SDIWG:Action Items 20090318

2009-03-20T12:44:41Z

Bkirschn:

SDIWG:Action Items 20090318

2009-03-19T14:57:36Z

Bkirschn:

SDIWG:Action Items 20090116

2009-02-06T19:39:53Z

Bkirschn:

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

'''Who''': Natasha, Ivo, Beth 
'''Background''': [[SDIWG:Action_Items_20081219| See meeting Notes of 12/19/2008]]

== Discussion and Current Status (2009-01-16): ==
* Natasha: BioPortal has been updated with latest biositemaps data
* Ivo: iTools does a weekly reload of biositemaps (rdf/xml) found using Yahoo search engine (note this search only finds 2 biositemap files)
* Beth: Biositemaps registration application is now available
* All: Follow up via email on action items -- next meeting end of January or when (updated) Biositemaps Editor and Biositemaps Search applications are ready for review

== Action Items (2009-01-16): ==
* Csongor
** Update Biositemaps Editor with the following by end of January:
*** browse-mode (possibly with click-able urls; possibly with namespace displayed)
*** allow invalid classes
*** support multiple resource types
*** support harmonized CTSA biositemaps information model:
**** Properties removed: byline
**** Properties added: contact_person_phone, resource_sharable, documentation_available, technical_support
**** Properties optional: biositemap_author not displayed for CTSA
*** Remove 'Save to Disk' button (unimplemented; perhaps replace 'Open It' with 'View and Save')
* Ivo
** <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
*** 1/23/09 XML & RDF both in use?
** <strike>Publish IATR and CCB biositemap file on UCLA/CCB server</strike> (done)
* Beth
** Retire biositemap XML files from biositemaps.org web site once iTools has been updated to make use of biositemap registry
** <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
** 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)
** 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
* Peter
** 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 January-February 2009 (Beth and Peter) ==
* 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
* 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).
* Feature request: CTSA asked if defintions of BRO/IM terms can be displayed in editor with mouse over (or similar)
* 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.
* Discussion: 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?

SDIWG:Action Items 20090116

2009-02-06T19:37:36Z

Bkirschn:

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

'''Who''': Natasha, Ivo, Beth 
'''Background''': [[SDIWG:Action_Items_20081219| See meeting Notes of 12/19/2008]]

== Discussion and Current Status (2009-01-16): ==
* Natasha: BioPortal has been updated with latest biositemaps data
* Ivo: iTools does a weekly reload of biositemaps (rdf/xml) found using Yahoo search engine (note this search only finds 2 biositemap files)
* Beth: Biositemaps registration application is now available
* All: Follow up via email on action items -- next meeting end of January or when (updated) Biositemaps Editor and Biositemaps Search applications are ready for review

== Action Items (2009-01-16): ==
* Csongor
** Update Biositemaps Editor with the following by end of January:
*** browse-mode (possibly with click-able urls; possibly with namespace displayed)
*** allow invalid classes
*** support multiple resource types
*** support harmonized CTSA biositemaps information model:
**** byline dropped
**** properties added
**** biositemap_author not displayed for CTSA
*** Remove 'Save to Disk' button (unimplemented; perhaps replace 'Open It' with 'View and Save')
* Ivo
** <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
*** 1/23/09 XML & RDF both in use?
** <strike>Publish IATR and CCB biositemap file on UCLA/CCB server</strike> (done)
* Beth
** Retire biositemap XML files from biositemaps.org web site once iTools has been updated to make use of biositemap registry
** <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
** 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)
** 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
* Peter
** 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 January-February 2009 (Beth and Peter) ==
* 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
* 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).
* Feature request: CTSA asked if defintions of BRO/IM terms can be displayed in editor with mouse over (or similar)
* 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.
* Discussion: 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?

