Mar2010 ontology report

Ontology Development Report - March 2010

I. Ontology Development

• SourceForge
  • Items opened: 127
  • Items closed: 128
  • Items still open: 239
    • assigned: 150
    • unassigned: 89

• Completed content items
  • Various SourceForge items

• Content items in progress
  • Signaling
  • 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
  • Becky Foulger from UniProt is joining us until the May 14th 2010
  • GO bibliography has 3164 entries

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