NAMIC Wiki - User contributions [en]

2010 CCA Retreat

2010-06-10T23:33:40Z

Rubin:

=Introduction=
This is a one-day retreat for the clinical computational anatomy project of NAC. The purpose is to review the state of this project and formulate strategic plans.

=Date and Location:=
*June 18 2010
*1249 Boylston St. 2nd floor demo room
*Start at 8.30

=Agenda=
*2006 Brain atlas (Ron Kikinis, Michael Halle, Daniel Rubin)
**scene
**scene snap shots
**DTI
*Query atlas (Wendy Plesniak)
**quick demo
**brainstorming for generalizing
**discuss incorporation of vtk infoviz
*Ontology tools (Michael Halle, Jim Miller, Daniel Rubin)
**RadLex
**integrating ontologies into Slicer

=Participants=
*Ron Kikinis
*Michael Halle
*Florin Talos
*Daniel Rubin
*Jim Miller
*Steve Pieper
*Wendy Plesniak
*Nicole Aucoin
*Dominik Meier

SDIWG:Meeting Minutes 20080919

2008-09-19T05:02:06Z

Rubin: /* Tcon Agenda */

==NCBC Joint Working Group Meeting==

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

===Notes===
''Friday September 19, 2008: 2:30-3:30 PM EST'' 
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]'' 
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]'' 
Save the date for the next SDWIG tcon/Connect, three months from now: Friday December 19, 2008

===Tcon Agenda===

*Roll Call/Note-taker (Will Schroeder) (5 min)
*Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20080516|May 16, 2008]] (5 min)
*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)
* Explicitely define '''Tiger Team''':
*Status check on '''three working groups''':
**[[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.]
*** [[Meeting_Minutes_20080919_Lysters8 | Peter Lyster's 8 Action Items (August 2008)]]
***Plans for adoption within and beyond NCBCs.
***[[Media:Biositemaps_white_paper_v4.0.doc | Biositemaps white paper v4.0]] (Needs Updating: Peter, Ivo, Daniel).
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]
* 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

 

===Minutes===
* '''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]]
* Attendees:
* '''Biositemaps Resourceome Update'''
**
**
* '''Scientific Ontologies Update'''
**
**
* '''Driving Biological Projects and Impact Update'''
**
**
* '''Meeting Schedule''':
**

===Action Items===
*
*
*

===Appendix: Biositemaps white paper===
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,
* querying,
* composing or combining, and
* mining software tools and information resources on the Internet.

SDIWG:Meeting Minutes 20080919

2008-09-19T03:05:27Z

Rubin:

==NCBC Joint Working Group Meeting==

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

===Notes===
''Friday September 19, 2008: 2:30-3:30 PM EST'' 
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]'' 
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]'' 
Save the date for the next SDWIG tcon/Connect, three months from now: Friday December 19, 2008

===Tcon Agenda===

*Roll Call/Note-taker (Will Schroeder) (5 min)
*Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20080516|May 16, 2008]] (5 min)
*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)
* Explicitely define '''Tiger Team''':
*Status check on '''three working groups''':
**[[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/38407 Biomedical Resource Ontology (BRO)] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]
*** [[Meeting_Minutes_20080919_Lysters8 | Peter Lyster's 8 Action Items (August 2008)]]
***Plans for adoption within and beyond NCBCs.
***[[Media:Biositemaps_white_paper_v4.0.doc | Biositemaps white paper v4.0]] (Needs Updating: Peter, Ivo, Daniel).
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]
* 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

 

===Minutes===
* '''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]]
* Attendees:
* '''Biositemaps Resourceome Update'''
**
**
* '''Scientific Ontologies Update'''
**
**
* '''Driving Biological Projects and Impact Update'''
**
**
* '''Meeting Schedule''':
**

===Action Items===
*
*
*

===Appendix: Biositemaps white paper===
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,
* querying,
* composing or combining, and
* mining software tools and information resources on the Internet.

