SDIWG:Action Items 20081121 - Revision history

Bkirschn at 21:48, 18 December 2008

2008-12-18T21:48:45Z

Bkirschn at 13:46, 16 December 2008

2008-12-16T13:46:40Z

Bkirschn at 13:45, 16 December 2008

2008-12-16T13:45:09Z

Bkirschn at 13:42, 16 December 2008

2008-12-16T13:42:09Z

Bkirschn at 22:02, 8 December 2008

2008-12-08T22:02:50Z

Bkirschn at 18:17, 4 December 2008

2008-12-04T18:17:43Z

Bkirschn at 18:17, 4 December 2008

2008-12-04T18:17:16Z

Bkirschn at 18:16, 4 December 2008

2008-12-04T18:16:00Z

Bkirschn at 17:54, 4 December 2008

2008-12-04T17:54:46Z

Bkirschn at 17:54, 4 December 2008

2008-12-04T17:54:18Z

← Older revision		Revision as of 21:48, 18 December 2008
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	* NCBC-CTSA Team Action Items		* 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,...)		** 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,...)
		+
		+
		+	Go to [[SDIWG:Action_Items_20081203 \| Action Items (12-3-2008)]]

← Older revision		Revision as of 13:46, 16 December 2008
Line 1:		Line 1:
	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		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)

	== Action Items (2008-11-21): ==		== Action Items (2008-11-21): ==

← Older revision		Revision as of 13:45, 16 December 2008
Line 1:		Line 1:
	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		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)

	== Action Items (2008-11-21): ==		== Action Items (2008-11-21): ==

@@ Line 1: / Line 1: @@
 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): ==
+== Action Items (2008-11-21): ==
 * NCBC Team Action Items

@@ Line 13: / Line 13: @@
 * 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 (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)

@@ Line 44: / Line 44: @@
 *** Natasha: will email group when problems are resolved
-* Modify the BioPortal to index biositemaps corpus over more than BRO--see Beth's API
+* 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

@@ Line 25: / Line 25: @@
 ** 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
 * 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
@@ Line 36: / Line 36: @@
 ** Action Items:
 *** <strike>Ivo: will provide email describing documentation needed for iTools to consume current biositemaps corpus</strike> (done)
-*** Beth: Update biositemaps website with provided documentation
+*** <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

@@ Line 18: / Line 18: @@
 ** 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>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)