Difference between revisions of "Manager 20November2013"

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[[Category:GO_Managers_Meetings]]
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==New Agenda Items==
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=== Reference Proteomes ===
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* Do we use the reference proteomes in GO as default?
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* Do we sync with QfO or with UniProt?
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* How do we deal with async issues, e.g. PAINT?
 +
 +
CM: provided summary.
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 +
There are two GAF files at GOA for human, 1) goa_human and 2) goa_ref_human.
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Which file should an user use for say enrichment analysis? #1 has all annotations and #2 has annotations for genes in the reference_proteome set. Which file should GOC provide on its FTP/AMIGO?
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Also some of the IDs in the QFO file don't match the ones in the ref.proteome set. Seems like data synchronization problem between UniProt, QFO and GOA.
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JB: this is an important issue
 +
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SL: can we move to a faster release cycle with QfO
 +
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CM: issue with synchrony
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SL: we can automatically update PAINT GAFs
 +
 +
PT: we can switch to two (PANTHER) releases a year. monthly is aggressive
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RH: GOA monthly
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RH: Reference proteome is based on QfO
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CM: it's a synchrony issue. We need to be working to the same release
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JB: lot's of QC goes in. every 6 months.
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ACTION: CM will write a proposal. Help from PT and SL.
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SL: we have to be careful not to lose anything when we provide the
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reference as default
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JB: what about other species.
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 +
CM: depends on the MOD. For other non-MOD species make sure anything
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we project annotations to in PAINT
 +
 +
RH: new QuickGO will allow projection to reference proteome
 +
 +
CM : docs should be synced
 +
 +
ACTION: RH will add goa_ref_human to GOC release
 +
 +
===Annotations to non-UniProtKB identifiers===
 +
 +
*Collecting use cases for non-UniProtKB identifiers for common annotation tool.
 +
**email was sent to seven groups to ask for identifiers specifications.  So far, responses from AgBase, BHF-UCL, and WB.
 +
 +
KVA: CAF/protein2go - need to annotate to non-uniprot IDs. Sent
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spreadsheet with sruver of kinds of identifiers people want to use.
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ACTION: everyone to fill in spreadsheet
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SL: this arose from RNA central.
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KVA: orphan genes, ncRNAs, complexes.
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KVA: this is mostly just a survey
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===Enhancing Taxon Constraints===
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The ontology group has created a new ticket and sub-tickets:
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* https://www.ebi.ac.uk/panda/jira/browse/GO-217
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There are some technical issues to take care of, and making taxon constraints often leads to time-consuming refactors -these ultimately improve the ontology but take effort away from other priorities. Do we have some deadline and metric of success for the next meeting in Texas?
 +
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JL: taxon constraint jamboree. Will be much easier in future
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PT: we want to add more
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SL: need a report for PAINT
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ACTION: SL to coordinate with Heiko to get Jenkins/taxon reports on
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PAINT files
 +
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PT: we calculate age of every gene. combine this with annotations. +1
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for Jamboree
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ACTION: have a taxon jamboree before texas meeting
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===Contribute to 2013 GOC Progress Report===
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Please send updates to Judy and she will incorporate.  Judy will post drafts for review.
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JB: PIs will generate new report. Need by end of december. Still
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awaiting info on carryover.
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ACTION: Rama set up new page for pubs
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===GO help===
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The number of people on the rota has gone down to 9, will be 8 in January. Some groups aren't on the rota at all - can we volunteer people please?
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RB: Becky leaving in January, need more people.
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SL: volunteer Moni
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==Action points from last meeting ==
 
==Action points from last meeting ==
  
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'''Action Item:''' Draft a GO_REF for BP annotations inferred from Phenotype Ontology annotations that documents curation pipeline and entities included in the With/From column, e.g. Variation IDs, RNAi experiment IDs, Phenotype Ontology terms, Paper IDs.  [Kimberly]
 
