SDIWG:Action Items 20081203

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Action Items (2008-12-03):

  • Unify API(s)
    • Csongor: I started working on the "Lightweight API", i.e. the REST web services that will process biositemaps and will return an XML representation that can be consumed by iTools...
    • Beth: I've started working on a 'consumer' api that locates and queries biositemaps... (
    • The Stanford/NCIBI Biositemap APIs provide complimentary functionality and should be merged
    • Csongor's RDF-to-XML webservice provides expected/needed functionality for iTools to consume current RDF biositemaps
    • Action Items:
  • Document knowledge of Google access to Biositemaps corpus and other access issue (DONE)
    • Biositemaps registry at (with email to register new biositemaps url) is acceptable in the short-term; long-term we should find a more scalable solution (currently Google & Yahoo search engines do not provide reliable indexing of biositemaps rdf files)
  • Agree on official location of BRO and IM and easily accessible functions to download them (DONE)
    • bioportal is official location of BRO & is official location of IM
    • Action Items:
      • Natasha: provide a virtual url that will always point to the latest version of the BRO (done)
      • Beth: Update biositemaps web site with virtual url (done)
  • Finalize process for backward compatibility of BRO and IM (deprecation etc...)
    • 1. Software needs to be flexible (graceful handling of undefined classes)
    • 2. New Policy: don't delete classes and move to deprecated sub-tree (annotate with a recommended valid class)
    • Action Items:
      • Beth: Document policy on biositemaps webpage (done)
      • Csongor: Update API & Biositemaps Editor to allow invalid classes
  • Get back to NCBC liaisons and (i) generate full corpus of NCBC biositemaps and (ii) expose biositemaps consistently to the Internet according to practices that Beth will disseminate
    • Action Items:
      • Beth & Peter: follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)
  • Get iTools to consume biositemaps corpus
    • Csongor's XML-to-RDF web service provides Ivo needed functionality. Both Beth and Csongor's API use 13-14 MB in jars, so the only way to avoid this overhead is to parse the serialized XML version of the biositemaps from this service.
    • Action Items:
      • Ivo: will provide email describing documentation needed for iTools to consume current biositemaps corpus (done)
      • Beth: Update biositemaps website with provided documentation (done)
      • Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service (12-18-08 Update: Complete excepting BRO query & navigation)
  • Get BioPortal to consume biositemaps corpus
    • There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal
    • Action Items:
      • Natasha: will email group when problems are resolved
  • Modify the BioPortal to index biositemaps corpus over more than BRO
    • Action Items:
      • Beth: will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing
  • Modify Biositemaps Editor to support multiple resource types
    • Action Items:
      • Csongor: to be done early next year (January 2009)