Feb2010 ontology report

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Ontology Development Report - February 2010

I. Ontology Development

  • SourceForge
    • Items opened: 147
    • Items closed: 201
    • Items still open: 237
      • assigned: 164
      • unassigned: 73
  • Completed content items
    • Signaling: The signaling branch has been committed and the project is being carried forward by Becky Foulger. [Jen]
    • Taxon triggers: The files are now in their permanent location in cvs and most of the problematic annotations and mappings have been fixed. The ontology issues are being worked on. The project will be taken over by Jane and a new member of staff at GOA. [Jen]
    • Various SourceForge items
  • Content items in progress
    • Further discussion on aligning with ChEBI for cross-products (Midori, Chris, Jane, David, ChEBI curators); David and Tanya visiting Cambridge in March to standardize GO implicit chemical ontology
    • Kidney development meeting follow-up work in progress [Midori & David]
    • Working on two new sets of PAMGO terms, see [1] and [2] [Jane]
    • Added a new set of terms for axon-related cellular components in collaboration with NIF (Neuroscience Information Framework) [Jane & Chris]
    • Review of internal cross-product sets such as BP-xp-self and CC-xp-self continues; see plan to add internal cross-products. (Jen, Jane, Midori, Chris, David, Tanya)
    • Continuing to add function-process part-of links in gene_ontology_write.obo and gene_ontology_ext.obo (David, Tanya)
    • Work continues on overhauling terms related to viruses (Jane)
    • Quality control continues as usual - reports generated by Chris (cronjobs)
      • Reasoner-based implied links for new regulation terms - also see above (David, Tanya)
      • Multiple part_of parents (several GO curators, especially Tanya & David)
      • Abduced links [[3]](David, Tanya)
      • Problematic regulates terms [[4]](David, Tanya)
  • Publications
    • Manuscript on Taxon triggers almost ready for submission to BMC Bioinformatics (Jen, Chris)
    • New PAMGO paper "Unifying themes in microbial associations with animal and plant hosts described using the Gene Ontology" ready for submission to Microbiology and Molecular Biology Reviews
    • Case studies for publication on "revisability" of GO, proposed and coordinated by Sabina Leonelli - in progress (Midori, Jane, Alex, Karen C)
    • Continued from November & December:
      • Resuming work on manuscript on regulates relations (Jane, Midori, David, Chris, Tanya, maybe other annotators)
  • Anything else
    • Jen going on maternity leave from the 1st March 2010 to the 28th February 2011.
    • Becky Foulger from UniProt is joining us until the May 14th 2010
    • GO bibliography has 3164 entries

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