Difference between revisions of "SDIWG:Meeting Minutes 20080222"

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*Roll Call/Note-taker (Henry Chueh) (5 min)
 
*Roll Call/Note-taker (Henry Chueh) (5 min)
 
*Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20071116|Nov 16, 2007]] (5 min)
 
*Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20071116|Nov 16, 2007]] (5 min)
−
*NCBC All Hand Meeting, 2008. Planning & Brainstorm discussion (Peter, Karin, All)
+
*NCBC All Hands Meeting, August 13-15, 2008. Planning & Brainstorm discussion (Peter, Karin, All)
 
*Status check on three working groups: [[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Biositemaps Resourceome]], [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]], [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]
 
*Status check on three working groups: [[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Biositemaps Resourceome]], [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]], [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]
−
*Demo on Biomedical Resource Ontology (NCBO staff) which is stable development environment for the BRO and repository in BioPortal.  This is a key component of the Biositemaps effort.
+
*Demo on Biomedical Resource Ontology (see [[Media:BRO_Requirements.doc | BRO Requirements document]]) (Daniel Rubin).  The demo will describe a stable development environment for the BRO and repository in BioPortal.  This is a key component of the Biositemaps effort.
−
**Overview of white paper (‘the biositemaps concept’) (Daniel, Ivo, Peter)  
+
**Overview of [[Media:Biositemaps-white-paper-v2.2.doc | white paper]] (‘the biositemaps concept’) (Daniel, Ivo, Peter)  
 
**Overview of (i) collaborative development environment for BRO and (ii) BioPortal repository of BRO (how is BRO accessed through API?) (Daniel)  
 
**Overview of (i) collaborative development environment for BRO and (ii) BioPortal repository of BRO (how is BRO accessed through API?) (Daniel)  
 
**Overview of how iTools accesses the current corpus of three proto-biositemaps (google”filtetype:xml biositemap”). (Ivo)  
 
**Overview of how iTools accesses the current corpus of three proto-biositemaps (google”filtetype:xml biositemap”). (Ivo)  
 
**Overview of plan for next 2 to 4 months (Peter)  
 
**Overview of plan for next 2 to 4 months (Peter)  
−
***(1) In the next two months NCBO develops a stable platform for content development and content repository in bioportal relating to the resource ontology, culminating in ½ to 1 day tcon with authorized seven Center reps to finalize v1.0 resource ontology (I may add rep from NITRC and NIF, Bill Bug).  NCBO is generating and executing the plan for the ‘stable platform’
+
***(1) In the next two months NCBO develops a stable platform for content development and content repository in bioportal relating to the Biomedical Resource Ontology (BRO), culminating in ½ to 1 day tcon with authorized seven Center reps to finalize v1.0 resource ontology (I may add rep from NITRC and NIF, Bill Bug).  NCBO is generating and executing the plan for the ‘stable platform’.  It is likely that this will involve some merging of the development process with NIF and NITRC, but that is yet to be resolved.
−
***(2) After that I call each PI and get personal commitment to create biositemaps.xml content on their web sites.
+
***(2) After that Lyster contacts each PI and get personal commitment to create biositemaps.xml content on their web sites.
 
*
 
*
 
*
 
*
 
*Upcoming meetings: AMIA translational, Zac, ...
 
*Upcoming meetings: AMIA translational, Zac, ...
−
*NCBC Consortium authorship policies (Peter; Open Discussion with output a list of bullet ideas)
+
*Next 2 meeting date (Friday May 16 2:30 PM ET and three months after that)
−
*Discussion of [[Media:Biositemaps-white-paper-v2.2.doc | Biositemaps white paper]] and of authorship (see more details in 'Appendix' below).
 
