https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=Hkhagler 2026-06-05T20:19:07Z User contributions MediaWiki 1.35.9 https://www.bioontology.org//mediawiki/index.php?title=OCI:Main_Page&diff=6788 2008-04-15T15:17:09Z

<p>Hkhagler: /* Conference Call Information */</p> <hr /> <div>=OCI - Ontology for Clinical Investigations=<br /> <br /> ==About OCI==<br /> <br /> The goal of the OCI Working Group is to foster the creation and dissemination of a reference ontology (high-quality controlled structured vocabulary) for the annotation of the results of clinical trials.<br /> <br /> ==Recent Developments==<br /> <br /> ==Conference Call Information==<br /> * '''Next OCI conference call: Thursday, April 17 at 10am CDT, 11am EDT, 17:00 Germany, 13:00 UCT(GMT).'''<br /> * [[Conference Call Schedule]]<br /> * [[Call-in Information]]<br /> * [[Conference Call Agendas]]<br /> * [[Conference Call Minutes]]<br /> * [[Action Items]]<br /> <br /> ==Meetings==<br /> * [[Upcoming Meetings]]<br /> * [[Meetings Attended]]<br /> <br /> ==Communities and Working Group (WG) Participants==<br /> * [[OCI WG Chairs]]<br /> * [[OCI Curators]]<br /> * [[Other members of OCI WG]]<br /> <br /> ==Draft version of OCI==<br /> <br /> ==Ontology Development Items==<br /> * [[Design Principles]]<br /> * [[Term Lists]]<br /> * [[High-level Concepts]]<br /> * [[High-level Concepts v0.2]]<br /> * [[Initial OCI-OBI Mapping]]<br /> * [[OCI Term Compilation (Jennifer)]]<br /> * [[OBI v0.6.6 Schematic]]<br /> <br /> ==OCI Development Policies==<br /> * [[Ontology Metadata Policy (from OBI)]]<br /> * [[OCI Check-out Procedure Policy]]<br /> * [[OCI Working Group Membership Policy]]<br /> <br /> ==Publications==<br /> <br /> OCI Google group: http://groups.google.com/group/OCInv<br /> <br /> OCI Google mailing list: mailto:OCInv@googlegroups.com<br /> <br /> OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)<br /> <br /> ==OCI Wiki information==</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=OCI:Main_Page&diff=6760 2008-04-10T15:03:15Z

<p>Hkhagler: /* Conference Call Information */</p> <hr /> <div>=OCI - Ontology for Clinical Investigations=<br /> <br /> ==About OCI==<br /> <br /> The goal of the OCI Working Group is to foster the creation and dissemination of a reference ontology (high-quality controlled structured vocabulary) for the annotation of the results of clinical trials.<br /> <br /> ==Recent Developments==<br /> <br /> ==Conference Call Information==<br /> * '''Next OCI conference call: Thursday, April 17 at 10am CST, 11am EST, 17:00 Germany, 14:00 UCT(GMT).'''<br /> * [[Conference Call Schedule]]<br /> * [[Call-in Information]]<br /> * [[Conference Call Agendas]]<br /> * [[Conference Call Minutes]]<br /> * [[Action Items]]<br /> <br /> ==Meetings==<br /> * [[Upcoming Meetings]]<br /> * [[Meetings Attended]]<br /> <br /> ==Communities and Working Group (WG) Participants==<br /> * [[OCI WG Chairs]]<br /> * [[OCI Curators]]<br /> * [[Other members of OCI WG]]<br /> <br /> ==Draft version of OCI==<br /> <br /> ==Ontology Development Items==<br /> * [[Design Principles]]<br /> * [[Term Lists]]<br /> * [[High-level Concepts]]<br /> * [[High-level Concepts v0.2]]<br /> * [[Initial OCI-OBI Mapping]]<br /> * [[OCI Term Compilation (Jennifer)]]<br /> * [[OBI v0.6.6 Schematic]]<br /> <br /> ==OCI Development Policies==<br /> * [[Ontology Metadata Policy (from OBI)]]<br /> * [[OCI Check-out Procedure Policy]]<br /> * [[OCI Working Group Membership Policy]]<br /> <br /> ==Publications==<br /> <br /> OCI Google group: http://groups.google.com/group/OCInv<br /> <br /> OCI Google mailing list: mailto:OCInv@googlegroups.com<br /> <br /> OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)<br /> <br /> ==OCI Wiki information==</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Schedule&diff=6759 2008-04-10T15:02:35Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> <br /> '''Meeting changes'''<br /> *NOTE Switch from 2 and 4 back to 1 and 3 Thursdays.