SDIWG:Action Items 20090116

2009-02-05T14:49:37Z

Bkirschn:

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

'''Who''': Natasha, Ivo, Beth 
'''Background''': [[SDIWG:Action_Items_20081219| See meeting Notes of 12/19/2008]]

== Discussion and Current Status (2009-01-16): ==
* Natasha: BioPortal has been updated with latest biositemaps data
* Ivo: iTools does a weekly reload of biositemaps (rdf/xml) found using Yahoo search engine (note this search only finds 2 biositemap files)
* Beth: Biositemaps registration application is now available
* All: Follow up via email on action items -- next meeting end of January or when (updated) Biositemaps Editor and Biositemaps Search applications are ready for review

== Action Items (2009-01-16): ==
* Csongor
** Update Biositemaps Editor with the following by end of January:
*** browse-mode (possibly with click-able urls; possibly with namespace displayed)
*** 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)
*** Remove 'Save to Disk' button (unimplemented; perhaps replace 'Open It' with 'View and Save')
* Ivo
** <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
*** 1/23/09 XML & RDF both in use?
** <strike>Publish IATR and CCB biositemap file on UCLA/CCB server</strike> (done)
* Beth
** Retire biositemap XML files from biositemaps.org web site once iTools has been updated to make use of biositemap registry
** <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
** 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)
** 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
* Peter
** 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 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 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?

SDIWG:Action Items 20090116

2009-02-02T13:53:07Z

Bkirschn:

SDIWG:Action Items 20090116

2009-01-27T14:05:34Z

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

SDIWG:Action Items 20090116

2009-01-16T21:45:43Z

Bkirschn:

2009-01-16T19:52:15Z

SDIWG: NCBC Resource Yellow Pages and Software Ontologies

2009-01-16T19:50:47Z

Bkirschn:

This is the main page for the NIH Roadmap National Centers for Biomedical Computing (NCBC) Working Group titled: Resource Yellow Pages and Biomedical Software Classification

[http://www.ncbcs.org/ Top page of ncbcs.org web site which is maintained by the NCBCs themselves]

[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]

[http://www.na-mic.org/Wiki/index.php/SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers NCBC Working Group Discussion threads, tcons, Breeze/Access minutes]

=== The leads for this Working Group are [http://www.loni.ucla.edu/~dinov/ Ivo Dinov] ([http://www.loni.ucla.edu/CCB CCB]) and [http://smi-web.stanford.edu/people/rubin/ Daniel Rubin] ([http://bioontology.org NCBO]) ===

=== Mission Statement===
The goals of this working group (lead by the [[Tiger_team_biositemaps|Tiger Team]]) are: (1) Develop a Visualization interface (iTools) to enable query and browsing of the NCBC tools, and potentially access to a broad range of biomedical software tools; (2) Develop a software classification scheme that can be used broadly to enable query tools (such as iTools) and tagging of biomedical software tools; (3) Develop technologies that will enable convenient and rapid application development and pipelines across diverse heterogeneous hardware and software environments.

----

Latest works is focusing on the Biositemaps effort. You can go to [http://www.Biositemaps.org www.Biositemaps.org] for further information.

[http://www.loni.ucla.edu/iToolssvc/ncbc_iTools.html Click here to use PROTOTYPE iTools:] This will allow you to visually browse tools according to their classifications, or to search keywords and other descriptors. Note there there are two kinds of views: (1) the visual Hyperbolic viewer, and (2) the more traditional hierarchical interface.

[http://iTools.loni.ucla.edu/ NCBC iTools Development Page:] This is the main developers page for the iTools project, which is a visualization interface to enable query and browsing of the NCBC tools, and potentially access to a broad range of biomedical software tools.

[http://bioontology.org/projects/ontologies/SoftwareOntology/ Software Classification Development Page:] This is the main developers page for the project to develop a common Software Tools Ontology that can be used to improve query and browsing in the iTools project and for more general efforts at classifying biomedical software tools.

----

=== Archive Activies ===

* [[SDIWG:NCBC_Software_Classification|NCBC DRAFT Software Classification and Ontologies Page]]
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_071806_RequiredFields Required/Minimal] & [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_071806_ToolSpecificFields Optional and Resource-specific] Resource Description Fields
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_2006_OtherArchives Other Efforts to develop archives of resources]

=== Update on Biomedical Resource Ontology (BRO) ===
The ontology of software tools and resources ("Biomedical Resource Ontology (BRO)") has been attracting interest not only amongst NCBCs, but from other NIH programs and related external projects (such as BIRN, ICBP, and IATR). The current ontology is available in read-only format (http://bioontology.org/projects/ontologies/SoftwareOntology/).
A core group of individuals interested in developing the ontology into a more robust resource recently came together to begin developing the Software Ontology collaboratively: Daniel Rubin, Ivo Dinov, William Bug, Mayrann Martone, and David Kennedy. They are editing the ontology using Protege in collaborative mode, enabling multiple people to edit the ontology.
If other people in the community are interested in participating in developing the Software Ontology and gaining edit access, please contact Daniel Rubin. The meeting minutes (below) has the latest news on this thread...

