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===Notes===
 
===Notes===
−
''Friday September 19, 2009: 2:30-3:30 PM EST''<br>
+
''Friday September 19, 2008: 2:30-3:30 PM EST''<br>
 
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br>
 
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]''<br>
 
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br>
 
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]''<br>
−
<b>Save the date for the next SDWIG tcon/Connect, three months from now: Friday December 19, 2009</b>
+
<b>Save the date for the next SDWIG tcon/Connect, three months from now: Friday December 19, 2008</b>
  
 
===Tcon Agenda===
 
===Tcon Agenda===
  
−
*Roll Call/Note-taker (Joy Ku) (5 min)
+
*Roll Call/Note-taker (Will Schroeder) (5 min)
−
*Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20080222|Feb. 22, 2008]] (5 min)
+
*Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20080516|May 16, 2008]] (5 min)
−
*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].  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]
−
* State of [http://www.biositemap.org Biositemaps] and [[Media:Biositemaps_white_paper_v4.0.doc | Biositemaps white paper v4.0]] (Peter, Ivo, Daniel) and [http://na-mic.org/Wiki/index.php/SDIWG:Meeting_Minutes_20080416 Biomedical Resource Ontology (BRO) ]
 
−
* Programmatic and translational-research interactions with other initiatives (CTSA, BIRN, and so on)
 
−
* Overview of plan for next 2 months (Peter)
 
−
* State of the Roadmap Initiative
 
−
* Other Progress reports
 
−
* Next 2 meeting date (2008 NCBC AHM) - we may need a prep-meeting in early August!
 
 
* Questions/Information Sharing
 
* Questions/Information Sharing
 +
*  From May 16 SDIWG, any progress on: Setting up a booth at the annual neuroscience meeting.  There’s great interest in the tools being developed.  If agenda for meeting isn’t set, holding a session to talk about the tools would be even more effective
  
 
<br>
 
<br>
  
 
===Minutes===
 
===Minutes===
−
* '''Note taker''': [Suggested order of note takers for future meetings: '''Joy Ku (this one)'''; Schroeder; Floratos; Rubin; Jags, Dinov, Murphy]
+
* '''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_20080222|Feb 22, 2008 Minutes]]
+
* Review of [[SDIWG:Meeting_Minutes_20080516|May 16, 2008 Minutes]]  
−
* Attendees: Peter Lyster (NIH/NIGMS), Joy Ku (Simbios), Jeanette Schmidt (Simbios), Natasha Noy (NCBO), Mark Musen (NCBO), Csonger Nyulas (NCBO), Ivo Dinov (CCB), David States (NCIBI), Zac Kohane (i2b2), Brian Athey (NCIBI), Jim Cavalcoli (NCIBI), Beth Kirschner (NCIBI), Karin Remington (NIH/NIGMS), John Matochik (NIH/NIAAA), Yuan Liu (NIH/NINDS), Jennie Larkin (NIH/NHLBI), Aris Floratos (MAGNet), Will Schroeder (NA-MIC), German Cavelier (NIH/NIMH)  
+
 
 +
* 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'''
−
** Goal is to get the first version of the biomedical resource ontology (BRO) finalized and approved by the seven centers within the next month, before the all-hands meeting.  Currently, the group is streamlining it—they want flatten it out, simplify it.  The current decision is to develop the BRO and delay any attempts to reconcile it with other ontologies that exist.  This is just one field in the biositemap.xml file.  This could provide direction for the SDIWG Ontology working group. 
+
** 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.  
−
** Need a tool for creating the annotations. This is being created by NCBO.  Natasha will take the lead with Ivo and Bill Bug.  David is to be added to this list. Natasha is creating the environment using Protégé. The first user will be iTools.  After finishing this, the team will build it out to the 7 centers. Send Peter an email if you want to be involved earlier.
+
* '''Scientific Ontologies Update'''
−
** Need adoption of biositemaps by all seven centers before the all-hands meeting. Only 3 of 7 centers are linking right now on the BISTI page. Peter pointed out that all 7 centers have contributed to iTools, in the alpha version. What would help is conversion of tools on iTools into xml files.  Ivo says that you can’t currently do this, but maybe they could create a tool for this.
+
** 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.
−
** Proposal to create a demo to show how biositemaps could be used to link up tools and data.  Want to tell a story that wouldn’t happen with an individual center.  One possibility is diabetes.  How would this relate to imagery? This will branch off as a separate working group.
+
* '''Driving Biological Projects and Impact Update'''
−
***The paper on iTools added a demo for searching for data and tools through iTools. It was a proof of concept of integrating pieces into a workflow. Ivo volunteered to show how this was done, perhaps with another Tcon.
+
** 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.
−
***Peter mentioned that inputs and outputs weren’t well-described in his white paper on biositemaps on purpose, pending version 2.0, which will be a more Semantic Web-enabled tool but it wasn’t on the current agenda
+
 
−
* '''Other Working Groups Update''':  Scientific Ontologies and NCBC Driving Biological Projects Interactions and Impact need to branch off. They need to finalize efforts and think about setting up new working groups for after the all hands meeting.
+
* '''Meeting Schedule''':
−
* '''Meeting Schedule''': Need more meetings. Tcon the 3rd Friday of every month was proposed. Next Tcon would be June 20th. It was pointed out that the ISMB mtg and others conflict with July Tcon. Action: Suggest times for summer and then decide what works
+
 
−
* '''All Hands Meeting'''
+
=== NCBC DBPs===
−
** Karin is excited about the second day’s afternoon discussions and wants to coordinate dialogs between different centers. Are there people in other communities to invite, e.g., in other programs? Suggestions included CTSA, NIST, and BIRN. Action: Group will do a follow-up with PIs to provide input on this.
+
* [http://cms.loni.ucla.edu/CCB/research.aspx?id=2538 CCB DBPs]:
−
** Idea suggested to possibly switch demo to evening of 1st night and do working groups morning of 2nd night to get more quality time. Problem is with hotel space.
+
** [https://cms.loni.ucla.edu/WorkArea/linkit.aspx?LinkIdentifier=id&ItemID=3418 Identifying Age Related Atrophy Using Levelset Registration of Embedded Maps]
−
** Yuan suggested having a demo for the biomedical society to learn what wonderful tools have been developed so we can work together. While a demo is scheduled, Yuan emphasized the the need to invite the people, not just program directors. Invite other groups.
+
** [https://cms.loni.ucla.edu/WorkArea/linkit.aspx?LinkIdentifier=id&ItemID=3420 Developmental Origin of Phenotypic Variation in Drosophila Melanogaster]
−
** Idea came up about setting up a booth at the annual neuroscience meeting. There’s great interest in the tools being developed. If agenda for meeting isn’t set, holding a session to talk about the tools would be even more effective.
+
** [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]
 +
* [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===
−
* Get the first version of the biomedical resource ontology (BRO) finalized and approved by the seven centers within the next month, before the all hands meeting. 
+
* TBD
−
* Natasha and the TIGER team will create environment for annotating.  After finishing this, the team will build it out to the 7 centers. 
 
−
* All 7 centers need to adopt and create biositemaps for their tools before the all hands meeting.
 
−
* Scientific Ontologies and NCBC Driving Biological Projects Interactions and Impact need to finalize efforts and think about setting up new working groups for after the all hands meeting.
 
−
* Need to solicit and finalize summer Tcon times.
 
−
* Follow-up with PIs to provide input on Karin’s request for who to invite to the all hands meeting (specifically for the 2nd day’s afternoon discussion)
 
  
 
===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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