<br /> *See Conference Call In info for new telecon phone number<br /> <br /> <br /> '''Scheduled meetings:'''<br /> *Next meeting April 17 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany<br /> *BIWEEKLY (every 1nd and 3th Thursday) starting March 6, 2008 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=OCI:Main_Page&diff=6656 2008-03-20T15:05:31Z

<p>Hkhagler: /* Conference Call Information */</p> <hr /> <div>=OCI - Ontology for Clinical Investigations=<br /> <br /> ==About OCI==<br /> <br /> The goal of the OCI Working Group is to foster the creation and dissemination of a reference ontology (high-quality controlled structured vocabulary) for the annotation of the results of clinical trials.<br /> <br /> ==Recent Developments==<br /> <br /> ==Conference Call Information==<br /> * '''Next OCI conference call: Thursday, March 20 at 10am CST, 11am EST, 17:00 Germany, 14:00 UCT(GMT).'''<br /> * [[Conference Call Schedule]]<br /> * [[Call-in Information]]<br /> * [[Conference Call Agendas]]<br /> * [[Conference Call Minutes]]<br /> * [[Action Items]]<br /> <br /> ==Meetings==<br /> * [[Upcoming Meetings]]<br /> * [[Meetings Attended]]<br /> <br /> ==Communities and Working Group (WG) Participants==<br /> * [[OCI WG Chairs]]<br /> * [[OCI Curators]]<br /> * [[Other members of OCI WG]]<br /> <br /> ==Draft version of OCI==<br /> <br /> ==Ontology Development Items==<br /> * [[Design Principles]]<br /> * [[Term Lists]]<br /> * [[High-level Concepts]]<br /> * [[High-level Concepts v0.2]]<br /> * [[Initial OCI-OBI Mapping]]<br /> * [[OCI Term Compilation (Jennifer)]]<br /> * [[OBI v0.6.6 Schematic]]<br /> <br /> ==OCI Development Policies==<br /> * [[Ontology Metadata Policy (from OBI)]]<br /> * [[OCI Check-out Procedure Policy]]<br /> * [[OCI Working Group Membership Policy]]<br /> <br /> ==Publications==<br /> <br /> OCI Google group: http://groups.google.com/group/OCInv<br /> <br /> OCI Google mailing list: mailto:OCInv@googlegroups.com<br /> <br /> OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)<br /> <br /> ==OCI Wiki information==</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Agendas&diff=6613 2008-03-06T20:16:47Z

<p>Hkhagler: /* Conference Call Agendas */</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> = Conference Call Agendas =<br /> <br /> <br /> ==March 20, 2008==<br /> *Term Review Complete - Future Directions?<br /> <br /> ==March 6, 2008==<br /> *Review Terms in Google Docs<br /> <br /> <br /> ==February 21, 2008==<br /> *Review Terms in Google Docs<br /> *Discuss Use Cases that are needed to match with the terms<br /> *Next Steps<br /> <br /> ==January 25, 2008==<br /> *Review Terms in Google Docs<br /> *Discuss Use Cases that are needed to match with the terms<br /> *Next Steps<br /> <br /> ==November 29==<br /> *Continue working on Google Docs Terms and Definitions&lt;br&gt;<br /> <br /> ==August 10==<br /> 1. Overview of the BRIDG project by Doug Fridsma&lt;br&gt;<br /> <br /> <br /> ==August 2==<br /> 1. Overview of the CDISC Terminology project by Bron Kisler&lt;br&gt;<br /> 2. Brief review of Jim Zhengs text mining approach for identifying clinical terms from clinical protocols&lt;br&gt;<br /> <br /> ==May 10==<br /> 1. Review the recent work that several people have added&lt;br&gt;<br /> 2. Review the goals and organization of the workshop&lt;br&gt;<br /> 3. Discuss how