SDIWG:Action Items 20090116

Go back to top level of Resourcome working group discussion pages http://na-mic.org/Wiki/index.php/SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies

Who: Natasha, Ivo, Beth
Background: See meeting Notes of 12/19/2008

Discussion and Current Status (2009-01-16):

• Natasha: BioPortal has been updated with latest biositemaps data
• Ivo: iTools does a weekly reload of biositemaps (rdf/xml) found using Yahoo search engine (note this search only finds 2 biositemap files)
• Beth: Biositemaps registration application is now available
• All: Follow up via email on action items -- next meeting end of January or when (updated) Biositemaps Editor and Biositemaps Search applications are ready for review

Action Items (2009-01-16):

• Csongor
  • Update Biositemaps Editor with the following by end of January:
    • browse-mode (possibly with click-able urls; possibly with namespace displayed)
    • allow invalid classes
    • support multiple resource types
    • support harmonized CTSA biositemaps information model:
      • byline dropped
      • properties added
      • biositemap_author not displayed for CTSA
    • Remove 'Save to Disk' button (unimplemented; perhaps replace 'Open It' with 'View and Save')
• Ivo
  • Send Natasha IATR biositemap.xml file to be translated to RDF (Done)
  • Update iTools to make use of biositemap registry and cease using XML biositemap files by January 23rd
    • 1/23/09 XML & RDF both in use?
  • Publish IATR and CCB biositemap file on UCLA/CCB server (done)
• Beth
  • Retire biositemap XML files from biositemaps.org web site once iTools has been updated to make use of biositemap registry
  • Forward proposed set of biositemap logos developed by UM graphic designer for consideration (done)
  • Develop biositemaps search application based on BiositemapsConsumer prototype API described at https://appserver.ctaalliance.org/~bkirschn/biositemaps/ (initial release by end of January)
    • Initial release available at http://appserver.ctaalliance.org:8080/biositemap-search-tool/index.html
  • Work with Csongor to combine above BiositemapsConsumer API with existing BRO api (https://bmir-gforge.stanford.edu/gf/project/biositemaps/scmsvn/)
• Natasha
  • Translate IATR biositemap.xml into biositemap.rdf format (done)
  • Provide updated definition of available and proposed web services based on proposed list at bottom of [1] discussion. Note that some of these services are already available, some can be developed, and some will not be developed (tabled pending further discussion)
  • Email Joy at Stanford to review biositemap web site after above minimum requirements are met (e.g. here is where your current biositemap, how to view, update, etc.) when above action items have been resolved
  • BioPortal will leverage combined biositemaps API (when available, see above) to support more frequent/live updates of biositemaps data
• Peter
  • Follow up with other NCBC's requesting updated biositemap.rdf data once above action items have been resolved

Follow-up Issues from CTSA Harmonization Calls January-February 2009 (Beth and Peter)

• Feature request: Create capability to 'version' the BRO/IM, in particular, so that any particular biositemap.rdf file can be traced back to a particular version vx.y.z of the BRO/IM. An incremental way to do this is to create a list of deprecated terms in the BRO/IM. Thus the editor or any query tools could at least check with the depracated list if there are problems with interpreting unknown items in a particualar biositemaps.rdf. Here is a description of the discussion from 20090130. Using Versioning in BRO namespace attribute (Peter writes: Can we think of a way of identifying the version (or 'epoch') of BRO and IM in a biositemaps file. This is for the case where over time folks use different epochs and there will need to be some way of tracking the BRO and IM so that consumers can 'validate'.). This issue came up in discussion with CTSA team. The reason it may be an issue is if there are two biositemaps.rdf files in two different places created at different times from different versions of BRO/IM, then will that not cause problems for the querey tool (e.g., if an ontology class is moved within the hierarchy, then how will iTools or Michigan query tool know what kind of tree to display or traverse? Solution: expose versions of BRO/IM (v1.1 v1.2 etc.) and modify the Editor to install a pointer to the appropiate version of BRO/IM
• Feature request: Create a new ontology "Related_Biomedical_Areas_of_Research_and_Activities" (using classes that will be provided by MBecich and PLyster and NWhelan) and enable new discriptor in the Editor with this new ontology. This will handle almost all of the old terms from the Area Priority List (APL).
• Feature request: CTSA asked if defintions of BRO/IM terms can be displayed in editor with mouse over (or similar)
• Feature request: CTSA team ask of Wikipedia entries can be used, where possible, for BRO/IM definitions.
• Feature request from 20090206 'query tool' tcon (Beth, Harpreet, Nancy, Peter, Jian): add a button to Biositemaps editor to automatically publish a biositemaps file (presumably the file will be published on Stanford/NCBO server.
• Discussion: NIF-Biositemaps harmonization is now focused on developing a common (agreed upon) lexicon. How do we generate this, and what technologies need to be in place to allow NIF and Biositemaps to maintain alignment to the same lexicon?