−
*Next 2 meeting dates set
 
 
*Questions/Information Sharing
 
*Questions/Information Sharing
  
 
<br>
 
<br>
 +
==Minutes==
  
−
==Appendix: Biositemaps white paper==
+
Note taker: (Peter Lyster) [Suggested order of note takers for future meetings: Chueh (this one); Sherman; Schroeder; Floratos; Rubin; Jags, Dinov]
−
*'''[[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Biositemaps Resourceome]]''' (Ivo Dinov, Daniel Rubin, Will Schroeder, Beth Kirschner, Karen Skinner, Zohara Cohen, Bill Bug, Peter Lyster)
+
*Review of [[SDIWG:Meeting_Minutes_20071116|November 16, 2007 Minutes]]
−
**The biositemaps [[Media:Biositemaps-white-paper-v2.2.doc | white paper]] presents description of prototype for distributed architecture to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining software tools and information resources on the Internet.  Each site which intends to contribute to the inventory instantiates a file on its Internet site ‘biositemap.xml’ which conforms to a defined schema and is tagged by a resource ontology. The prototype schema may be found at http://www.ncbcs.org/biositemaps/biositemaps-v04.xsd A good reference for XML editors is at http://en.wikipedia.org/wiki/Xml_editor e.g., we are using XMLmind. The prototype resource ontology may be found at http://bioontology.org/projects/ontologies/SoftwareOntology/
+
*Attendees:  Daniel Rubin, Ivo Dinov, Karen Skinner, Karin Remington, David Kennedy, Olivier Bodenreider
−
**Further postings will be made at the NCBC portal at http://www.ncbcs.org/biositemaps/
+
**Daniel showed Biomedical Resource Ontology (BRO) and other ontologies/terminologes (e.g., NCI Thesaurus) in Bioportal
−
**TBD: Long-term plan for maintenance of schema and resource ontology (hosting, versioning, ownership,...).  Converge on contents of schema and resource ontology with appropriate parties.  This will amount to a v1.0 release (i.e., figure out where to stop now and leave extensions to a later date). Resolve issues of locating the biositemaps content (hard-wired, crawl,...)
+
**Daniel described the link between the BRO and Ontrez which is the NCBO tool for curated indexing of resources (this uses the terminologies, including BRO that are in Bioportal); Daniel shows the Mapping capability
−
**Status of the NCBC iTools, which is uses the biositemaps. (production) http://www.loni.ucla.edu/iToolssvc/ncbc_iTools.html/http://iTools.loni.ucla.edu and (dev) http://netulla.loni.ucla.edu:8080/iToolssvc/ncbc_iTools.html/http://www.loni.ucla.edu/twiki/bin/view/CCB/iTools.
+
**There was a general discussion of the development environment for the BRO—currently it exits as (i) the primary content is in Daniel’s private repository (CVS) (thus the full complement of old versions are not propagated into BioPortal, although BioPortal does show the difference between the current and immediately previous version); (ii) annotations that can be entered directly into Bioportal. 
 +
**Daniel will put the current BRO on a Stanford gforge where it can be used by the NCBC SDIWG contacts to agree on a common BRO.   
 +
**Daniel has written, after the tcon, a brief description for immediate conversion from biositemaps based on xml to biositemaps: First, we will translated BRO to OWL (BRO.owl) and create a new class in the BRO ontology called "ResourceDescription" which represents the collection of all descriptions of resources (each instance of this class will be equivalent to a single resource description in a biositemaps.xml file). Then BRO.owl would be published to the Web so the world can reference this class and create instances of it; the preferred tool for doing that will be Protege. So each NCBC would launch protege, then open the URL to the BRO.owl file, and create instances of the ResourceDescription class for each tool they wish to describe (what they are doing is creating a new OWL file which stores only instances of the ResourceDescription class). Then they save their OWL file and publish it on the Web on their own server (we'll call that file a ResourceDescription.owl file; Peter would prefer if it were named the biositemaps.owl for the sake of continuity). Then Ontrez (this has been since renamed the Resources Tab) would consume the ResourceDescription.owl files from all NCBCs that are published to the Web and index them using BRO, resulting in a demo similar to that I showed today. But now we're totally operating within Semantic Web technologies--others on the Semantic Web could also consume the ResourceDescription.owl files for their own purposes independent of Ontrez.  This change would require Ivo to do some re-coding so that iTools consumes (parses) the ResourceDescription.owl files instead of parsing the biositemaps.xml files. This should not be a very tedious operation, and only need be done once.
 +
**Overview of plan for next 2 to 4 months (Peter)  
 +
***(1) In the next two months NCBO develops a stable platform for content development and content repository in bioportal relating to the Biomedical Resource Ontology (BRO), culminating in ½ to 1 day tcon with authorized seven Center reps to finalize v1.0 resource ontology (I may add rep from NITRC and NIF, Bill Bug).   NCBO is generating and executing the plan for the ‘stable platform’. It is likely that this will involve some merging of the development process with NIF and NITRC, but that is yet to be resolved.
 +
***(2) After that Lyster contacts each PI and get personal commitment to create biositemaps.xml content on their web sites.
  