'''Action Item:''' Draft a GO_REF for BP annotations inferred from Phenotype Ontology annotations that documents curation pipeline and entities included in the With/From column, e.g. Variation IDs, RNAi experiment IDs, Phenotype Ontology terms, Paper IDs.  [Kimberly]
  
Draft:
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'''Draft:'''
  
GO_REF:0000058
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''GO_REF:0000058''
  
Gene Ontology annotation through association of Phenotype Ontology terms with GO Biological Process terms
+
''Gene Ontology annotation through association of Phenotype Ontology terms with GO Biological Process terms''
  
WB
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''WB''
  
Transitive assignment of GO terms based on mappings between Phenotype Ontology terms and GO Biological Process terms.  GO terms are obtained from a file, generated manually by WormBase curators, containing mappings to Worm Phenotype Ontology (WPO) terms.  Annotations using this reference may contain one or more of the following in the With/From column (column 8) of the gene association file: 1) A variation or RNAi identifier that indicates the perturbation that produced the phenotype, 2) The Phenotype Ontology term ID, 3) A reference identifier for the publication that reported the phenotype.  Mapping files ''will be made available'' here:  http://www.geneontology.org/external2go/wbphenotype2go.
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''Transitive assignment of GO terms based on mappings between Phenotype Ontology terms and GO Biological Process terms.  GO terms are obtained from a file, generated manually by WormBase curators, containing mappings to Worm Phenotype Ontology (WPO) terms.  Annotations made using this reference may contain one or more of the following in the With/Fro column (Column 8): 1) A variation or RNAi identifier used by WB to indicate the perturbation; 2) The WPO term; 3) A reference identifier for the publication that reported the phenotype.  Mapping files ''will be made available'' here:  http://www.geneontology.org/external2go/wbphenotype2go.''
  
 
'''Action Item:''' Update documentation about what can be included in the With/From column for IMP annotations to include paper identifiers. [Rachael, Rama]
 
'''Action Item:''' Update documentation about what can be included in the With/From column for IMP annotations to include paper identifiers. [Rachael, Rama]
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'''Action Item:''' Assemble use cases where phenotype-based annotations would be either misleading or inconsistent with manual GO annotation practices. [GO Curators]
 
'''Action Item:''' Assemble use cases where phenotype-based annotations would be either misleading or inconsistent with manual GO annotation practices. [GO Curators]
 
=== Reference Proteomes ===
 
 
* Do we use the reference proteomes in GO as default?
 
* Do we sync with QfO or with UniProt?
 
* How do we deal with async issues, e.g. PAINT?
 
  
  
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Ideas: enrichment analysis strategies, MGI's phenotype to BP pipeline, apoptosis
 
Ideas: enrichment analysis strategies, MGI's phenotype to BP pipeline, apoptosis
 +
 +
http://gocwiki.geneontology.org/index.php/GO_Managers#Ideas.2FTopics_for_Biocuration_meeting
  
 
==Discussion points==
 
==Discussion points==

Latest revision as of 12:18, 27 June 2014

New Agenda Items

Reference Proteomes

  • Do we use the reference proteomes in GO as default?
  • Do we sync with QfO or with UniProt?
  • How do we deal with async issues, e.g. PAINT?

CM: provided summary.

There are two GAF files at GOA for human, 1) goa_human and 2) goa_ref_human. Which file should an user use for say enrichment analysis? #1 has all annotations and #2 has annotations for genes in the reference_proteome set. Which file should GOC provide on its FTP/AMIGO? Also some of the IDs in the QFO file don't match the ones in the ref.proteome set. Seems like data synchronization problem between UniProt, QFO and GOA.

JB: this is an important issue

SL: can we move to a faster release cycle with QfO

CM: issue with synchrony

SL: we can automatically update PAINT GAFs

PT: we can switch to two (PANTHER) releases a year. monthly is aggressive

RH: GOA monthly

RH: Reference proteome is based on QfO

CM: it's a synchrony issue. We need to be working to the same release

JB: lot's of QC goes in. every 6 months.

