Difference between revisions of "SDIWG:Meeting Minutes 20070518"

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* Roll Call/Note-taker (Rubin) (5 min)
 
* Roll Call/Note-taker (Rubin) (5 min)
  
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* Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20070216|February 16, 2006]] (5 min)
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* Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20070216|February 16, 2007]] (5 min)
  
 
* Progress in three working groups
 
* Progress in three working groups
 
** '''[[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]''' (Zak Kohane, Mark Musen, and Suzi Lewis, 15 min)
 
** '''[[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]''' (Zak Kohane, Mark Musen, and Suzi Lewis, 15 min)
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*** TBD
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*** enter draft agenda items here
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** '''[[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Yellow Pages and Resourceome]]''' (Ivo Dinov, Daniel Rubin, Bill Lorensen, Jonathan Dugan, 15 min)
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** '''[[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Yellow Pages and Resourceome]]''' (Ivo Dinov, Daniel Rubin, Will Schroeder, Jonathan Dugan, 15 min)
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*** Past Progress
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*** Status of [http://www.loni.ucla.edu/twiki/bin/view/CCB/iTools iTools]
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**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_2006_OtherArchives Other Attempts to provide archives of SW and tool resources]
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*** [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_iTools_Usage iTools Usage]
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**** Proposed set of '''[http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_071806_RequiredFields Required/Minimal]''' Resource Description Fields
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*** [http://netulla.loni.ucla.edu:8080/itools/ncbc_iTools.html Use iTools Now]
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**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_071806_ToolSpecificFields '''Optional''' and '''Resource-specific''' description fields]
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** '''[[SDIWG:_NCBC_DBP_Interactions_and_Impact|NCBC Driving Biological Projects Interactions and Impact]]''' (Aris Floratos, Brian Athey, Russ Altman, 15 min)
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**** [http://bioontology.org/projects/ontologies/SoftwareOntology/ Current Ontological Description of the NCBC Tool Yellow-Pages]
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*** enter draft agenda items here
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**** [http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_103106_ResourceDef Types of CompBio Resources]?
 
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**** [[SDIWG:NCBC_Software_Classification | Center described 3-5 resources]]?
 
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*** Status of NCBC '''''[http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_iTools iTools]'''''
 
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**** V1 (v 0.1, 10/12/06)
 
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**** V4 (v 0.4, 02/13/07)
 
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*** Sugested Action Items for the YPR WG:
 
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**** Each Center should ensure that they have [[SDIWG:NCBC_Software_Classification|6-12 SW Resources described according to these templates]]
 
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**** Test, comment and revise iTools. How does it compare with other similar efforts?
 
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** '''[[SDIWG:_NCBC_Systems_Biology|Applications of Systems Biology, Modeling, and Analysis]]''' (Aris Floratos, Brian Athey, Russ Altman, 15 min)
 
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*** TBD
 
  
 
=== Minutes ===
 
=== Minutes ===
  
−
Note taker: (Aris Floratos)
+
Note taker: (Daniel Rubin)
  
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* Review of 11/17/06 minutes
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* Review of [[SDIWG:Meeting_Minutes_20070216|February 16, 2007 Minutes]]
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** '''[[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Yellow Pages and Resourceome]]'''
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*
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** '''[[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]'''
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#Attending: Peter Lyster, Ivo Dinov, Aris Floratos, Arthus Castle, Zohara Cohen, Daniel Rubin, David States, Jeanette Schmidt, Karen Skinner, Mark Musen, Michael Montegut, Shawn Murphy, Terry Weymouth, Brian Athey, Will Schroeder, David Kennedy, Zak Kohane
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** '''[[SDIWG:_NCBC_Systems_Biology|Applications of Systems Biology, Modeling, and Analysis]]'''
+
#iTools and Ontology of Software Tools (Ivo Dinov)
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#*We have populated iTools with the metadata for each of the NCBC tools. Right now, this presents a center-specific view of tools. This will be changed to display according to the software tools ontology.
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Zak Kohane outlined the process via which the Scientific Ontologies SIG reviewed a select set of ontologies and vocabularies. A summary list along with the a broad assessment of overall "quality" has been compiled by Suzie Lewis and is available at www.berkeleybop.org/sowg/table.cgi. In addition to being an inventory for the vocabularies and ontologies that tbe NCBCs use intenally, the SIG hopes that this list will be a useful starting point to non-experts seeking to identify ontologies/terminologies appropriate for use in their work. Zak recognized that there is a  gap in the set of vocabularies reviewed, namely in the area of imaging and neuroscience and he solicited help in identifying the main players in these domains. Daniel Rubin offered to help in this direction.
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#*At this point, each NCBC should review the software tool ontology to make sure they are happy with it.
−
 