=== Biositemaps Archive Meeting Minutes ===
Top level sites

[[SDIWG:Software_and_Data_Integration_Working_Group|Top page of SDIWG web site]]

[http://www.na-mic.org/Wiki/index.php/SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers NCBC Working Group Discussion threads, tcons, Breeze/Access minutes]

Specific Minutes relating to Biositemaps Development

* [[SDIWG:Action_Items_20090116 | Status and Action Items (01-16-2009)]]
* [[SDIWG:Action_Items_20081219 | Status and Action Items (12-19-2008)]]
* [[SDIWG:Action_Items_20081203 | Status and Action Items (12-3-2008)]]
* [[SDIWG:Action_Items_20081121 | Status and Action Items (11-21-2008)]]
* [[SDIWG:Meeting_Minutes_20081001|Biomedical Resource Ontology and Biositemaps: Tiger Team Subprojects and Biositemaps Shakeout (10/1/08)]]
* [[SDIWG:Meeting_Minutes_20080919|Biomedical Resource Ontology and Biositemaps: NCBC working group minutes (9/19/08)]]
* [[SDIWG:Meeting_Minutes_20080716|Biomedical Resource Ontology and Biositemaps: Four Activities Description (7/16/08)]]
* [[SDIWG:Meeting_Minutes_20080530|Biomedical Resource Ontology and Biositemaps Development Path Tcon (5/30/08)]]
* [[SDIWG:Meeting_Minutes_20080416|Biomedical Resource Ontology (BRO) Tcon (4/16/08)]]
* [[SDIWG:Meeting_Minutes_20061117|Joint NCBC Working Group TCon (11/17/06)]]
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_103106 TCon 10/31/06]
* [[SDIWG:Meeting_Minutes_20060818|NCBC SDIWG/Working-Group TCon (Fri., 08/18/06)]]
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_071806PM Tue 07/18/06, PM] - [http://www.bisti.nih.gov/ahm2006/agenda.htm NCBC Workgroup Reports (20 minutes per group), 1-2 PM]
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_071806AM Tue 07/18/06, AM] - [http://www.bisti.nih.gov/ahm2006/agenda.htm Concurrent NCBC Workgroup Meetings, 10AM - 12PM]
* [[SDIWG:Meeting_Minutes_20060616|Fri 06/16/06]] -- Includes examples of Meta-data and XMLTology descriptions of 1-5 SW Tools from all 7 NCBCs
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_061506 Fri 06/15/06]
* [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_042806 Fri 04/28/06]

SDIWG:Action Items 20081219

2009-01-16T19:29:51Z

Bkirschn:

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

Who: Natasha, Csongor, Ivo, Beth, Peter

== Discussion and Action Items (2008-12-19): ==

* What is minimum that is absolutely necessary? mechanism to publish: create form (auto-add to registry & email & widget for human-authentication)
** Action: Natasha - weekly update of bioportal with latest biositemaps
** Action: Ivo - weekly update of iTools already done
** Action: Beth - <strike>document the fact that HTTP will inform last date/time of biositemaps file update</strike> (done)
** Action: Beth - <strike>registration form for adding biositemaps to registry</strike> (done)
** Action: Beth - Grep-like application against all biositemaps (Use Csongor's editor in browse only for presentation)
** Action: Csongor - browseable mode for biositemaps editor

* Do we have a good information model? Do we have good documentation?
** Action: Someone (Natasha?) to 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.)

* Note: Csongor back on January 8th

* Note: Next meeting on 1-16-2008 (Beth to email reminder in January)

== Outstanding action items: ==

* Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)
** Csongor & I need to talk about this, but given all the editor work that is on Csongor's plate, I believe Michigan should be able to do this work

* Csongor: Update Biositemaps Editor to allow invalid classes
** Csongor, can this be done by end of January?

* Beth & Peter: follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)
** wait on this until other outstanding issues are completed
** <strike>comment out deprecated classes for now</strike> (done)

* Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service
** Ivo/Natasha: Outstanding issues listed in followup email

* There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal
** Natasha: early January release should fix this

* Beth: will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing
** While we didn't get a chance to discuss this on the CTSA call, Michigan is willing to work on this with a target date early in 2009 (an exact date wouldn't be available until we can get our team to meet after the holidays).

