SDIWG:Action Items 20090116 - Revision history

Bkirschn: /* Action Items (2009-01-16): */

2009-02-12T16:20:09Z

Action Items (2009-01-16):

Bkirschn at 19:39, 6 February 2009

2009-02-06T19:39:53Z

Bkirschn at 19:37, 6 February 2009

2009-02-06T19:37:36Z

Lysterp at 19:26, 6 February 2009

2009-02-06T19:26:34Z

Lysterp at 19:15, 6 February 2009

2009-02-06T19:15:57Z

Lysterp at 18:49, 6 February 2009

2009-02-06T18:49:07Z

Bkirschn at 14:49, 5 February 2009

2009-02-05T14:49:37Z

Lysterp at 00:30, 5 February 2009

2009-02-05T00:30:44Z

Lysterp at 00:26, 5 February 2009

2009-02-05T00:26:37Z

Lysterp at 00:26, 5 February 2009

2009-02-05T00:26:18Z

@@ Line 30: / Line 30: @@
 ** <strike>Forward proposed set of biositemap logos developed by UM graphic designer for consideration</strike> (done)
 ** Develop biositemaps search application based on BiositemapsConsumer prototype API described at https://appserver.ctaalliance.org/~bkirschn/biositemaps/ (initial release by end of January)
-*** Initial release available at http://appserver.ctaalliance.org:8080/biositemap-search-tool/index.html
+*** Initial release available at http://appserver.ctaalliance.org:8080/biositemaps/search/basic
 ** Work with Csongor to combine above BiositemapsConsumer API with existing BRO api (https://bmir-gforge.stanford.edu/gf/project/biositemaps/scmsvn/)
 * Natasha
 ** <strike>Translate IATR biositemap.xml into biositemap.rdf format</strike> (done)
-** Provide updated definition of available and proposed web services based on proposed list at bottom of [http://na-mic.org/Wiki/index.php/SDIWG:Action_Items_20081219|2008-12-19] discussion. Note that some of these services are already available, some can be developed, and some will not be developed (tabled pending further discussion)
+** <strike>Provide updated definition of available and proposed web services based on proposed list at bottom of [http://na-mic.org/Wiki/index.php/SDIWG:Action_Items_20081219|2008-12-19] discussion. Note that some of these services are already available, some can be developed, and some will not be developed (tabled pending further discussion)</strike> (done)
 ** Email 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
 ** BioPortal will leverage combined biositemaps API (when available, see above) to support more frequent/live updates of biositemaps data

@@ Line 17: / Line 17: @@
 *** support multiple resource types
 *** support harmonized CTSA biositemaps information model:
-**** byline dropped
+**** Properties removed: byline
-**** properties added
+**** Properties added: contact_person_phone, resource_sharable, documentation_available, technical_support
-**** biositemap_author not displayed for CTSA
+**** Properties optional: biositemap_author not displayed for CTSA
 *** Remove 'Save to Disk' button (unimplemented; perhaps replace 'Open It' with 'View and Save')
 * Ivo

@@ Line 16: / Line 16: @@
 *** allow invalid classes
 *** support multiple resource types
-*** support harmonized CTSA biositemaps information model (byline dropped, several other properties added, biositemap_author not displayed for CTSA)
+*** support harmonized CTSA biositemaps information model:
 *** Remove 'Save to Disk' button (unimplemented; perhaps replace 'Open It' with 'View and Save')
 * Ivo