SDIWG:Meeting Minutes 20080919

2008-09-19T03:02:44Z

Rubin: /* Tcon Agenda */

SDIWG:Meeting Minutes 20080919

2008-09-19T03:02:20Z

Rubin: /* Tcon Agenda */

==NCBC Joint Working Group Meeting==

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

===Notes===
''Friday September 19, 2008: 2:30-3:30 PM EST'' 
''Please contact Peter Lyster for information [mailto:lysterp@mail.nih.gov Peter Lyster]'' 
''[[SDIWG:Software_Engineering_Body_of_Knowledge_Across_NCBC_Biocomputing_Centers | SDIWG Meetings Page]]'' 
Save the date for the next SDWIG tcon/Connect, three months from now: Friday December 19, 2008

===Tcon Agenda===

*Roll Call/Note-taker (Will Schroeder) (5 min)
*Minutes from most recent SDIWG tcon [[SDIWG:Meeting_Minutes_20080516|May 16, 2008]] (5 min)
*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)
* Explicitely define '''Tiger Team''':
*Status check on '''three working groups''':
**[[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)] and the [http://biositemaps.bioontology.org/editor/ Information Model (IM) which is encapsulated in the Biositemaps Editor. Please try it out.]
*** [[Meeting_Minutes_20080919_Lysters8 | Peter Lyster's 8 Action Items (August 2008)]]
***Plans for adoption within and beyond NCBCs.
***[[Media:Biositemaps_white_paper_v4.0.doc | Biositemaps white paper v4.0]] (Needs Updating: Peter, Ivo, Daniel).
** [[SDIWG:_NCBC_Scientific_Ontologies|Scientific Ontologies]]
** [http://www.ncbcs.org/dbp_interactions.html NCBC Driving Biological Projects Interactions and Impact]
* 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

 

===Minutes===
* '''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]]
* Attendees:
* '''Biositemaps Resourceome Update'''
**
**
* '''Scientific Ontologies Update'''
**
**
* '''Driving Biological Projects and Impact Update'''
**
**
* '''Meeting Schedule''':
**

===Action Items===
*
*
*

===Appendix: Biositemaps white paper===
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,
* querying,
* composing or combining, and
* mining software tools and information resources on the Internet.

Comments on Imaging and Neuroinformatics Ontologies

2007-02-16T20:44:58Z

Rubin:

I would like to suggest that the Software Ontologies working group consider the following terminologies to fulfill the needs for the neuroinformatics and radiology domains:

1. Neuroinformatics: BIRNLex (http://xwiki.nbirn.net:8080/xwiki/bin/view/%20BIRN-OTF-Public/Home) is being developed by members of the Ontology Task Force in BIRN. They are also working in coordination with the NCBO, the Ontology for Biomedical Investigation (OBI) community, and the radiology community in developing this terminology. A draft of BIRNLex is available, and it will soon be released publicly.

2. Radiology: The Radiology Society of North America (RSNA) is sponsoring the development of RadLex (http://radlex.org), a comprehensive terminology for the radiology domain. RadLex had its initial release in November 2006. RadLex development is being coordinated with other terminology efforts, such as BIRNLex, OBI, and SNOMED.

SDIWG: NCBC Scientific Ontologies

2007-02-16T20:39:25Z

Rubin:

=== This is the main page for the NIH Roadmap National Centers for Biomedical Computing (NCBC) Working Group titled: Scientific Ontologies ===

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

 Contacts for this Working Group are Zak Kohane (isaac_kohane@harvard.edu), Suzi Lewis(suzi@fruitfly.org), and Mark Musen (musen@stanford.edu)

 

----

 '''The following are important output from the Scientific Ontologies working group, with most recent at the top, and we welcome comments from the community'''

* [http://www.berkeleybop.org/sowg/table.cgi Suzi Lewis Compilation of proposed ontologies and data standards selected for use by the NCBCs, as of February 2007.] Additional information can be found in the [http://homepage.mac.com/isaac.kohane/blogwavestudio/LH20050109125630/LHA20070210191150/index.html Working Group Meeting Minutes 20070209]

* [[PrelimResultsSOWG1|Preliminary Results from Scientific Ontologies WG #1]]

* [[The_States_8|Proposal for common reference ontologies/vocabularies (The States 8)]]

* [[Commentary_on_States_8|Commentary on States 8]]

* [[Top_down_becoming_bottom_up|Need for (semi-)automated ontology mapping ]]

* [[Comments_from_Bill_Bug|Comments from Bill Bug]]

* [[Comments_on_Imaging_and_Neuroinformatics_Ontologies]]

 

----

* [[Upcoming_meetings|Upcoming meetings of relevance to science ontologies]]

 

----

'''Highlights from Scientific Ontologies TCONs'''
* [http://homepage.mac.com/isaac.kohane/blogwavestudio/LH20050109125630/LHA20070210191150/index.html Meeting Minutes 20070209]

* [[Meeting_Minutes_20060601|Meeting Minutes 20060601]]