Annotation Conf. Call 2017-11-14
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Revision as of 07:02, 14 November 2017 by Vanaukenk
- 1 Meeting URL
- 2 Agenda
- 3 Minutes
Ontology Term Requests - Reminder
- Refresher on information required for term requests:
- Term name
- Term definition
- dbxrefs (e.g. GOC:kmv)
- If you need help with parentage or definitions, the ontology editors can help with this, but please make a first-pass attempt at parentage and defs to help expedite the ticket.
- Guideline for Contributing to the Ontology
- We need to have groups properly captured in the Assigned By field of output GPAD files
- All current and future Noctua curators who are associated with one or more curation groups need to fill out the groups field in their entry in the users.yaml file
- Full path: https://github.com/geneontology/go-site/blob/master/metadata/users.yaml
- Groups are entered as URLs, e.g. http://www.wormbase.org, in single quotes
- If curators belong to multiple annotation groups, the first group will be considered the default
- To change groups in Noctua, select from the drop-down list next to the curator name in the upper right of the tool
- Attribution with GO-CAM exports to GOC annotation files
Direct Annotation to High Level Terms
- Manual annotation to uninformative high-level terms is strongly discouraged
- See: improving specificity by banning high level terms #1648
- For example: direct annotation to 'transport' (GO:0006810) is one case where a more specific annotation can likely be made
- In AmiGO, there are 53 experimentally supported annotations to 'transport'.
- Can groups check these annotations to see if a more granular term is appropriate?
- Once you've checked the annotations, please remove yourself from the Assignee list on the ticket, so we know you've finished
- Unresolved annotations according to group:
(7) PseudoCAP (Fiona Brinkman) (2) GR (Pankaj)
- PomBase has a list of >1300 high-level terms that have a 'do not manually annotate' flag
- The proposal is to work through this list so annotations are consistent amongst all GOC members
- Review cAMP-mediated GPCR signaling pathway annotations
HTP Evidence Codes
- New HTP paper google spreadsheet for potential HTP papers annotated using the GO:Sheet laballed:"Over_40_per_evidencecode"
- 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"
- 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!
Protein Complexes Working Group
- Birgit is spearheading this working group
- Doodle poll
- First meeting, Thursday, November 16th, 8am PST or 7:30am PST ? (11am or 10:30am EST, 4pm or 3:30pm UMT)
- Use the same Zoom as for the annotation calls
- On call: