SDIWG:Action Items 20081121

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

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... (http://appserver.ctaalliance.org/~bkirschn/biositemaps/index.html)
  • 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:
    • Csongor's software project (https://bmir-gforge.stanford.edu/gf/project/biositemaps/scmsvn/) is password protected (use 'anonymous' for username and an empty password)
    • Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)

• Document knowledge of Google access to Biositemaps corpus and other access issue (DONE)
  • Biositemaps registry at http://www.ncbcs.org/biositemaps/biositemap.registry (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 & biositemaps.org 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

• 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)

Archived Action Items (2008-11-21):

• NCBC Team Action Items
  • codify API(s) (Csongr-Beth-Ivo)
    • 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...
  • document knowledge of Google access to Biositemaps corpus and other access issue (Beth)
  • agree on official location of BRO and IM and easily accessible functions to download them (Csongor-Daniel)
  • finalize process for backward compatibility of BRO and IM (deprecation etc...) (Csongor-Beth)
  • 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 (Peter)
  • get iTools to consume biositemaps corpus (Ivo)
  • get BioPortal to consume biositemaps corpus (Csongor-Daniel)
  • modify the BioPortal to index biositemaps corpus over more than BRO--see Beth's API (Csongor-Beth)
    • Daniel: ...providing a search box for people to search by tools using text queries... Harpreet might be able to do in conjunction with the CTSA supplement
  • Modify Biositemaps Editor to support multiple resource types (Csongor)
• NCBC-CTSA Team Action Items
  • harmonize BRO-IM with CTSA IM; clarify which fields should reside in BRO and which in IM. Overall goal is improve biositemaps as format for exchanging information about resources, and reuse tools (Technical Tiger Team: Beth, Csongor, Kevin,...)