we think the CTO could be useful (use cases)&lt;br&gt;<br /> <br /> ==May 3==<br /> *Discussion of High-Level BFO-OBI Structure<br /> *Discussion of new added terms<br /> *Plans for CTO Workshop<br /> *Action items for the coming week<br /> <br /> ==April 19==<br /> '''1. Ontology of Biomedical Investigation'''<br /> *a. Overview of OBI core (Fostel, tentative)<br /> '''2. CTO development approach (with deadlines and milestones)'''<br /> *a. Goals for completion by May16th<br /> *b. Status of proposed steps<br /> **term list assembly<br /> **term list merging<br /> **term positioning into branches<br /> **term CTO definition<br /> '''3. High-level concept branches'''<br /> <br /> '''4. Others'''<br /> <br /> ==April 12==<br /> '''1. CTO Working Group (WG) Organization'''<br /> *a. Are current assignments acceptable?<br /> *b. Need a secretary<br /> *c. Responsibilities<br /> *d. Schedule of calls<br /> '''2. Development and WG policies in general'''<br /> *a. Draft metadata and CTO check-out policies<br /> *b. CTO WG membership policy<br /> '''3. Ontology Organization'''<br /> *a. Relationship with the BFO<br /> *b. Relationship with the OBI<br /> '''4. CTO scope'''<br /> *a. Definition of the CTO domain<br /> *b. Relationship with other ontologies<br /> '''5. CTO development approach (with deadlines and milestones)'''<br /> *a. Proposed steps<br /> **term list assembly<br /> **term list merging<br /> **term positioning into branches<br /> **term CTO definition<br /> *b. Goals for completion by May 16th<br /> *c. Managing discussion threads<br /> '''6. Information objects as dependent continuants (if time)'''</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Schedule&diff=6612 2008-03-06T20:15:43Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> <br /> '''Meeting changes'''<br /> *NOTE Switch from 2 and 4 back to 1 and 3 Thursdays.<br /> *See Conference Call In info for new telecon phone number<br /> <br /> <br /> '''Scheduled meetings:'''<br /> *Next meeting March 20 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany<br /> *BIWEEKLY (every 1nd and 3th Thursday) starting March 6, 2008 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_03/06/08_Conference_Call&diff=6611 2008-03-06T20:15:19Z

<p>Hkhagler: New page: Go back to OCI:Main Page Present on the call: Jennifer Fostel, Herb Hagler, &lt;br&gt; 1. Completed all of the items in the googledocs spreadsheet&lt;br&gt; 2. Jennifer has agreed to cleanup t...</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Jennifer Fostel, Herb Hagler, <br /> &lt;br&gt;<br /> <br /> 1. Completed all of the items in the googledocs spreadsheet&lt;br&gt;<br /> 2. Jennifer has agreed to cleanup the document for submission to OBI&lt;br&gt;<br /> 3. Will cover next steps and future directions during next meeting&lt;br&gt;<br /> <br /> Next call scheduled for March 20th at 10 am Central, 11 am Eastern, 1700 Germany.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Minutes&diff=6610 2008-03-06T20:11:58Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> * [[Minutes from 03/06/08 Conference Call]]<br /> * [[Minutes from 02/21/08 Conference Call]]<br /> * [[Minutes from 01/10/08 Conference Call]]<br /> * [[Minutes from 10/11/07 Conference Call]]<br /> * [[Minutes from 08/30/07 Conference Call]]<br /> * [[Minutes from 08/10/07 Conference Call]]<br /> * [[Minutes from 08/02/07 Conference Call]]<br /> * [[Minutes from 07/19/07 Conference Call]]<br /> * [[Minutes from 06/28/07 Conference Call]]<br /> * [[Minutes from 05/10/07 Conference Call]]<br /> * [[Minutes from 05/03/07 Conference Call]]<br /> * [[Minutes from 04/19/07 Conference Call]]<br /> * [[Minutes from 04/12/07 Conference