https://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20081203&feed=atom&action=historySDIWG:Action Items 20081203 - Revision history2024-03-28T11:02:08ZRevision history for this page on the wikiMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20081203&diff=33865&oldid=prevBkirschn at 21:51, 18 December 20082008-12-18T21:51:18Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*** <strike>Ivo: will provide email describing documentation needed for iTools to consume current biositemaps corpus</strike> (done)</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*** <strike>Ivo: will provide email describing documentation needed for iTools to consume current biositemaps corpus</strike> (done)</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Get BioPortal to consume biositemaps corpus</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>* Get BioPortal to consume biositemaps corpus</div></td></tr>
</table>Bkirschnhttps://www.na-mic.org/w/index.php?title=SDIWG:Action_Items_20081203&diff=33669&oldid=prevBkirschn: 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<p>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): ...</p>
<p><b>New page</b></p><div>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<br />
<br />
== Action Items (2008-12-03): ==<br />
<br />
* Unify API(s) <br />
** 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...<br />
** Beth: I've started working on a 'consumer' api that locates and queries biositemaps... (http://appserver.ctaalliance.org/~bkirschn/biositemaps/index.html)<br />
** The Stanford/NCIBI Biositemap APIs provide complimentary functionality and should be merged<br />
** Csongor's RDF-to-XML webservice provides expected/needed functionality for iTools to consume current RDF biositemaps<br />
** Action Items:<br />
*** <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) <br />
*** Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)<br />
<br />
* Document knowledge of Google access to Biositemaps corpus and other access issue (DONE)<br />
** 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)<br />
<br />
* Agree on official location of BRO and IM and easily accessible functions to download them (DONE)<br />
** bioportal is official location of BRO & biositemaps.org is official location of IM<br />
** Action Items:<br />
*** <strike>Natasha: provide a virtual url that will always point to the latest version of the BRO</strike> (done)<br />
*** <strike>Beth: Update biositemaps web site with virtual url</strike> (done)<br />
<br />
* Finalize process for backward compatibility of BRO and IM (deprecation etc...)<br />
** 1. Software needs to be flexible (graceful handling of undefined classes) <br />
** 2. New Policy: don't delete classes and move to deprecated sub-tree (annotate with a recommended valid class)<br />
** Action Items:<br />
*** <strike>Beth: Document policy on biositemaps webpage</strike> (done)<br />
*** Csongor: Update API & Biositemaps Editor to allow invalid classes<br />
<br />
* 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<br />
** Action Items:<br />
*** Beth & Peter: follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)<br />
<br />
* Get iTools to consume biositemaps corpus<br />
** 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.<br />
** Action Items:<br />
*** <strike>Ivo: will provide email describing documentation needed for iTools to consume current biositemaps corpus</strike> (done)<br />
*** <strike>Beth: Update biositemaps website with provided documentation</strike> (done)<br />
*** Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service<br />
<br />
* Get BioPortal to consume biositemaps corpus<br />
** There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal<br />
** Action Items:<br />
*** Natasha: will email group when problems are resolved<br />
<br />
* Modify the BioPortal to index biositemaps corpus over more than BRO<br />
** Action Items:<br />
*** Beth: will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing<br />
<br />
* Modify Biositemaps Editor to support multiple resource types<br />
**Action Items:<br />
*** Csongor: to be done early next year (January 2009)</div>Bkirschn