* Modify Biositemaps Editor to support multiple resource types
** Csongor: to be done early next year (January 2009)

* Modify Biositemaps Editor to support harmonized CTSA biositemaps information model:
** Csongor: update editor
** Question: Can Harpreet to write converter?

* The expanded/harmonized biositemap has 25 possible properties which should be reviewed/trimmed down if possible
** Byline will be dropped
** Language and platform kept as optional
** biositemap_author kept as optional (note that CTSA wants this not displayed in the editor -- they see it as a disincentive)

* A significant outcome of the harmonizing call was the much broader definition of what is a Biomedical Resource that CTSA uses. Nancy and Harpreet were planning on following up with their proposed additions to the BRO first week of January

==Biositemaps Web-Services Specifications==
===I. Biomedical Resource Ontology (BRO) ontology===
* (http://bioportal.bioontology.org/virtual/1104). The following methods/functions will be valuable:
** getBRO(): returns an XML with the complete current BRO hierarchy (starts with BRO root node)
** getParents(BRONode): returns an XML with the meta-data of all the parents (in the BRO hierarchy), given BRONode. Most of the time there will be 1 parent, but there may be many
** getChildren(BRONode): returns an XML with the meta-data of all the children (in the BRO hierarchy), given BRONode
** getPartialBRO(BRONode): returns an XML with the meta-data of the BRO sub-hierarchy starting with BRONode
** getSiblings(BRONode): returns an XML with the meta-data of all the siblings (in the BRO hierarchy) of the given BRONode (same hierarchy level)

===II. Information Model (IM)===
* http://www.ncbcs.org/biositemaps/formatDescription.html. The following methods/functions will be valuable:
** getBiositemapsIM(): returns an XML with the meta-data of all the required/formal IM fields, their properties and descriptions. Like in: http://www.ncbcs.org/biositemaps/formatDescription.html
** getBiositemapsIM_Property(int): returns an XML with the property-name of the IM field index by "int".
** getBiositemapsIM_Description(int): returns an XML with the description of the provided IM field index by "int"
** getBiositemapsIM_Description(property): returns an XML with the description of the provided IM property-name
** getBiositemapsIM_Optional(property): returns an XML with the triples (name, property, value) of all non-standard, optional and non-core IM fields.

===III. General Biositemaps.RDF web-service that provide not only the standard/required/IM meta-data, but any project/center/field- specific meta-data provided by the Biositemap creator/curator===
: That is, we can have a center that has created a new Biositemap.RDF object, which contains the triple (name=NewField; property=NewProperty; value=NewValue). Suppose, "NewField" is *not* in the Biositemaps IM. We still need to provide services for people/ tools to retrieve this triple in XML, just like we allow retrieval of IM fields. This may be relatively easy, once we have the first two extensions (I. and II.).

==[http://itools.ccb.ucla.edu/ iTools] processing (consumption/production) of Biositemaps.RDF==
* Date: 01/14/09
* Status of the current implementation of [http://itools.ccb.ucla.edu/ iTools] Yahoo-WebSearch of Biositemaps.RDF
** [http://itools.ccb.ucla.edu/ iTools] WebSearch starts automatically every Friday morning. It may also be manually started by admins.
** After the completion of the auto WebSearch, [http://itools.ccb.ucla.edu/ iTools] starts is own custom designed Web-Crawler, which traverses the entire http://www.biositemap.org/ domain and extracts all Biositemap.RDF objects there.
** Finally [http://itools.ccb.ucla.edu/ iTools] combines both the Web-Search and the Web-Crawler results in the iTools SandBox. There are no identifiers indicating how was a Biositemaps.RDF object obtained (via web-search or web-crawling).
* [http://itools.ccb.ucla.edu/ iTools] uses its own parser to parse Biositemap.RDF documents. There are 2 reasons for not using the [http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf NCBO provided Biositemap.RDF web-service]:
** The Biositemaps.XML genereated by this service does not provide a valid Biositemap.XML result (it's incompatible with the (legacy) Biositemaps.xml schema/format).
** The RDF --> XML web-service converter only rewrites the RDF tags, so one needs yet another follow-up parser applied to the resulting XML object. Thus, the iTools client uses its own parser to minimize the overhead.
* All Biositemaps.RDF clients (machines or humans), including [http://itools.ccb.ucla.edu/ iTools], will need an [http://www.ncbcs.org/biositemaps/formatDescription.html IM] parser web-service, as [[SDIWG:Action_Items_20081219#II._Information_Model_.28IM.29 | described above]].