Call]]</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_02/21/08_Conference_Call&diff=6548 2008-02-21T19:13:26Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Jim Zheng, Jennifer Fostel, Herb Hagler, Christian Cocos&lt;br&gt;<br /> <br /> 1. Herb and Richard working with the CTSA metadata development group&lt;br&gt;<br /> 2. The Metadata group has a few use cases that will serve to focus further term developments&lt;br&gt;<br /> 3. Completed about 80 terms today, more 2 wks from now&lt;br&gt;<br /> <br /> Next call scheduled for March 6th at 10 am Central, 11 am Eastern, 1700 Germany.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Agendas&diff=6547 2008-02-21T19:09:49Z

<p>Hkhagler: /* Conference Call Agendas */</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> = Conference Call Agendas =<br /> <br /> <br /> <br /> ==March 6, 2008==<br /> *Review Terms in Google Docs<br /> <br /> <br /> ==February 21, 2008==<br /> *Review Terms in Google Docs<br /> *Discuss Use Cases that are needed to match with the terms<br /> *Next Steps<br /> <br /> ==January 25, 2008==<br /> *Review Terms in Google Docs<br /> *Discuss Use Cases that are needed to match with the terms<br /> *Next Steps<br /> <br /> ==November 29==<br /> *Continue working on Google Docs Terms and Definitions&lt;br&gt;<br /> <br /> ==August 10==<br /> 1. Overview of the BRIDG project by Doug Fridsma&lt;br&gt;<br /> <br /> <br /> ==August 2==<br /> 1. Overview of the CDISC Terminology project by Bron Kisler&lt;br&gt;<br /> 2. Brief review of Jim Zhengs text mining approach for identifying clinical terms from clinical protocols&lt;br&gt;<br /> <br /> ==May 10==<br /> 1. Review the recent work that several people have added&lt;br&gt;<br /> 2. Review the goals and organization of the workshop&lt;br&gt;<br /> 3. Discuss how we think the CTO could be useful (use cases)&lt;br&gt;<br /> <br /> ==May 3==<br /> *Discussion of High-Level BFO-OBI Structure<br /> *Discussion of new added terms<br /> *Plans for CTO Workshop<br /> *Action items for the coming week<br /> <br /> ==April 19==<br /> '''1. Ontology of Biomedical Investigation'''<br /> *a. Overview of OBI core (Fostel, tentative)<br /> '''2. CTO development approach (with deadlines and milestones)'''<br /> *a. Goals for completion by May16th<br /> *b. Status of proposed steps<br /> **term list assembly<br /> **term list merging<br /> **term positioning into branches<br /> **term CTO definition<br /> '''3. High-level concept branches'''<br /> <br /> '''4. Others'''<br /> <br /> ==April 12==<br /> '''1. CTO Working Group (WG) Organization'''<br /> *a. Are current assignments acceptable?<br /> *b. Need a secretary<br /> *c. Responsibilities<br /> *d. Schedule of calls<br /> '''2. Development and WG policies in general'''<br /> *a. Draft metadata and CTO check-out policies<br /> *b. CTO WG membership policy<br /> '''3. Ontology Organization'''<br /> *a. Relationship with the BFO<br /> *b. Relationship with the OBI<br /> '''4. CTO scope'''<br /> *a. Definition of the CTO domain<br /> *b. Relationship with other ontologies<br /> '''5. CTO development approach (with deadlines and milestones)'''<br /> *a. Proposed steps<br /> **term list assembly<br /> **term list merging<br /> **term positioning into branches<br /> **term CTO definition<br /> *b. Goals for completion by May 16th<br /> *c. Managing discussion threads<br /> '''6. Information objects as dependent continuants (if time)'''</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_02/21/08_Conference_Call&diff=6546 2008-02-21T19:06:44Z

