Difference between revisions of "SDIWG:Meeting Minutes 20080919"

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*Roll Call/Note-taker (Will Schroeder) (5 min)
 
*Roll Call/Note-taker (Will Schroeder) (5 min)
 
*Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20080516|May 16, 2008]] (5 min)
 
*Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20080516|May 16, 2008]] (5 min)
−
*Debrief NCBC All Hands Meeting, August 13-15, 2008. Logistics, Planning & Brainstorming discussion (Peter, Karin, All)
+
*Debrief [http://meetings.nigms.nih.gov/index.cfm?event=home&ID=4095 NCBC All Hands Meeting, August 13-15, 2008]. Logistics, Planning & Brainstorming discussion (Peter, Karin, All)
 
*Status check on '''three working groups''':  
 
*Status check on '''three working groups''':  
−
** [[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Biositemaps Resourceome]]
+
**[[SDIWG:_NCBC_Resource_Yellow_Pages_and_Software_Ontologies|Biositemaps Resourceome]]
−
*** State of [http://www.biositemap.org Biositemaps] and [[Media:Biositemaps_white_paper_v4.0.doc | Biositemaps white paper v4.0]] (Needs Updating: Peter, Ivo, Daniel).  The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/38407 Biomedical Resource Ontology (BRO)] and the [http://bmir-protege-dev1.stanford.edu/bro2/ Information Model (IM)]
+
***State of [http://www.biositemap.org Biositemaps].  The underlying technology for Biositemaps is the [http://bioportal.bioontology.org/visualize/38610 Biomedical Resource Ontology (BRO) V2.1] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]
 +
*** The [[Tiger_team_biositemaps | <b> Tiger Team</b>]] is working on this phase of biositemaps.
 +
*** If you want to view the working group thread, suggest you start at the [[SDIWG:Meeting_Minutes_20080716 | Four basic activities, Authoring/Consuming of Biositemaps/BRO]]
 +
*** [[Meeting_Minutes_20080919_Lysters8 | Peter Lyster's 8 Action Items (August 2008)]]
 +
*** [[Plans for adoption within and beyond NCBCs | Plans for adoption within and beyond NCBCs]]
 +
***[[Media:Biositemaps_white_paper_v4.0.doc | Biositemaps white paper v4.0]] (Needs Updating: Peter, Ivo, Daniel).
 +
***[[Cheat Sheet for NCBC Leads to adopt Biositemaps | Cheat Sheet for NCBC Leads to adopt Biositemaps]]
 +
***[[Ongoing activities of Biositemaps team | Ongoing activities of Biositemaps team]]
 
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]
 
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]
 
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]
 
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]
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===Minutes===
 
===Minutes===
 
* '''Note taker''': [Suggested order of note takers for future meetings: '''Will Schroeder (this one)'''; Floratos; Rubin; Jags, Dinov, Murphy, Ku]
 
* '''Note taker''': [Suggested order of note takers for future meetings: '''Will Schroeder (this one)'''; Floratos; Rubin; Jags, Dinov, Murphy, Ku]
−
* Review of [[SDIWG:Meeting_Minutes_20080516|May 16, 2008 Minutes]]
+
* Review of [[SDIWG:Meeting_Minutes_20080516|May 16, 2008 Minutes]]  
−
* Attendees:
+
 
 +
* Attendees: Peter Lyster (NIH/NIGMS), Will Schroeder (NA-MIC), Ivo Dinov (CCB), Daniel Rubin (NCBO), Brian Haugen (OD), Joy Ku (Simbios), Jerry Li (NCI), Brian Athey (NCIBI), Gil Omenn (NCIBI), David States (NCIB), Aris Floratos (MAGNet), William Lau (CIT), John Matochik (NIAAA), Karen Skinner (NIDA), Nanwei Cao (NIAAA), Beth Kirschner (NCIBI)
 
* '''Biositemaps Resourceome Update'''
 
* '''Biositemaps Resourceome Update'''
−
**  
+
** Ivo talked about using BRO to collecting notes in annotation field. Go to http://www.ncbcs.org/biositemaps/ to see current site information. Went through top eight action items http://www.na-mic.org/Wiki/index.php/Meeting_Minutes_20080919_Lysters8. Please make sure your site information is up to date.
−
**
 
 
* '''Scientific Ontologies Update'''
 
* '''Scientific Ontologies Update'''
−
**
+
** Committee decided that writing a paper on ontology evaluation is a good idea. Expected time frame for first draft is Thanksgiving time frame. General anectode that ontology has relatively unknown and their is a hungry community for them. Journal of Biomedical Informatics is a possible target. One disadvantage is that we want to reach the biomedical scientists. Nature of Medicine might be another place. We were wondering about metrics for evaluation ontologies.
−
**
 
 
* '''Driving Biological Projects and Impact Update'''
 
* '''Driving Biological Projects and Impact Update'''
−
**
+
** Brian: Believes that the NCBCs will be evaluated based on what highlights/discoveries have been enabled by the NCBCs? how they impact health problems, which may be more important, comparatively than the infrastructure developments. Advocating a special Simbios issue of glossy mag to highlight NCBC contributions. Put on an event on as a panel to discuss NCBC contributions. Brian also talked about NCI-related caBIG Knowledge Center and contributions to the data sharing initiative. Joyce led discussion on 32-page glossy mag (Biomedical Computing Review), wondering how to divvy this up across publication space/time. We talked about winter and spring issues as possibilities. Karen recommended shooting for December deadline.
−
**
+
 
