Annotation Conf. Call 2017-11-14: Difference between revisions
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*[https://github.com/geneontology/go-ontology/blob/master/CONTRIBUTING.md Guideline for Contributing to the Ontology] | *[https://github.com/geneontology/go-ontology/blob/master/CONTRIBUTING.md Guideline for Contributing to the Ontology] | ||
== Attribution | == Noctua -Infrastructure == | ||
=== Annotation Attribution === | |||
*We need to have groups properly captured in the Assigned By field of output GPAD files | *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 | *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 | ||
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*If curators belong to multiple annotation groups, the first group will be considered the default | *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 | *To change groups in Noctua, select from the drop-down list next to the curator name in the upper right of the tool | ||
== Annotation QC == | == Annotation QC == | ||
Revision as of 12:53, 10 November 2017
Meeting URL
Agenda
Ontology Term Requests - Reminder
- Refresher on information required for term requests:
- Term name
- Parents
- Term definition
- Reference(s)
- 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
Noctua -Infrastructure
Annotation Attribution
- 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
Annotation QC
- 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?
- Annotations according to group:
(8) EcoCyc (7) EcoliWiki (7) MGI (7) PseudoCAP (6) SGD (5) UniProt (4) BHF-UCL (3) RGD (3) TAIR (2) GR (1) SynGO
- 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
Ontology Updates
- Pascale:
- Transcription factor activity refactor
- Molecular Function terms describing 'transcription factors'
- See: Make parent term for transcription factor activity
- See: Transcription factor branch refactoring: overview of annotations of TFIIIC and TFIIB complexes
GOC Meetings Cambridge
- Review key action items from signaling workshop and GOC meeting
- GOC Cambridge 2017 Meeting Minutes
- Focus on annotation to signaling pathways
- Adoption of expanded set of BP relations
- Review use of contributes_to and colocalizes_with
- Noctua into full production mode
- Meetings on second and fourth Wednesdays at 8am PST to discuss issues
- Representation of protein complexes, and their constituent members, in GO and GO-CAM models
- Review HTP annotations
Minutes
- On call:
Annotation QC
- Action Item: Need curators to review experimental annotations to 'transport'
- Report back on any annotations that can't reasonably be transferred to a more granular term
- We will continue to look at the PomBase list and prioritize additional flags and error checks
Ontology Updates
- Will merge DNA binding transcription factor activity into nucleic acid binding transcription factor activity
- Goal: trying to more easily distinguish 'general' transcription factors (generally only described wrt pol II TFs) from specific, regulatory TFs
- Pascale will tag groups/people if annotations need review
- Pascale, Karen, Paul T. will discuss further
GOC Cambridge Meetings
Signaling Pathways
- Will follow-up on signaling workshop with items using the go-annotation tracker
HTP Evidence Codes
- Helen will finish updating guidelines
- How doe the HTP evidence codes map up to existing GO evidence codes?
- They are in a separate branch, although still experimental.