Difference between revisions of "SDIWG:Action Items 20081121"

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== Action Items (2008-12-03): ==
 
== Action Items (2008-12-03): ==
  
* Unify API(s) (Csonogr-Beth-Ivo)
+
* 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...
 
** 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)
 
** Beth: I've started working on a 'consumer' api that locates and queries biositemaps... (http://appserver.ctaalliance.org/~bkirschn/biositemaps/index.html)
** The two APIs provide complimentary functionality and should be merged
+
** 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:
 
** 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)       
 
*** <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)       
*** Ivo: RDF-to-XML webservice provides expected/needed functionality; will work on incorporating into iTools
 
 
*** Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)
 
*** 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 (Beth)
+
* 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 involving search engines
 
** 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 involving search engines
  
* Agree on official location of BRO and IM and easily accessible functions to download them (Csongor-Daniel)
+
* Agree on official location of BRO and IM and easily accessible functions to download them
 
** bioportal is official location of BRO & biositemaps.org is official location of IM
 
** bioportal is official location of BRO & biositemaps.org is official location of IM
 
** Action Items:
 
** Action Items:
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*** <strike>Beth: Update biositemaps web site with virtual url</strike> (done)
 
*** <strike>Beth: Update biositemaps web site with virtual url</strike> (done)
  
* Finalize process for backward compatibility of BRO and IM (deprecation etc...) (Csongor-Beth)
+
* Finalize process for backward compatibility of BRO and IM (deprecation etc...)
 
** 1. Software needs to be flexible (graceful handling of undefined classes)  
 
** 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)
 
** 2. New Policy: don't delete classes and move to deprecated sub-tree (annotate with a recommended valid class)
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*** Beth: Document policy on biositemaps webpage
 
*** Beth: Document policy on biositemaps webpage
  
* 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 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:
 
** Action Items:
 
*** Beth & Peter:  follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)
 
*** 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 (Ivo)
+
* 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.
 
** 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:
 
** Action Items:
 
*** <strike>Ivo: will provide email describing documentation needed for iTools to consume current biositemaps corpus</strike> (done)
 
*** <strike>Ivo: will provide email describing documentation needed for iTools to consume current biositemaps corpus</strike> (done)
 
*** Beth: Update biositemaps website with provided documentation
 
*** Beth: Update biositemaps website with provided documentation
 +
*** Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service
  
* Get BioPortal to consume biositemaps corpus (Csongor-Daniel)
+
* 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
 
** There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal
 
** Action Items:
 
** Action Items:
 
*** Natasha: will email group when problems are resolved
 
*** Natasha: will email group when problems are resolved
  
* Modify the BioPortal to index biositemaps corpus over more than BRO--see Beth's API (Csongor-Beth)
+
* Modify the BioPortal to index biositemaps corpus over more than BRO--see Beth's API
 
** Daniel had emailed that "...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"  
 
** Daniel had emailed that "...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"  
 
** Action Items:
 
** Action Items:
 
*** Beth:  will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing
 
*** Beth:  will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing
  
* Modify Biositemaps Editor to support multiple resource types (Csongor)
+
* Modify Biositemaps Editor to support multiple resource types
 
**Action Items:
 
**Action Items:
 
*** Csongor:  to be done early next year (January 2009)
 
*** Csongor:  to be done early next year (January 2009)

Revision as of 13:53, 4 December 2008

Home < 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:
  • Document knowledge of Google access to Biositemaps corpus and other access issue (done)
  • Agree on official location of BRO and IM and easily accessible functions to download them
    • 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:
      • Csongor: Update API & Biositemaps Editor to allow invalid classes
      • Beth: Document policy on biositemaps webpage
  • 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
      • 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--see Beth's API
    • Daniel had emailed that "...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"
    • 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,...)