@@ Line 38: / Line 38: @@
 == Follow-up Issues from CTSA Harmonization Calls January-February 2009 (Beth and Peter) ==
-* Using Versioning in BRO namespace attribute (Peter writes: ''Can we think of a way of identifying the version (or 'epoch') of BRO and IM in a biositemaps file.  This is for the case where over time folks use different epochs and there will need to be some way of tracking the BRO and IM so that consumers can 'validate'.'').  This issue came up in discussion with CTSA team. The reason it may be an issue is if there are two biositemaps.rdf files in two different places created at different times from different versions of BRO/IM, then will that not cause problems for the querey tool (e.g., if an ontology class is moved within the hierarchy, then how will iTools or Michigan query tool know what kind of tree to display or traverse?  Solution: expose versions of BRO/IM (v1.1 v1.2 etc.) and modify the Editor to install a pointer to the appropiate version of BRO/IM
+* Feature request: Create capability to 'version' the BRO/IM, in particular, so that any particular biositemap.rdf file can be traced back to a particular version vx.y.z of the BRO/IM. An incremental way to do this is to create a list of deprecated terms in the BRO/IM. Thus the editor or any query tools could at least check with the depracated list if there are problems with interpreting unknown items in a particualar biositemaps.rdf. Here is a description of the discussion from 20090130.  Using Versioning in BRO namespace attribute (Peter writes: ''Can we think of a way of identifying the version (or 'epoch') of BRO and IM in a biositemaps file.  This is for the case where over time folks use different epochs and there will need to be some way of tracking the BRO and IM so that consumers can 'validate'.'').  This issue came up in discussion with CTSA team. The reason it may be an issue is if there are two biositemaps.rdf files in two different places created at different times from different versions of BRO/IM, then will that not cause problems for the querey tool (e.g., if an ontology class is moved within the hierarchy, then how will iTools or Michigan query tool know what kind of tree to display or traverse?  Solution: expose versions of BRO/IM (v1.1 v1.2 etc.) and modify the Editor to install a pointer to the appropiate version of BRO/IM
-* CTSA asked if defintions of BRO/IM terms can be displayed in editor with mouse over (or similar)
+* Feature request: Create a new ontology "Related_Biomedical_Areas_of_Research_and_Activities" (using classes that will be provided by MBecich and PLyster and NWhelan) and enable new discriptor in the Editor with this new ontology. This will handle almost all of the old terms from the Area Priority List (APL).
-* CTSA team ask of Wikipedia entries can be used, where possible, for BRO/IM definitions.
+* Feature request: CTSA asked if defintions of BRO/IM terms can be displayed in editor with mouse over (or similar)
-* NIF-Biositemaps harmonization is now focused on developing a common (agreed upon) lexicon.  How do we generate this, and what technologies need to be in place to allow NIF and Biositemaps to maintain alignment to the same lexicon?
+* Feature request: CTSA team ask of Wikipedia entries can be used, where possible, for BRO/IM definitions.
 * Feature request from 20090206 'query tool' tcon (Beth, Harpreet, Nancy, Peter, Jian): add a button to Biositemaps editor to automatically publish a biositemaps file (presumably the file will be published on Stanford/NCBO server.

@@ Line 39: / Line 39: @@
 == Follow-up Issues from CTSA Harmonization Calls January-February 2009 (Beth and Peter) ==
 * Using Versioning in BRO namespace attribute (Peter writes: ''Can we think of a way of identifying the version (or 'epoch') of BRO and IM in a biositemaps file.  This is for the case where over time folks use different epochs and there will need to be some way of tracking the BRO and IM so that consumers can 'validate'.'').  This issue came up in discussion with CTSA team. The reason it may be an issue is if there are two biositemaps.rdf files in two different places created at different times from different versions of BRO/IM, then will that not cause problems for the querey tool (e.g., if an ontology class is moved within the hierarchy, then how will iTools or Michigan query tool know what kind of tree to display or traverse?  Solution: expose versions of BRO/IM (v1.1 v1.2 etc.) and modify the Editor to install a pointer to the appropiate version of BRO/IM
-* CTSA asked if defintions of BRO/IM terms can be displayed in editor with mouse over (or similear)
+* CTSA asked if defintions of BRO/IM terms can be displayed in editor with mouse over (or similar)
 * CTSA team ask of Wikipedia entries can be used, where possible, for BRO/IM definitions.
 * NIF-Biositemaps harmonization is now focused on developing a common (agreed upon) lexicon.  How do we generate this, and what technologies need to be in place to allow NIF and Biositemaps to maintain alignment to the same lexicon?
 * Feature request from 20090206 'query tool' tcon (Beth, Harpreet, Nancy, Peter, Jian): add a button to Biositemaps editor to automatically publish a biositemaps file (presumably the file will be published on Stanford/NCBO server.

← Older revision		Revision as of 18:49, 6 February 2009
Line 42:		Line 42:
	* CTSA team ask of Wikipedia entries can be used, where possible, for BRO/IM definitions.		* CTSA team ask of Wikipedia entries can be used, where possible, for BRO/IM definitions.
	* NIF-Biositemaps harmonization is now focused on developing a common (agreed upon) lexicon. How do we generate this, and what technologies need to be in place to allow NIF and Biositemaps to maintain alignment to the same lexicon?		* NIF-Biositemaps harmonization is now focused on developing a common (agreed upon) lexicon. How do we generate this, and what technologies need to be in place to allow NIF and Biositemaps to maintain alignment to the same lexicon?
		+	* Feature request from 20090206 'query tool' tcon (Beth, Harpreet, Nancy, Peter, Jian): add a button to Biositemaps editor to automatically publish a biositemaps file (presumably the file will be published on Stanford/NCBO server.

