Annotation Conf. Call 2018-03-13
Agenda
GOC Meeting, NYU, New York, NY, May 12-14th
- Reminder to register, and reserve your hotel room before April 6th if staying at the Shelburne NYC
- Logistics
- Agenda
20th Anniversary GO Meeting, Montreal, CA
- Dates set for Oct 17-20
HTP Annotation Guidelines
- Helen has added documentation on the use of HTP evidence codes to the wiki:
- Guide to GO Evidence Codes
- Annotation standards for HTP proteomics experiments
- How best to capture the combination of a published paper's experiment combined with secondary curator evaluation using some other methodology? New combinatorial evidence code and paper plus a GO reference? (This would be a change to our reference practice.)
- Review RCA evidence code - Please can the groups listed below review their RCA annotations and decide if they'd still like to keep them and if RCA is still the appropriate evidence code?
- TAIR
- MGI
- SGD
- RGD
- CAFA
UniProt vs UniProtKB
- UniProt = contributed by
- UniProtKB = annotated entities
- This ticket is still open - are we just waiting for groups to have their software team implement and the changes to make their way to the GO website?
- Is everyone also using UniProtKB as a prefix in the With/From field?
Annotation Review
- Annotation review is being driven by annotation QC and ontology development
- Goal here is for correct and consistent annotation
- Prioritize by:
- Annotations that are incorrect
- Annotations to terms that are being made obsolete or updated in the ontology
- Annotations to high level terms that are not informative
- Annotations to grouping terms for which more granular, informative terms exist (maybe weren't found initially or were created after the annotation was made)
- Prioritize by:
- Tickets are created in the geneontology/go-annotation repo on github
- Currently, 59 open tickets labeled with Annotation Review in geneontology/go-annotation
- Tickets are assigned to representatives of the annotation groups that need to perform the review
- Once review is done, please remove yourself from the assignee list AND record the action in the accompanying Google spreadsheet linked from the github ticket
- Spreadsheet on GO Annotation Google drive with specific annotations, suggestions
- Tickets to review:
- Review annotation for GPCR
- Several different spreadsheets for this ticket:
- positive regulation of cAMP biosynthetic process - NOTE: two different sheets
- 2 annotations (CACAO)
- Cholera toxin stimulates cAMP production in CHO cells (via stimulation of Gsalpha) Stabilization of the tertiary structure of the cholera toxin A1 subunit inhibits toxin dislocation and cellular intoxication.
- 6 annotations (CAFA)
- 12 annotations (UniProt)
- 2 annotations (CACAO)
- positive regulation of cAMP biosynthetic process - NOTE: two different sheets
- Review annotations to receptor activity
- 4 annotation (AgBase)
- 40 annotations (MGI)
- 2 annotations (SGN)
- 1 annotation (TIGR)
- 46 annotations (UniProt)
- Review annotations to palate development
- 14 annotations (BHF-UCL)
- Review annotations to mRNA cleavage
- 1 annotation (SWIP)
Annotation Requests
- There are some tickets in geneontology/go-annotation that are requesting annotation
- We'd like to assign these to groups
GO-CAM/Noctua
- Next call tomorrow, Wednesday, March 14th at 11:00am EDT (see Google calendar)
Protein Complexes Working Group
- Next call this Thursday, March 15th at 10:30am EDT (see Google calendar)
Minutes
- On call: Chris, David H., Dustin, Edith, Eric, George, Giulia, Harold, Helen, Karen, Kevin, Kimberly, Laurent-Phillipe, Li, Liz, Pascale, Petra, Rachael, Rob, Sabrina, Sage, Shur-Jen, Suzi A, Suzi L, Tanya, Val
New Consoritum Members
- Laurent-Phillipe - with Paul T.'s group but based in Berkeley
- Dustin - also with Paul T's groups
NYU Meeting
- Need to check with Peter D. about the Monday night group rate
Infrastructure
- PAINT annotations - now being directly injected into GO Central
- Will be screened out when they come back in from the MOD
- Consumption of derived GPAD files from GO-CAM models
- How will this pipeline work ? MGI will be the test case for this pipeline.