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#*Tools will appear in multiple places in the taxonomy
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In response to questions/suggestions from Gil Ommenn and Brian Athey, it was agreed that the Scientific Ontologies SIG will also produce representative use cases, outlining how ontologies/terminologies are used in practice.
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#*The current content of iTools has not yet been vetted. The content should be labeled "prototype" and representatives at each NCBC should review the current content.
−
 
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#*Users can update the software tools metadata directly in iTools or send requests to Ivo
−
Ivo Dinov reviewed the process that led to the definition of the minimum resource descriptors and Dan Rubin's software classification ontology and proceeded to discuss the iTools framework (www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_iTools) and demonstrate the Java prototype front end. The demo outlined several supported search modes as well as the ability of the tool to "scrape" updates to tool description information from Web pages that follow the format of the Resource descriptions on the SDIWG wiki.
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#*The iTools site has documentation and screen shots
−
 
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#Scientific Ontologies (Zak Kohane)
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Suzie Lewis observed that the scraping approach useb by the iTools could be used to also process the listing of terminologies produced by the Ontologies SIG and allow then to be presented/searched via the iTools application.
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#*The effort was inteneded to be pragmatic. Results of initial work is a spreadsheet that lists curated ontologies that are endorsed, used and critiqued, and those not quite ready for prime time.
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#*Zak is writing a paper on this. People can contribute use cases.
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A discussion followed about what is the proper manner to release and start using the iTools framework. Suggestions were made taht NIH should centrally host the database and portal, so as to offer the approrpiate branding and central entry point for the general public to access the NCBC resources. One idea was to develop a NCBC-specific web site (e.g., ncbc.org; or nih.ncbc.org) for that purpose. Peter Lyster said that there have been internal discussion in NIH about this topic and some ideas (such as having a central entry point to the NCBC resource listing from NCBI or some other institute) have been vetted.
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#*Action items for everyone: review the spreadsheet and make sure you agree. Contribute use cases to Zak for the manuscript.  
−
 
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#*This effort isn't an "endorsement" activity. This is more akin to a "Consumer Reports" in which each ontology is described according to various criteria.  
−
Brian Athey and Aris Floratos commented on the upcoming March telecon of the Systems Biology SIG and the idea of developing a suite of software tools comprising resources from mulitple NCBCs which will be leveraged in the context of various DBPs. The question came up of how we achieve a good balance between tool development and tool adoption and how we advertise and promote the various tools, in particular since the adoption of these tools by the community will, to a large extent, determine the impact and usefulness of the NCBC program as whole and its potential for renewed funding. Peter Lyster commented that there is no concerted effort at the time wihtin NIH to promote the NCBC tools, rather there are a number of ongoing initiatives like caBIG, BIRN, etc that are procedding in parallel. One course of action might be to start with having the iTools hosted at CCB and then move gradually towards bringing the repository within NIH as an updated NCBC page on the BISTI site (or elsewhere) is created. Peter also said that he will ask John Whitmarsh to get back to the PIs regarding the current plans for the program evaluation.
+
#DBP Interactions (Brian Athey)
 +
#*Had recent meeting on March 16. Discussion was about how via a new web site and future meetings, we coud form parternships related to NCBCs.  
 +
#*We should set up a web site where people could find out which meetings people will be attending. We should be connecting at these meetings to work together.
 +
#*Created a draft taxonomy of the DBPs. It's important to put a broad map of DBPs across all the NCBCs that would be available to reviewers. Will be posting an updated taxonomy of DBPs and invite all NCBCs to review this.
 +
#*It would help researchers looking for collaborations if all DBPs could be found in a central place.
 +
#Other issues
 +
#*Upcoming review: The NCBCs will be reviewed in a whole in the upcoming review. We could use ncbcs.org to post material at a high level shows the work NCBCs are doing--Highlights, bullets, powerpoints to show off the best of the NCBCs and of the whole program.  
 +
#*Suggestion was made to update the web site with this additional information. Emails to update the site should be Jim Cavicoli. Reps from each center should send any updated paragraph description of their center: Ivo for CCB, Daniel for NCBO, Jeanette for SIMBIOS, Brian and Will for NA-MIC, and Aris for MAGNET, and Zak for I2B2.
  
