Tasks/Priorities 2012 (Archived): Difference between revisions

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[[Category:Archived]]
===Tasks due 1st May 2012===
===Tasks due 1st May 2012===


# Implementation of the JIRA project management software for the GO Consortium
# Implementation of the JIRA project management software for the GO Consortium
# Common Annotation Framework. Determine the directions and deliverables for the next year.
# [http://wiki.geneontology.org/index.php/Common_Annotation_Framework_Specification Common Annotation Framework]: Determine the directions and deliverables for the next year.
# Full documentation of the minimal/ideal annotation format, including the gp2protein, gp2rna formats.
# Full documentation of the minimal/ideal annotation format including the:
 
#* minimal GAF
====Task management requests====
#* gp2protein
 
#* gp2rna (groups who annotate to ncRNAs should create a gp2rna file)
We need to be able to start relying on other GO-NIH funded curators for contributions. Perhaps also set up some focused working group meetings to make headway.
#* orphan gps IDs that have annotations
# 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 ===
=== Other Projects ===
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- ''annotation and software activity''
- ''annotation and software activity''


====Non-redundant set of annotations====
* Round 1: discussion on what constitutes a redundant annotation was held on March 13th (http://gocwiki.geneontology.org/index.php/Annotation_Conf._Call,_March_13,_2012)
* Round 2: Recap decisions on redundancy. Then: 1) how do col-16 and col-17 fit in the non-redundant set
====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


'''5. Public engagement on the value of the annotation_extension data'''
====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 [http://wiki.geneontology.org/index.php/Mock-ups_of_new_GOC_Annotation_pages here]
* However, documenation takes a large amount of time, requiring a focused effort.


- dedicated open call inviting go_friends folk?
* 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.


- email targetting tool developers, informing them of the annotation_extension resource?
Subtasks: finalize guidance for transcription and apoptosis, from the ontology redevelopment efforts.


- publication showcasing the value of the annotation_extension resource?
==== Evidence Codes ====


- '' all managers?''
* Discuss new evidence code requirements with the GOC
* Resolve evidence code for MF-BP, BP-CC inferences
* Discuss [http://wiki.geneontology.org/index.php/Evidence_Code_Ontology_%28ECO%29 Mapping of ECO to GO] at an annotation call


==== Extended annotation format (increased expressivity)====
==== Annotation Relations ====


===== Chain of evidence =====
==== QC checks ====


http://wiki.geneontology.org/index.php/Chain_of_Evidence
* integrating centrally created annotations (reciprocals/inferrred).  


* Working group needs to be set up to determine how best to represent chains of evidence and report options back to the annotation groups.
* Collaborate with the software group as to how to implement for best impact.
* 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 cod) and evidence code for inferences based on inter-ontology links


====Non-redundant set of annotations====
==== Community annotation tool ====
* Round 1: discussion on what constitutes a redundant annotation was held on March 13th (http://gocwiki.geneontology.org/index.php/Annotation_Conf._Call,_March_13,_2012)
* Round 2: how do col-16 and col-17 fit in the non-redundant set


====Annotating to Complexes as Objects====
open up CANTO in some form to the public, communication with emerging annotation groups
* Come up with pipleline/specs to annotate Complexes as objects.
----
** sort out contributes_to qualifier
** how to propagate annotations to subunits


# Clean up existing documentation on wiki and move to the GO website.
# Create new documentation for existing file formats: annotation/mapping files, annotation guidance (already mentioned, and set as a prioritised task for this next quarter)
# Annotation documentation guidance; what constitutes a redundant annotation, clarification of contributes_to qualifier. Specific guidance for transcription and apoptosis.
# Discuss and resolve new annotation methods: annotating to protein complexes, mapping of ECO to GO ev. codes, annotation relations
# define pipeline for PAINT curation and GOC annotation targets - to be coordinated with PAINT folks
# define pipeline for PAINT curation and GOC annotation targets - to be coordinated with PAINT folks
# Evidence codes. Mapping of ECO to GO evidence codes. Resolve evidence code for MF-BP, BP-CC inferences
# QC checks, integrating centrally created annotations (reciprocals/inferrred). We need to collaborate with the software group as to how to implement for best impact.
# open up CANTO in some form to the public, communication with emerging annotation groups
# [[Transition_to_OWL]]
# [[Transition_to_OWL]]
# [[TermGenie]] templates
# [[TermGenie]] templates
Line 101: Line 116:
# formal specification of expressive annotations in OWL
# formal specification of expressive annotations in OWL


===Action Items from the February 2012 GO Consortium meeting===
===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


ACTION: PIs need to determine the most important items to be communicated for metrics on annotation quality/efficiency improvements. These need to be displayed separately for NIH-funded and the full GO Consortium efforts.
1) Making an online training tutorials for GO ontology development, for the EBI-resource website


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

Latest revision as of 06:08, 12 April 2019

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