|---|---|
AgBase | 29 | ||
ARUK-UC | 2 | ||
BHF-UCL | 19 | ||
dictyBase | 9 | Y | |
Ecoliwiki | 9 | ||
FlyBase | 62 | ||
MGI | 32 | ||
MTBBASE | 10 | ||
ParkinsonsUK-UCL | 5 | ||
PomBase | 9 | Y | |
RGD | 2 | ||
SGD | 43 | ||
TAIR | 84 | ||
UniProt | 88 | ||
WB | 16 | Y | 5 -> HTP code; 7 -> UniProt; 4 -> no change in evidence code, but will review annotations generally |
ZFIN | 24 | Y |
- It would be great if each group could go over these (may take some time) and indicate if the paper/experiment was HTP and what action was taken on the spreadsheet.
- More concise version of HTP guidelines. Please use and give feedback!
- Instructions for updating evidence codes in Protein2GO
- First, send the request to goa@ebi.ac.uk, not to Tony directly.
- Second, clearly list the PMID you like to have updated.
- Finally, list the specific HTP ECO code you would like to use for the annotations from the PMID you listed.
- Note that not all annotations from a given paper will need to be switched to an HTP code, only those for which the group specifies the evidence code to switch.
Minutes
- On call: Edith, George, Giulia, Harold, Helen, Karen, Kimberly, Midori, Pascale, Paul T., Penelope, Petra, Ruth, Sabrina, Shur-Jen, Stan, Tanya
Infrastructure
users.yaml file
- Link to users.yaml QC report
- AI: Curators need to check if they are listed in the report and update their groups and uris, as needed.
- Please contact Kimberly or Seth if you need help with this. Thx.
- Please keep in mind that the report is generated as part of the new build and a new attempt is made every night.
- This means that 1) if the load fails the report may not be there (which is a good thing) and 2) there will times every day during regeneration when the report is not yet there.
Annotation Review
Signaling Project
adenylate cyclase-activating G-protein coupled receptor signaling pathway
- Review annotation for GPCR
- We discussed cases where it didn't appear that annotations wrt regulation of cAMP signaling or regulation of adenylate cyclase could not be re-housed to adenylate cyclase-activating GPCR signaling pathway
- AI: Harold created regulation terms for regulation of the signaling pathway. See: NTR 'regulation of adenylate cyclase-activating G protein coupled receptor signaling pathway
- Other cases still under discussion: regulation of adenylate cyclase activity by competitive binding to an activator and regulation of cAMP signaling but via an uncharacterized pathway