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) |
+ | ** 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 two APIs provide complimentary functionality and should be merged | ||
+ | ** Action Items: | ||
+ | *** Csongor's software project (https://bmir-gforge.stanford.edu/gf/project/biositemaps/scmsvn/) is password protected -- Ivo should register account and Csongor can provide access | ||
+ | *** 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) | ||
− | == Action Items (2008-11-21): == | + | * Document knowledge of Google access to Biositemaps corpus and other access issue (Beth) |
+ | ** 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) | ||
+ | ** 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...) (Csongor-Beth) | ||
+ | ** 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 (Peter) | ||
+ | ** 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 (Ivo) | ||
+ | ** 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) | ||
+ | *** Beth: Update biositemaps website with provided documentation | ||
+ | |||
+ | * Get BioPortal to consume biositemaps corpus (Csongor-Daniel) | ||
+ | ** 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 (Csongor-Beth) | ||
+ | ** 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 (Csongor) | ||
+ | **Action Items: | ||
+ | *** Csongor: to be done early next year (January 2009) | ||
+ | |||
+ | == Archived Action Items (2008-11-21): == | ||
* NCBC Team Action Items | * NCBC Team Action Items | ||
Line 17: | Line 64: | ||
** get iTools to consume biositemaps corpus (Ivo) | ** get iTools to consume biositemaps corpus (Ivo) | ||
** get BioPortal to consume biositemaps corpus (Csongor-Daniel) | ** 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 | *** 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) | ** Modify Biositemaps Editor to support multiple resource types (Csongor) | ||
− | |||
* 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,...) |
Revision as of 16:45, 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) (Csonogr-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... (http://appserver.ctaalliance.org/~bkirschn/biositemaps/index.html)
- The two APIs provide complimentary functionality and should be merged
- Action Items:
- Csongor's software project (https://bmir-gforge.stanford.edu/gf/project/biositemaps/scmsvn/) is password protected -- Ivo should register account and Csongor can provide access
- 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)
- Document knowledge of Google access to Biositemaps corpus and other access issue (Beth)
- 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)
- 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...) (Csongor-Beth)
- 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 (Peter)
- 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 (Ivo)
- 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
- Get BioPortal to consume biositemaps corpus (Csongor-Daniel)
- 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 (Csongor-Beth)
- 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 (Csongor)
- 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,...)