−
==Minutes==
 
−
 
−
Note taker: (Henry Chueh) [Suggested order of note takers for future meetings: Chueh (this one); Sherman; Schroeder; Floratos; Rubin; Jags, Dinov]
 
−
*Review of [[SDIWG:Meeting_Minutes_20070921|Sept 21, 2007 Minutes]]
 
−
*Attendees: 
 
 
*Go over dates for next year's meetings:
 
*Go over dates for next year's meetings:
 
** AMIA Summit on Translational Bioinformatics, San Francisco, http://www.amia.org/inside/releases/2007/translationalbioinformaticssummit_pr2007.pdf, March 10-12 2008  
 
** AMIA Summit on Translational Bioinformatics, San Francisco, http://www.amia.org/inside/releases/2007/translationalbioinformaticssummit_pr2007.pdf, March 10-12 2008  
 
** Health Informatics April 11, 2008, Boston, MA - Health Informatics (Zak?) Need a link.
 
** Health Informatics April 11, 2008, Boston, MA - Health Informatics (Zak?) Need a link.
 
** NCBC All Hands Meeting, date August 13-15, Bethesda
 
** NCBC All Hands Meeting, date August 13-15, Bethesda
 +
** SDWGI meets once every 3 months 11:30 AM (Pacific), third Fri of the month.
 
*
 
*
−
*
+
 
−
*
 
−
* SDWGI meets once every 3 months 11:30 AM (Pacific), third Fri of the month.
 
−
*
 
 
==Action Items==
 
==Action Items==
−
*  
+
* Convert Biositemaps method to owl
−
*
+
* Convene SDIWG tcon (probably lasting 1/2 day to agree on a common BRO)
 +
**Overview of plan for next 2 to 4 months (Peter)
 +
***(1) In the next two months NCBO develops a stable platform for content development and content repository in bioportal relating to the Biomedical Resource Ontology (BRO), culminating in ½ to 1 day tcon with authorized seven Center reps to finalize v1.0 resource ontology (I may add rep from NITRC and NIF, Bill Bug).  NCBO is generating and executing the plan for the ‘stable platform’.  It is likely that this will involve some merging of the development process with NIF and NITRC, but that is yet to be resolved.
 +
***(2) After that Lyster contacts each PI and get personal commitment to create biositemaps.xml content on their web sites.
 +
 
 +
 
 +
==Appendix: Biositemaps white paper==
 +
*'''[[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Biositemaps Resourceome]]''' (Ivo Dinov, Daniel Rubin, Will Schroeder, Beth Kirschner, Karen Skinner, Zohara Cohen, Bill Bug, Peter Lyster)
 +
**The biositemaps [[Media:Biositemaps-white-paper-v2.2.doc | white paper]] presents description of prototype for distributed architecture to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining software tools and information resources on the Internet.  Each site which intends to contribute to the inventory instantiates a file on its Internet site ‘biositemap.xml’ which conforms to a defined schema and is tagged by a resource ontology. The prototype schema may be found at http://www.ncbcs.org/biositemaps/biositemaps-v04.xsd A good reference for XML editors is at http://en.wikipedia.org/wiki/Xml_editor e.g., we are using XMLmind.  The prototype resource ontology may be found at http://bioontology.org/projects/ontologies/SoftwareOntology/
 +
**The Biomedical Resource Ontology (BRO) (see [[Media:BRO_Requirements.doc | BRO Requirements document]]) is an extensible terminology for online electronic resources, intended to be an enabling technology for tools which improve query and access to online resources.
 +
**Further postings will be made at the NCBC portal at http://www.ncbcs.org/biositemaps/
 +
**Status of the NCBC iTools, which is uses the biositemaps. http://iTools.loni.ucla.edu

Latest revision as of 17:53, 7 March 2008

Home < SDIWG:Meeting Minutes 20080222

Agenda: NCBC Joint Working Group Meeting

Top page of SDIWG web site

Notes

Friday February 22, 2008: 2:30 -- 3:30 PM EST
Please contact Peter Lyster for information Peter Lyster
SDIWG Meetings Page
Save the date for the next SDWIG tcon/Connect, three months from now: Friday May 16, 2008

Tcon DRAFT Agenda

  • Roll Call/Note-taker (Henry Chueh) (5 min)
  • Minutes from most recent SDIWG tcon Nov 16, 2007 (5 min)
  • NCBC All Hands Meeting, August 13-15, 2008. Planning & Brainstorm discussion (Peter, Karin, All)
  • Status check on three working groups: Biositemaps Resourceome, Scientific Ontologies, NCBC Driving Biological Projects Interactions and Impact
  • Demo on Biomedical Resource Ontology (see BRO Requirements document) (Daniel Rubin). The demo will describe a stable development environment for the BRO and repository in BioPortal. This is a key component of the Biositemaps effort.
    • Overview of white paper (‘the biositemaps concept’) (Daniel, Ivo, Peter)
    • Overview of (i) collaborative development environment for BRO and (ii) BioPortal repository of BRO (how is BRO accessed through API?) (Daniel)
    • Overview of how iTools accesses the current corpus of three proto-biositemaps (google”filtetype:xml biositemap”). (Ivo)
    • Overview of plan for next 2 to 4 months (Peter)
      • (1) In the next two months NCBO develops a stable platform for content development and content repository in bioportal relating to the Biomedical Resource Ontology (BRO), culminating in ½ to 1 day tcon with authorized seven Center reps to finalize v1.0 resource ontology (I may add rep from NITRC and NIF, Bill Bug). NCBO is generating and executing the plan for the ‘stable platform’. It is likely that this will involve some merging of the development process with NIF and NITRC, but that is yet to be resolved.
      • (2) After that Lyster contacts each PI and get personal commitment to create biositemaps.xml content on their web sites.
  • Upcoming meetings: AMIA translational, Zac, ...
  • Next 2 meeting date (Friday May 16 2:30 PM ET and three months after that)
  • Questions/Information Sharing