===Important Note===
Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.

: ''BK: actually there is a center-name -- unfortunately the above IM is not alphabetically sorted, but the center property does exist along with organization.''

: ''ID: Yes, 'center' it is defined by IM, but if you see this example http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf, not all the resources have this field. If all resources are not guaranteed to have a clearly delineated center information, iTools will not be able to properly place these in the tabular/hyperbolic views.''

SDIWG:Action Items 20081219

2009-01-16T15:41:18Z

Bkirschn:

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

Who: Natasha, Csongor, Ivo, Beth, Peter

== Discussion and Action Items (2008-12-19): ==

* What is minimum that is absolutely necessary? mechanism to publish: create form (auto-add to registry & email & widget for human-authentication)
** Action: Natasha - weekly update of bioportal with latest biositemaps
** Action: Ivo - weekly update of iTools already done
** Action: Beth - <strike>document the fact that HTTP will inform last date/time of biositemaps file update</strike> (done)
** Action: Beth - registration form for adding biositemaps to registry
** Action: Beth - Grep-like application against all biositemaps (Use Csongor's editor in browse only for presentation)
** Action: Csongor - browseable mode for biositemaps editor

* Do we have a good information model? Do we have good documentation?
** Action: Someone (Natasha?) to 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.)

* Note: Csongor back on January 8th

* Note: Next meeting on 1-16-2008 (Beth to email reminder in January)

== Outstanding action items: ==

* Beth & Csongor: work on merging apis (complimentary functionality) upon his return from Australia (week of Dec. 15)
** Csongor & I need to talk about this, but given all the editor work that is on Csongor's plate, I believe Michigan should be able to do this work

* Csongor: Update Biositemaps Editor to allow invalid classes
** Csongor, can this be done by end of January?

* Beth & Peter: follow up with NCBC centers to publish & update biositemaps (note I2B2 & CCB use deprecated classes that need to be updated)
** wait on this until other outstanding issues are completed
** <strike>comment out deprecated classes for now</strike> (done)

* Ivo: Update iTools application to consume new biositemaps RDF files via RDF-to-XML web service
** Ivo/Natasha: Outstanding issues listed in followup email

* There are problems with the database or bioportal that need to be resolved in order to expose NCBC resources on bioportal
** Natasha: early January release should fix this

* Beth: will clarify who will develop biositemaps search application following CTSA call regarding BRO/IM harmonizing
** While we didn't get a chance to discuss this on the CTSA call, Michigan is willing to work on this with a target date early in 2009 (an exact date wouldn't be available until we can get our team to meet after the holidays).

* Modify Biositemaps Editor to support multiple resource types
** Csongor: to be done early next year (January 2009)

* Modify Biositemaps Editor to support harmonized CTSA biositemaps information model:
** Csongor: update editor
** Question: Can Harpreet to write converter?

* The expanded/harmonized biositemap has 25 possible properties which should be reviewed/trimmed down if possible
** Byline will be dropped
** Language and platform kept as optional
** biositemap_author kept as optional (note that CTSA wants this not displayed in the editor -- they see it as a disincentive)

* A significant outcome of the harmonizing call was the much broader definition of what is a Biomedical Resource that CTSA uses. Nancy and Harpreet were planning on following up with their proposed additions to the BRO first week of January

==Biositemaps Web-Services Specifications==
===I. Biomedical Resource Ontology (BRO) ontology===
* (http://bioportal.bioontology.org/virtual/1104). The following methods/functions will be valuable:
** getBRO(): returns an XML with the complete current BRO hierarchy (starts with BRO root node)
** getParents(BRONode): returns an XML with the meta-data of all the parents (in the BRO hierarchy), given BRONode. Most of the time there will be 1 parent, but there may be many
** getChildren(BRONode): returns an XML with the meta-data of all the children (in the BRO hierarchy), given BRONode
** getPartialBRO(BRONode): returns an XML with the meta-data of the BRO sub-hierarchy starting with BRONode
** getSiblings(BRONode): returns an XML with the meta-data of all the siblings (in the BRO hierarchy) of the given BRONode (same hierarchy level)