@@ Line 19: / Line 19: @@
 *** Remove 'Save to Disk' button (unimplemented; perhaps replace 'Open It' with 'View and Save')
 * Ivo
-** Send Natasha IATR biositemap.xml file to be translated to RDF (Done)
+** <strike>Send Natasha IATR biositemap.xml file to be translated to RDF</strike> (Done)
 ** Update iTools to make use of biositemap registry and cease using XML biositemap files by January 23rd
-** Publish IATR and CCB biositemap file on UCLA/CCB server
+*** 1/23/09 XML & RDF both in use?
 * Beth
 ** Retire biositemap XML files from biositemaps.org web site once iTools has been updated to make use of biositemap registry
-** Forward proposed set of biositemap logos developed by UM graphic designer for consideration
+** <strike>Forward proposed set of biositemap logos developed by UM graphic designer for consideration</strike> (done)
 ** Develop biositemaps search application based on BiositemapsConsumer prototype API described at https://appserver.ctaalliance.org/~bkirschn/biositemaps/ (initial release by end of January)
 ** Work with Csongor to combine above BiositemapsConsumer API with existing BRO api (https://bmir-gforge.stanford.edu/gf/project/biositemaps/scmsvn/)
 * Natasha
-** Translate IATR biositemap.xml into biositemap.rdf format
+** <strike>Translate IATR biositemap.xml into biositemap.rdf format</strike> (done)
 ** Provide updated definition of available and proposed web services based on proposed list at bottom of [http://na-mic.org/Wiki/index.php/SDIWG:Action_Items_20081219|2008-12-19] discussion. Note that some of these services are already available, some can be developed, and some will not be developed (tabled pending further discussion)
 ** Email 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

@@ Line 3: / Line 3: @@
 '''Who''': Natasha, Ivo, Beth<br>
 '''Background''': [[SDIWG:Action_Items_20081219| See meeting Notes of 12/19/2008]]
 == Discussion and Current Status (2009-01-16): ==
@@ Line 42: / Line 35: @@
 ** Follow up with other NCBC's requesting updated biositemap.rdf data once above action items have been resolved
-== Follow-up Issues from CTSA Harmonization Calls ==
+== Follow-up Issues from CTSA Harmonization Calls January-February 2009 (Beth and Peter) ==
-* Using Versioning in BRO namespace attribute (Peter writes: ''Can we think of a way of identifying the version (or 'epoch') of BRO and IM in a biositemaps file.  This is for the case where over time folks use different epochs and there will need to be some way of tracking the BRO and IM so that consumers can 'validate'.'')
+* Using Versioning in BRO namespace attribute (Peter writes: ''Can we think of a way of identifying the version (or 'epoch') of BRO and IM in a biositemaps file.  This is for the case where over time folks use different epochs and there will need to be some way of tracking the BRO and IM so that consumers can 'validate'.'').  This issue came up in discussion with CTSA team. The reason it may be an issue is if there are two biositemaps.rdf files in two different places created at different times from different versions of BRO/IM, then will that not cause problems for the querey tool (e.g., if an ontology class is moved within the hierarchy, then how will iTools or Michigan query tool know what kind of tree to display or traverse?  Solution: expose versions of BRO/IM (v1.1 v1.2 etc.) and modify the Editor to install a pointer to the appropiate version of BRO/IM

@@ Line 4: / Line 4: @@
 '''Background''': [[SDIWG:Action_Items_20081219| See meeting Notes of 12/19/2008]]
-== Action Items arising from CTSA-NIF-Biositemaps discussion during January 2009 (PMLyster) ==
+== Action Items arising from CTSA-NIF-Biositemaps discussion during January-February 2009 (PMLyster) ==
 * How do we track versions of BRO/IM that are used in any one biositemap file? This issue came up in discussion with CTSA team. The reason it may be an issue is if there are two biositemaps.rdf files in two different places created at different times from different versions of BRO/IM, then will that not cause problems for the querey tool (e.g., if an ontology class is moved within the hierarchy, then how will iTools or Michigan query tool know what kind of tree to display or traverse?  Solution: expose versions of BRO/IM (v1.1 v1.2 etc.) and modify the Editor to install a pointer to the appropiate version of BRO/IM
 * CTSA asked if defintions of BRO/IM terms can be displayed in editor with mouse over (or similear)