Minutes

Note taker: (Peter Lyster) [Suggested order of note takers for future meetings: Chueh (this one); Sherman; Schroeder; Floratos; Rubin; Jags, Dinov]

  • Review of November 16, 2007 Minutes
  • Attendees: Daniel Rubin, Ivo Dinov, Karen Skinner, Karin Remington, David Kennedy, Olivier Bodenreider
    • Daniel showed Biomedical Resource Ontology (BRO) and other ontologies/terminologes (e.g., NCI Thesaurus) in Bioportal
    • Daniel described the link between the BRO and Ontrez which is the NCBO tool for curated indexing of resources (this uses the terminologies, including BRO that are in Bioportal); Daniel shows the Mapping capability
    • There was a general discussion of the development environment for the BRO—currently it exits as (i) the primary content is in Daniel’s private repository (CVS) (thus the full complement of old versions are not propagated into BioPortal, although BioPortal does show the difference between the current and immediately previous version); (ii) annotations that can be entered directly into Bioportal.
    • Daniel will put the current BRO on a Stanford gforge where it can be used by the NCBC SDIWG contacts to agree on a common BRO.
    • Daniel has written, after the tcon, a brief description for immediate conversion from biositemaps based on xml to biositemaps: First, we will translated BRO to OWL (BRO.owl) and create a new class in the BRO ontology called "ResourceDescription" which represents the collection of all descriptions of resources (each instance of this class will be equivalent to a single resource description in a biositemaps.xml file). Then BRO.owl would be published to the Web so the world can reference this class and create instances of it; the preferred tool for doing that will be Protege. So each NCBC would launch protege, then open the URL to the BRO.owl file, and create instances of the ResourceDescription class for each tool they wish to describe (what they are doing is creating a new OWL file which stores only instances of the ResourceDescription class). Then they save their OWL file and publish it on the Web on their own server (we'll call that file a ResourceDescription.owl file; Peter would prefer if it were named the biositemaps.owl for the sake of continuity). Then Ontrez (this has been since renamed the Resources Tab) would consume the ResourceDescription.owl files from all NCBCs that are published to the Web and index them using BRO, resulting in a demo similar to that I showed today. But now we're totally operating within Semantic Web technologies--others on the Semantic Web could also consume the ResourceDescription.owl files for their own purposes independent of Ontrez. This change would require Ivo to do some re-coding so that iTools consumes (parses) the ResourceDescription.owl files instead of parsing the biositemaps.xml files. This should not be a very tedious operation, and only need be done once.
    • Overview of plan for next 2 to 4 months (Peter)
      • (1) In the next two months NCBO develops a stable platform for content development and content repository in bioportal relating to the Biomedical Resource Ontology (BRO), culminating in ½ to 1 day tcon with authorized seven Center reps to finalize v1.0 resource ontology (I may add rep from NITRC and NIF, Bill Bug). NCBO is generating and executing the plan for the ‘stable platform’. It is likely that this will involve some merging of the development process with NIF and NITRC, but that is yet to be resolved.
      • (2) After that Lyster contacts each PI and get personal commitment to create biositemaps.xml content on their web sites.

Action Items

  • Convert Biositemaps method to owl
  • Convene SDIWG tcon (probably lasting 1/2 day to agree on a common BRO)
    • Overview of plan for next 2 to 4 months (Peter)
      • (1) In the next two months NCBO develops a stable platform for content development and content repository in bioportal relating to the Biomedical Resource Ontology (BRO), culminating in ½ to 1 day tcon with authorized seven Center reps to finalize v1.0 resource ontology (I may add rep from NITRC and NIF, Bill Bug). NCBO is generating and executing the plan for the ‘stable platform’. It is likely that this will involve some merging of the development process with NIF and NITRC, but that is yet to be resolved.
      • (2) After that Lyster contacts each PI and get personal commitment to create biositemaps.xml content on their web sites.


Appendix: Biositemaps white paper

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