Version 128 (modified by val_wood, 9 years ago) (diff)


October 2012

Outstanding Action items from July

Action: Documentation task for curators; in progress

New Action items from July

Action: Curators look into acquiring data from strain collection in Japan Action: Curators to monitor web site for problems (ongoing) Action: Functional genomics views demo at next meeting (EBI) Action: Val to circulate non-redundant list of genome browser requests & feedback from community Action: PK et al. to create Jira tracker for Ensembl genome browser issues; PK to triage tickets Action: Diagnose the cause of the not synching of the update (Mark)


Updates from various Areas

Curation Update

  • All papers are triaged (upto ~August?)
  • Of 9510 papers 4602 are "curatable" with gene product specific information
  • 591 curation session (papers) in progress
  • 299 approved
  • 47 needing approval
  • 153 newer have been identified as community curatable, not sure how many in progress/ sent out but 19 have been completed and approved by community (5 from Ryoko Mandeville, Nurse lab)

Phenotype Ontology

  • 1625 phenotype terms
  • Reasoner deployed to check logical consistency
  • Midori has written a paper describing the ontology which will be submitted to Genome biology shortly

Chado loading

  • allele names, allele description, conditions now loaded into Chado
  • GO and BioGrid? export format nearly complete

Curation tool

  • Curtion tool individual data items are now "editable"
  • Curation tool deployed for pichia
  • Curation tool deployed for Ruth Loverings GO curation workshop at UCL

Review "Post-preview" and "GeneDB decommissioning" criteria & progress

Current jira status: Open 161 Closed/Resolved? 808 (was 150/655 last meeting, July)

Next priorities (Pombase website)

  1. Host new dataset with curation tool annotations (2000? check annotations)
  • This is now on stage/dev with a few tickets which still need to be cleared to get the new data hosted

The next dataset (nG 28) si the first one to include display of

  • All annotation from completed sessions curated in the curation tool
  • phenotype data with alleles
  • annotation extensions on GO data
  • manual human orthologs (final in Chado load 29)

Once this is done, curators can announce phenotypes, annotation extensions and new annotation from curation tool (and promote community curation) via pombelist. Once NG v29 is hosted, human ortholog data can be announced.

  1. GeneDB decommissioning tasks
    • Next prioities for Mark, 15 jira items
  1. Post GeneDB decommissioning tasks 16 items These are features which are provided by GeneDB, and used, but are not as critical. Provided they are replaced fairly quickly people can probably survive for a while if the old site is taken down
  1. Hosting genome wide datasets
  1. Unscheduled items (103)

Problems reported

  • wildcard search issue, lucene cannot accept wildcard at the front of search. Can we work around this somehow?

Meetings Attended/ Upcoming

  • GO meeting next week (Pasadena). Curators will attend remotely
  • proposed Workshop for 2013 (International meeting) straw poll?
  • Proposed Pombase 1-2 hour workshop at CRUK, with 1-2 hour curation tool demo and or jamboree


  • incentives for community curation, amazon voucher 'curator of the month'

  • Next meeting (doodle)