===II. Information Model (IM)===
* http://www.ncbcs.org/biositemaps/formatDescription.html. The following methods/functions will be valuable:
** getBiositemapsIM(): returns an XML with the meta-data of all the required/formal IM fields, their properties and descriptions. Like in: http://www.ncbcs.org/biositemaps/formatDescription.html
** getBiositemapsIM_Property(int): returns an XML with the property-name of the IM field index by "int".
** getBiositemapsIM_Description(int): returns an XML with the description of the provided IM field index by "int"
** getBiositemapsIM_Description(property): returns an XML with the description of the provided IM property-name
** getBiositemapsIM_Optional(property): returns an XML with the triples (name, property, value) of all non-standard, optional and non-core IM fields.

===III. General Biositemaps.RDF web-service that provide not only the standard/required/IM meta-data, but any project/center/field- specific meta-data provided by the Biositemap creator/curator===
: That is, we can have a center that has created a new Biositemap.RDF object, which contains the triple (name=NewField; property=NewProperty; value=NewValue). Suppose, "NewField" is *not* in the Biositemaps IM. We still need to provide services for people/ tools to retrieve this triple in XML, just like we allow retrieval of IM fields. This may be relatively easy, once we have the first two extensions (I. and II.).

==[http://itools.ccb.ucla.edu/ iTools] processing (consumption/production) of Biositemaps.RDF==
* Date: 01/14/09
* Status of the current implementation of [http://itools.ccb.ucla.edu/ iTools] Yahoo-WebSearch of Biositemaps.RDF
** [http://itools.ccb.ucla.edu/ iTools] WebSearch starts automatically every Friday morning. It may also be manually started by admins.
** After the completion of the auto WebSearch, [http://itools.ccb.ucla.edu/ iTools] starts is own custom designed Web-Crawler, which traverses the entire http://www.biositemap.org/ domain and extracts all Biositemap.RDF objects there.
** Finally [http://itools.ccb.ucla.edu/ iTools] combines both the Web-Search and the Web-Crawler results in the iTools SandBox. There are no identifiers indicating how was a Biositemaps.RDF object obtained (via web-search or web-crawling).
* [http://itools.ccb.ucla.edu/ iTools] uses its own parser to parse Biositemap.RDF documents. There are 2 reasons for not using the [http://rest.bioontology.org/biositemap-server/parse?url=http://portal.ncibi.org/biositemap.rdf NCBO provided Biositemap.RDF web-service]:
** The Biositemaps.XML genereated by this service does not provide a valid Biositemap.XML result (it's incompatible with the (legacy) Biositemaps.xml schema/format).
** The RDF --> XML web-service converter only rewrites the RDF tags, so one needs yet another follow-up parser applied to the resulting XML object. Thus, the iTools client uses its own parser to minimize the overhead.
* All Biositemaps.RDF clients (machines or humans), including [http://itools.ccb.ucla.edu/ iTools], will need an [http://www.ncbcs.org/biositemaps/formatDescription.html IM] parser web-service, as [[SDIWG:Action_Items_20081219#II._Information_Model_.28IM.29 | described above]].

===Important Note===
Note that in the new [http://www.ncbcs.org/biositemaps/formatDescription.html Biositemaps.RDF IM] there is no NCBC Center-name, which used to be a key tag in the old Biositemap.xml schema. This is now replaced by an [http://www.ncbcs.org/biositemaps/formatDescription.html Organization] tag. As a result of that, [http://itools.ccb.ucla.edu/ iTools] will not display NCBC-center-specific view in its tabular of graphical navigation panels.

''BK: actually there is a center-name -- unfortunately the above IM is not alphabetically sorted, but the center property does exist along with organization.''

SDIWG:Action Items 20081219

2009-01-13T14:54:11Z

Bkirschn:

SDIWG:Action Items 20081219

2009-01-12T15:18:11Z

Bkirschn:

SDIWG:Action Items 20081219

2009-01-08T21:09:51Z

2008-12-04T14:40:51Z

Bkirschn:

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): ==

''(tbd)''

== 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)
*** 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 the BioPortal to index biositemaps corpus over more than BRO--see Beth's API (Csongor-Beth)
** Modify Biositemaps Editor to support multiple resource types (Csongor)

* 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,...)