SDIWG:Action Items 20090212

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Who: Natasha, Ivo, Beth, Csongor, Peter
Background: See meeting Notes of 01/16/2009

Discussion and Current Status (2009-02-12):

• Csongor
  • The following biositemap editor enhancements should be available on a test server later today:
    • browse-mode (possibly with click-able urls; possibly with namespace displayed)
    • allow invalid classes
    • support multiple resource types
    • support harmonized CTSA biositemaps information model (through configurable layout enabled via url parameter)
      • Properties removed: byline
      • Properties added: contact_person_phone, resource_sharable, documentation_available, technical_support
      • Properties optional: biositemap_author not displayed for CTSA
    • Clickable URL when in browase mode
    • Backward compatibility of BRO maintained via:
      1. Virtual URL to ontology available for namespace definition
      2. Deprecated classes will be moved to 'deprecated' class hierarchy (not deleted)
      3. Existing biositemaps can be reviewed for use of deprecated classes via existing BioPortal and/or Search tools, or automatic mining of biositemaps. Owners of deprecated classes should be notified.
• Beth
  • Prototype search application available at http://appserver.ctaalliance.org:8080/biositemaps/search/basic http://portal.ncibi.org/biositemaps
• All
  • Legacy XML creates problem of out-of-date data
  • iTools can ingest either XML or RDF biositemaps, with preference to RDF
  • iTools only exports RDF biositemaps
  • Ivo would like legacy XML files retained in perpetuity due to published article reference
  • Suggestion to remove legacy XML and replace with redirects was tabled without agreement
• Peter
  • Nancy will handle converting CTSA MS Excel content to Biositemaps RDF content

Action Items (2009-02-12):

• Csongor
  • Biositemap Editor: Remove 'Save to Disk' button (unimplemented; perhaps replace 'Open It' with 'View and Save')
  • Biositemap Editor: Tool Tips (defintions of BRO/IM terms displayed in editor with mouse over)
  • Email/talke with 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
  • Support for CTSA relatedBiomedicalAreasOfResearchAndActivities addition to information model
• Beth
  • Work with Csongor to combine above BiositemapsConsumer API with existing BRO api (https://bmir-gforge.stanford.edu/gf/project/biositemaps/scmsvn/)
• Natasha
  • 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 (Beth notes minor invalid content within many biositemaps, such as invalid IM properties and invalid dates)
• All
  • Discuss and define method to 'stream-line' publication of biositemaps. Current process requires three manual steps:
    1. Create/edit biositemap
    2. Deploy biositemap to web server
    3. Publish biositemap via biositemaps registry http://www.ncbcs.org/biositemaps/publish.html

Feature Requests

• Develop, test, and install capability of synonyms for class names in BRO/Bioportal. This is a basic feature of ontological development, and is also related to the issues of provenance tracking and depracation (the latter of which is currently to be handled by assigning 'old' class names (and possibly synonyms) to a depracation bin. By formally allowing synonyms the BRO/Bioportal will be able to handle misspellings (in applications), resolution of collisions between different sides in a harmonization process, and just the usual need for multiple words to have the same meaning. This will also help in the process of alinging the lexicon with NIF. Aside from helping harmonization etc, this will also preserve the hierarchy in case of real synonyms. (Suggested by PLyster 20090218)
• Process for handling provenance which is lossless. Meaning: will enable users/consumers to know which epochs (lexicon and hierarchy) of BRO is applicable to a biositemaps.rdf. (Suggested by PLyster 20090218)
• Flexible extension to BIM (Information Model) in case an individual wants to create customized biositemaps, e.g., to display as web site (Suggested by PLyster 20090218)
• Extend Biositemaps API to support use of Biositemaps as exchange mechanism for information about resources (Suggested by PLyster 20080218)
• For some reason the site http://www.biositemaps.org/ does not work from my workstation at NIH. Any ideas? (Peter)