 
=== Attendees ===
 
=== Attendees ===

Latest revision as of 04:10, 19 May 2007

Home < SDIWG:Meeting Minutes 20070518

Agenda: NCBC Joint Working Group Meeting

Top page of SDIWG web site

Notes

Friday, May 18, 2007: 2:30 -- 3:30 PM EST
Please contact Peter Lyster for information Peter Lyster
SDIWG Meetings Page

TCon Agenda

  • Roll Call/Note-taker (Rubin) (5 min)

Minutes

Note taker: (Daniel Rubin)

  1. Attending: Peter Lyster, Ivo Dinov, Aris Floratos, Arthus Castle, Zohara Cohen, Daniel Rubin, David States, Jeanette Schmidt, Karen Skinner, Mark Musen, Michael Montegut, Shawn Murphy, Terry Weymouth, Brian Athey, Will Schroeder, David Kennedy, Zak Kohane
  2. iTools and Ontology of Software Tools (Ivo Dinov)
    • We have populated iTools with the metadata for each of the NCBC tools. Right now, this presents a center-specific view of tools. This will be changed to display according to the software tools ontology.
    • At this point, each NCBC should review the software tool ontology to make sure they are happy with it.
    • Tools will appear in multiple places in the taxonomy
    • The current content of iTools has not yet been vetted. The content should be labeled "prototype" and representatives at each NCBC should review the current content.
    • Users can update the software tools metadata directly in iTools or send requests to Ivo
    • The iTools site has documentation and screen shots
  3. Scientific Ontologies (Zak Kohane)
    • The effort was inteneded to be pragmatic. Results of initial work is a spreadsheet that lists curated ontologies that are endorsed, used and critiqued, and those not quite ready for prime time.
    • Zak is writing a paper on this. People can contribute use cases.
    • Action items for everyone: review the spreadsheet and make sure you agree. Contribute use cases to Zak for the manuscript.
    • This effort isn't an "endorsement" activity. This is more akin to a "Consumer Reports" in which each ontology is described according to various criteria.
  4. DBP Interactions (Brian Athey)
    • Had recent meeting on March 16. Discussion was about how via a new web site and future meetings, we coud form parternships related to NCBCs.
    • We should set up a web site where people could find out which meetings people will be attending. We should be connecting at these meetings to work together.
    • Created a draft taxonomy of the DBPs. It's important to put a broad map of DBPs across all the NCBCs that would be available to reviewers. Will be posting an updated taxonomy of DBPs and invite all NCBCs to review this.
    • It would help researchers looking for collaborations if all DBPs could be found in a central place.
  5. Other issues
    • Upcoming review: The NCBCs will be reviewed in a whole in the upcoming review. We could use ncbcs.org to post material at a high level shows the work NCBCs are doing--Highlights, bullets, powerpoints to show off the best of the NCBCs and of the whole program.
    • Suggestion was made to update the web site with this additional information. Emails to update the site should be Jim Cavicoli. Reps from each center should send any updated paragraph description of their center: Ivo for CCB, Daniel for NCBO, Jeanette for SIMBIOS, Brian and Will for NA-MIC, and Aris for MAGNET, and Zak for I2B2.

Attendees

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

Action Items

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