Bkirschn at 21:51, 18 December 2008

2008-12-18T21:51:18Z

Bkirschn: New page: 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): ...

2008-12-16T13:46:56Z

New page: 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): ...

New page

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:
*** <strike>Csongor's software project (https://bmir-gforge.stanford.edu/gf/project/biositemaps/scmsvn/) is password protected</strike> (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:
*** <strike>Natasha: provide a virtual url that will always point to the latest version of the BRO</strike> (done)
*** <strike>Beth: Update biositemaps web site with virtual url</strike> (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:
*** <strike>Beth: Document policy on biositemaps webpage</strike> (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:
*** <strike>Ivo: will provide email describing documentation needed for iTools to consume current biositemaps corpus</strike> (done)
*** <strike>Beth: Update biositemaps website with provided documentation</strike> (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)

@@ Line 37: / Line 37: @@
 *** <strike>Ivo: will provide email describing documentation needed for iTools to consume current biositemaps corpus</strike> (done)
 *** <strike>Beth: Update biositemaps website with provided documentation</strike> (done)
-*** Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service
+*** 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

SDIWG:Action Items 20081203 - Revision history

Bkirschn at 21:51, 18 December 2008

Bkirschn: New page: 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): ...