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Planning meeting Mon 15th August 2011 - Agenda

Minutes from previous meeting

1. Review of action items

completed action items

  • Val Write training session for new curator, Mark and Midori (training is in progress this month)
  • Val and Midori Finish tidying data for migration (should be complete by Monday)
  • Val and Midori Refine and describe annotation extensions (annotation extensions are now in use)
  • Val EMBL resubmission. This will allow all of the new genes/ gene structure changes to propagate through to Uniprot
  • Val circulate "names ideas" list
  • Pombeclub 10 May Val presented
  • Pombe 2011 June 27-30 Val, Midori, Mark Presented 3 posters. Mark presented Pombase in workshop. Val did an infomercial for community curation

ongoing items moved to tracker

  • Val Sequence update and versioning Versioning for Ensembl will start Pombase 1.1 where 1. Is the sequence assembly version and .1 is the annotation version. GeneDB files need backwardly naming: GeneDB 1_date GeneDB 2_date

outstanding action items

  • Val Finishing phenotype analysis for the Nurse lab (in progress)
  • Midori and I will scope out a proposal for the phenotype model in the next few weeks (still in progress, we know what we need to capture, need to think about how this will be done in practice)

2. Ensembl Group Update

These are the items labelled "blocker" and "critical" (login required to see lists):

Mark progress update

3. Curation Group update

i. Chado Loading

All GeneDB features loaded into Chado

  • See Types and Counts
  • All are annotated with Sequence Ontology (SO) terms
  • Loaded 25650 sequence features for fission yeast (Large number of "gene" is due to human and cerevisiae orthologs)

All functional annotations are mapped to controlled vocabularies

Annotation Extensions (NEW annotation type):

  • Post-composed terms used for annotation extensions
  • 340 annotations to 254 terms
  • We are the first MOD to use and submit GO annotation with annotation extensions (we are also using annotation_extension for other CVs)
  • Midori has added several entries to the small annotation extension relations ontology for use by GO annotation extension providers
  • We seem to be the first people to store annotation extensions in Chado. Kim has made the "method" available to other Chado developers.

Also loaded

  • pombe/cerevisiae ortholog table (sanity checked and fixed)
  • BioGRID physical and genetic interactions

Still to load

  • Target is and target of annotation extensions in old format
  • Some "localisation dependencies" annotated as IGI need migrating to annotation extensions
  • External GO data needs loading (pre-loading filters need to be written)
  • GOA (Interpro2GO, SPKWtoGO, Uniprot manual annotation)
    • Genome wide localisation data
    • PAINT annotation (ref geneomes)
    • Function Process link inferences
    • New annotation done in the curation tool is not yet loaded

ii. Curation and Ontology development ongoing tasks

PomBase SourceForge page


  • Chado 19 Open/ 16 Closed
  • Curation tasks 54 Open / 9 Closed
  • Documentation 8 Open / 1 Closed
  • Fission yeast phenotype 6 Open / 22 Closed
  • GO annotation 42 Open / 6 Closed
  • Sequence analysis 23 Open/ 9 Closed

GO ontology requests tracker PomBase group items Tracker

  • Gene Ontology requests 21 Open/ 12 Closed (does not include ~1800 closed legacy items)

General / Noteworthy

  • Phenotype ontology progress: about 450 terms; all have text definitions; about 90% have formal cross-product definitions (Midori)
  • EMBL submission (Val)
  • Submissions to PRO for GO "column 17" (Midori)
  • Tidying data for migration (mapping legacy qualifiers to annotation extensions, remapping obsoletions/typos/syntax errors and generally figuring out how some edge case annotations should be stored) (Val and Midori)
  • Training in progress. Annotation checklist will evolve into the curation documentation
  • describing annotation extensions
  • mapping modifications to MOD
  • mapping phenotypes to FYPO

iii. Curation Tool

SourceForge PomBase Curation Tool tracker

4. New Discussion Items

  • Is there ANYTHING we can use instead of RT?
  • Name of Gene Page -> Gene Summary Page
  • Requesting HTP dataset submissions (format/ sequence version)
  • Jira alerting (CC Val and Midori on all)
  • We need to do some serious testing when we know that the current data-sets are hosted.
  • Jurg asked about ability to view pages on phones, I told him this should/will be possible?
  • Access statistics, Monitoring usage of old vs new site
  • Interaction storage in Ensembl
  • Ontology browsing in Ensembl

5 Appointments

  • Antonia Lock started Aug 1st
  • Kim going back to New Zealand shortly

6. Timelines

  • Target for the preview (how long will it take to fix all critical?)
    • data equivalent to GeneDB pages

  • community curation launch - need workflow, literature triage, view of existing annotations by paper; may have more specifics to fill in

  • NAR paper (deadline today without extension). Will have 1st draft shortly

7. AOB

Minutes from this meeting

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