ACTION: CM will write a proposal. Help from PT and SL.

SL: we have to be careful not to lose anything when we provide the reference as default

JB: what about other species.

CM: depends on the MOD. For other non-MOD species make sure anything we project annotations to in PAINT

RH: new QuickGO will allow projection to reference proteome

CM : docs should be synced

ACTION: RH will add goa_ref_human to GOC release

Annotations to non-UniProtKB identifiers

  • Collecting use cases for non-UniProtKB identifiers for common annotation tool.
    • email was sent to seven groups to ask for identifiers specifications. So far, responses from AgBase, BHF-UCL, and WB.

KVA: CAF/protein2go - need to annotate to non-uniprot IDs. Sent spreadsheet with sruver of kinds of identifiers people want to use.

ACTION: everyone to fill in spreadsheet

SL: this arose from RNA central.

KVA: orphan genes, ncRNAs, complexes.

KVA: this is mostly just a survey

Enhancing Taxon Constraints

The ontology group has created a new ticket and sub-tickets:

There are some technical issues to take care of, and making taxon constraints often leads to time-consuming refactors -these ultimately improve the ontology but take effort away from other priorities. Do we have some deadline and metric of success for the next meeting in Texas?

JL: taxon constraint jamboree. Will be much easier in future PT: we want to add more SL: need a report for PAINT

ACTION: SL to coordinate with Heiko to get Jenkins/taxon reports on PAINT files

PT: we calculate age of every gene. combine this with annotations. +1 for Jamboree

ACTION: have a taxon jamboree before texas meeting

Contribute to 2013 GOC Progress Report

Please send updates to Judy and she will incorporate. Judy will post drafts for review.

JB: PIs will generate new report. Need by end of december. Still awaiting info on carryover.

ACTION: Rama set up new page for pubs

GO help

The number of people on the rota has gone down to 9, will be 8 in January. Some groups aren't on the rota at all - can we volunteer people please?

RB: Becky leaving in January, need more people.

SL: volunteer Moni

Action points from last meeting

Action Item: Draft a GO_REF for BP annotations inferred from Phenotype Ontology annotations that documents curation pipeline and entities included in the With/From column, e.g. Variation IDs, RNAi experiment IDs, Phenotype Ontology terms, Paper IDs. [Kimberly]

Draft:

GO_REF:0000058

Gene Ontology annotation through association of Phenotype Ontology terms with GO Biological Process terms

WB

Transitive assignment of GO terms based on mappings between Phenotype Ontology terms and GO Biological Process terms. GO terms are obtained from a file, generated manually by WormBase curators, containing mappings to Worm Phenotype Ontology (WPO) terms. Annotations made using this reference may contain one or more of the following in the With/Fro column (Column 8): 1) A variation or RNAi identifier used by WB to indicate the perturbation; 2) The WPO term; 3) A reference identifier for the publication that reported the phenotype. Mapping files will be made available here: http://www.geneontology.org/external2go/wbphenotype2go.

Action Item: Update documentation about what can be included in the With/From column for IMP annotations to include paper identifiers. [Rachael, Rama]

Action Item: Survey existing annotations to find suspect (outlier) BP annotations. [Suzi, Chris]

Action Item: Assemble use cases where phenotype-based annotations would be either misleading or inconsistent with manual GO annotation practices. [GO Curators]


BioCurator Meeting

  • What are GO's plans for the meeting?
  • Would be good to have a coordinated set of talks - start a wiki page for ideas?
  • Submit a paper for the Database issue? Just abstracts?
  • Who is going to the meeting?

Action Item: Add abstract deadline to GO calendar - DONE [Suzi]

Papers - November 15th, 2013

Abstract for Posters - February 10, 2014

Action Item: Create wiki page for ideas.

Ideas: enrichment analysis strategies, MGI's phenotype to BP pipeline, apoptosis

http://gocwiki.geneontology.org/index.php/GO_Managers#Ideas.2FTopics_for_Biocuration_meeting

Discussion points