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 | + | * 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 | + | ** 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) | ||
| − | |||
*** 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 ( | + | * 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 | + | * 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: | ||
| Line 21: | Line 21: | ||
*** <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... | + | * 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) | ||
| Line 28: | Line 28: | ||
*** 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 | + | * 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 | + | * 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 | + | * 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 | + | * 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 | + | * 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 17:53, 4 December 2008
Home < SDIWG:Action Items 20081121Go 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:
Csongor's software project (https://bmir-gforge.stanford.edu/gf/project/biositemaps/scmsvn/) is password protected(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 involving search engines
- 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)
- Action Items:
- 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)
- Action Items:
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)
- codify API(s) (Csongr-Beth-Ivo)
- 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,...)
