Tasks/Priorities 2012

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Tasks due 1st May 2012

  1. Implementation of the JIRA project management software for the GO Consortium
  2. Common Annotation Framework: Determine the directions and deliverables for the next year.
  3. Full documentation of the minimal/ideal annotation format including the:
    • minimal GAF
    • gp2protein
    • gp2rna (groups who annotate to ncRNAs should create a gp2rna file)
    • orphan gps IDs that have annotations
  4. An appropriate web-display for GOC users needs to be constructed, including statistics and statements on how the annotation set is changing in accordance to new format/focused annotation efforts.

Other Projects

Annotation_Extension field (col-16)

1. Clear, full guidance describing the data for the annotation_extension field Some documentation is in progress here: http://wiki.geneontology.org/index.php/Annotation_Extension

Actions needed:

- draft documentation to be finished (estimated time: 5 hours)

- documentation to be agreed by the GO Consortium annotation groups. This would initially be introduced in an annotation call, then a GO list discussion

- Annotation activity (estimated time to end doc: 2 months)


2. Annotation_extension QC checks to ensure quality of data

QC checks need to be agreed and implemented to enforce the agreed format. Many of the annotation_extension fields published by groups do not meet the current format specifications QCs would need to specify the overall format of the line and take into account the appropriate domain/scope of individual relations

- QCs to be formulated (general format QC, scope/domain restrictions applied to relationship usage QC, Protege web service for more advanced checks?)

- QCs to be agreed by GO Consortium (schedule GO annotation calls)

- QCs to be implemented on GOC-submitted files by the appropriate filtering mechanism

- Annotation QC and software activity


3. Relationships ontology

- relationships used in the annotation_extension field need to be agreed by both the ontology developers and annotators as being sufficiently descriptive for both annotations and logical definitions.

- relationship ontology needs to move out of scratch

- create a web-based visual represenation of the relationship ontology?

- ontology and annotation activity


4. Display the annotation_extension field in AmiGO - discussion on appropriate web display required at a GO Consortium annotation call?

- annotation and software activity

Non-redundant set of annotations

Extended annotation format (increased expressivity)

Chain of evidence

http://wiki.geneontology.org/index.php/Chain_of_Evidence

  • Working group needs to be set up to determine how best to represent chains of evidence and report options back to the annotation groups.
  • Concept of Annotation ID seems increasingly as an useful concept to deal with chain of evidence and to string annotations together. This is in the context of the recent discussions on ISS from IC (new ISC evidence code), complex IC statements and evidence code for inferences based on inter-ontology links
Annotating to Complexes as Objects
  • Come up with pipleline/specs to annotate Complexes as objects.
    • sort out contributes_to qualifier
    • how to propagate annotations to subunits

Annotation guidance documentation update

  • The annotation pages on the GO Consortium web site are out-of-date, incomplete and poorly ordered.
  • drafts of new annotation pages are being (slowly) developed by Rama and Emily here
  • However, documenation takes a large amount of time, requiring a focused effort.
  • Establish a group to work on documenation.
  • Decide what information is needed but missing from the website/wiki
  • Allocate writers of first drafts of pages.
  • Drafts passed to the GO list and then moved onto the GO website.

Subtasks: finalize guidance for transcription and apoptosis, from the ontology redevelopment efforts.

Evidence Codes

  • Discuss new evidence code requirements with the GOC
  • Resolve evidence code for MF-BP, BP-CC inferences
  • Discuss Mapping of ECO to GO at an annotation call

Annotation Relations

QC checks

  • integrating centrally created annotations (reciprocals/inferrred).
  • Collaborate with the software group as to how to implement for best impact.

Community annotation tool

open up CANTO in some form to the public, communication with emerging annotation groups


  1. define pipeline for PAINT curation and GOC annotation targets - to be coordinated with PAINT folks
  2. Transition_to_OWL
  3. TermGenie templates
    1. Regulation by
    2. Chemical entity templates
    3. Process-cell component templates
  4. LEGO prototype environment
  5. formal specification of expressive annotations in OWL

Ontology group task list

1. General ontology maintenance and development

A. SF simple term requests e.g. missing relationship, 1 - 10 new terms B. SF project requests: current open projects include - EC updates (200+ new terms), venoms (50+ new terms), Reactome enzymes (50+)

C. Review Automatic checks (eg. Jenkins, TG Gatekeeper)

D. Coordination with external groups (ChEBI, Reactome, InterPro)


2. Specialized ontology development (currently underway)

A. Viral terms.

1) Adding in terms to map to UniProtKB keywords for virus annotation. 2) Re-organizing top-level terms

B. Cardiac conduction.

1) Adding signaling pathway terms in the cardiac conduction node, based on the cardiac conduction workshop.

2) Consistency checking (mostly with the Cell Type Ontology) and tying in with SourceForge requests once the ontology structure is finalized.

C. Signaling

1) Next up: Reworking GPCR signaling

D. 'cell cycle' ontology

E. Apoptosis

F. MENGO (Microbial ENergy processes Gene Ontology Project)

3. Introduction of Cross-Products/Ontology engineering

A. Internal cross-products

1) CC X BP (underway)

B. External cross-products

2) ChEBI (underway)

3) Cell

4) Anatomy

C. Conversion to OWL/Protege

D. Define relationships for logical definitions of existing terms (in co-ordination with annotation groups)

4. Ontology Training and outreach

1) Making an online training tutorials for GO ontology development, for the EBI-resource website

2) Poster/presentations at external meetings/conferences, and participation in EBI Training and Open Days