 
* '''Meeting Schedule''':
 
* '''Meeting Schedule''':
−
**  
+
 
 +
=== NCBC DBPs===
 +
* [http://cms.loni.ucla.edu/CCB/research.aspx?id=2538 CCB DBPs]:
 +
** [https://cms.loni.ucla.edu/WorkArea/linkit.aspx?LinkIdentifier=id&ItemID=3418 Identifying Age Related Atrophy Using Levelset Registration of Embedded Maps]
 +
** [https://cms.loni.ucla.edu/WorkArea/linkit.aspx?LinkIdentifier=id&ItemID=3420 Developmental Origin of Phenotypic Variation in Drosophila Melanogaster]
 +
** [https://cms.loni.ucla.edu/WorkArea/linkit.aspx?LinkIdentifier=id&ItemID=3422 Mapping Brain Changes in HIV/AIDS]
 +
** [https://cms.loni.ucla.edu/WorkArea/linkit.aspx?LinkIdentifier=id&ItemID=3424 Vervet Genetics and Brain Morphology]
 +
** [http://cms.loni.ucla.edu/CCB/research.aspx?id=2538 Mapping Language Development Longitudinally]
 +
** [http://cms.loni.ucla.edu/CCB/research.aspx?id=2538 Mapping Brain Changes In Alzheimer's & Those at Risk]
 +
** [http://cms.loni.ucla.edu/CCB/research.aspx?id=2538 Mechanisms Underlying the Clinical Progression of MS and EAE]
 +
** [http://cms.loni.ucla.edu/CCB/research.aspx?id=2538 Genetic Influences on Brain Structure in Schizophrenia]
 +
* [http://bioontology.org/dbps.html NCBO DBPs]
 +
* [http://portal.ncibi.org/gateway/dbp.html NCIBI DBPs]
 +
* [http://magnet.c2b2.columbia.edu/projects.php MAGNet DBPs]
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* [http://simbios.stanford.edu/graduation.htm Simbios DBPs]
 +
* [http://www.na-mic.org/pages/Driving_Biological_Projects NAMIC DBPs]
 +
* [https://www.i2b2.org/about/collaborations.html I2B2 DBPs]
  
 
===Action Items===
 
===Action Items===
−
*
+
* TBD
−
*
 
−
*
 
  
 
===Appendix: Biositemaps white paper===
 
===Appendix: Biositemaps white paper===
−
The [http://www.biositemap.org biositemaps] [[Media:Biositemaps_white_paper_v4.0.doc | Biositemaps white paper v4.0]] presents description of prototype for distributed architecture to address  
+
The [http://www.biositemap.org biositemaps] [[Media:Biositemaps_white_paper_v4.0.doc | Biositemaps white paper v4.0 (Needs Updating)]] presents description of prototype for distributed architecture to address  
 
* locating,  
 
* locating,  
 
* querying,
 
* querying,
 
* composing or combining, and  
 
* composing or combining, and  
−
* mining software tools and information resources on the Internet.
+
* 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 11:57, 21 September 2008

Home < SDIWG:Meeting Minutes 20080919

NCBC Joint Working Group Meeting

Top page of SDIWG web site

Notes

Friday September 19, 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 December 19, 2008

Tcon Agenda


Minutes

  • Note taker: [Suggested order of note takers for future meetings: Will Schroeder (this one); Floratos; Rubin; Jags, Dinov, Murphy, Ku]
  • Review of May 16, 2008 Minutes
  • Attendees: Peter Lyster (NIH/NIGMS), Will Schroeder (NA-MIC), Ivo Dinov (CCB), Daniel Rubin (NCBO), Brian Haugen (OD), Joy Ku (Simbios), Jerry Li (NCI), Brian Athey (NCIBI), Gil Omenn (NCIBI), David States (NCIB), Aris Floratos (MAGNet), William Lau (CIT), John Matochik (NIAAA), Karen Skinner (NIDA), Nanwei Cao (NIAAA), Beth Kirschner (NCIBI)
  • Biositemaps Resourceome Update
  • Scientific Ontologies Update
    • Committee decided that writing a paper on ontology evaluation is a good idea. Expected time frame for first draft is Thanksgiving time frame. General anectode that ontology has relatively unknown and their is a hungry community for them. Journal of Biomedical Informatics is a possible target. One disadvantage is that we want to reach the biomedical scientists. Nature of Medicine might be another place. We were wondering about metrics for evaluation ontologies.
  • Driving Biological Projects and Impact Update
    • Brian: Believes that the NCBCs will be evaluated based on what highlights/discoveries have been enabled by the NCBCs? how they impact health problems, which may be more important, comparatively than the infrastructure developments. Advocating a special Simbios issue of glossy mag to highlight NCBC contributions. Put on an event on as a panel to discuss NCBC contributions. Brian also talked about NCI-related caBIG Knowledge Center and contributions to the data sharing initiative. Joyce led discussion on 32-page glossy mag (Biomedical Computing Review), wondering how to divvy this up across publication space/time. We talked about winter and spring issues as possibilities. Karen recommended shooting for December deadline.
  • Meeting Schedule:

NCBC DBPs

Action Items

  • TBD

Appendix: Biositemaps white paper

The biositemaps Biositemaps white paper v4.0 (Needs Updating) presents description of prototype for distributed architecture to address

  • locating,
  • querying,
  • composing or combining, and
  • mining software tools and information resources on the Internet.
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