<p>Hkhagler: New page: Go back to OCI:Main Page Present on the call: Jim Zheng, Jennifer Fostel, Herb Hagler, C&lt;br&gt; 1. Herb and Richard working with the CTSA metadata development group&lt;br&gt; 2. The Metadata...</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Jim Zheng, Jennifer Fostel, Herb Hagler, C&lt;br&gt;<br /> <br /> 1. Herb and Richard working with the CTSA metadata development group&lt;br&gt;<br /> 2. The Metadata group has a few use cases that will serve to focus further term developments&lt;br&gt;<br /> 3. Completed about 80 terms today, more 2 wks from now&lt;br&gt;<br /> <br /> Next call scheduled for March 6th at 10 am Central, 11 am Eastern, 1700 Germany.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Minutes&diff=6545 2008-02-21T19:01:12Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> * [[Minutes from 02/21/08 Conference Call]]<br /> * [[Minutes from 01/10/08 Conference Call]]<br /> * [[Minutes from 10/11/07 Conference Call]]<br /> * [[Minutes from 08/30/07 Conference Call]]<br /> * [[Minutes from 08/10/07 Conference Call]]<br /> * [[Minutes from 08/02/07 Conference Call]]<br /> * [[Minutes from 07/19/07 Conference Call]]<br /> * [[Minutes from 06/28/07 Conference Call]]<br /> * [[Minutes from 05/10/07 Conference Call]]<br /> * [[Minutes from 05/03/07 Conference Call]]<br /> * [[Minutes from 04/19/07 Conference Call]]<br /> * [[Minutes from 04/12/07 Conference Call]]</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=OCI:Main_Page&diff=6544 2008-02-21T18:59:00Z

<p>Hkhagler: /* Conference Call Information */</p> <hr /> <div>=OCI - Ontology for Clinical Investigations=<br /> <br /> ==About OCI==<br /> <br /> The goal of the OCI Working Group is to foster the creation and dissemination of a reference ontology (high-quality controlled structured vocabulary) for the annotation of the results of clinical trials.<br /> <br /> ==Recent Developments==<br /> <br /> ==Conference Call Information==<br /> * '''Next OCI conference call: Thursday, March 6 at 10am CST, 11am EST, 17:00 Germany, 14:00 UCT(GMT).'''<br /> * [[Conference Call Schedule]]<br /> * [[Call-in Information]]<br /> * [[Conference Call Agendas]]<br /> * [[Conference Call Minutes]]<br /> * [[Action Items]]<br /> <br /> ==Meetings==<br /> * [[Upcoming Meetings]]<br /> * [[Meetings Attended]]<br /> <br /> ==Communities and Working Group (WG) Participants==<br /> * [[OCI WG Chairs]]<br /> * [[OCI Curators]]<br /> * [[Other members of OCI WG]]<br /> <br /> ==Draft version of OCI==<br /> <br /> ==Ontology Development Items==<br /> * [[Design Principles]]<br /> * [[Term Lists]]<br /> * [[High-level Concepts]]<br /> * [[High-level Concepts v0.2]]<br /> * [[Initial OCI-OBI Mapping]]<br /> * [[OCI Term Compilation (Jennifer)]]<br /> * [[OBI v0.6.6 Schematic]]<br /> <br /> ==OCI Development Policies==<br /> * [[Ontology Metadata Policy (from OBI)]]<br /> * [[OCI Check-out Procedure Policy]]<br /> * [[OCI Working Group Membership Policy]]<br /> <br /> ==Publications==<br /> <br /> OCI Google group: http://groups.google.com/group/OCInv<br /> <br /> OCI Google mailing list: mailto:OCInv@googlegroups.com<br /> <br /> OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)<br /> <br /> ==OCI Wiki information==</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Schedule&diff=6543 2008-02-21T18:57:23Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> <br /> '''Meeting changes'''<br /> *NOTE Switch from 2 and 4 back to 1 and 3 Thursdays.<br /> *See Conference Call In info for new telecon phone number<br /> <br /> <br /> '''Scheduled meetings:'''<br /> *Next meeting March 6 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany<br /> *BIWEEKLY (every 1nd and 3th Thursday) starting March 6, 2008 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Schedule&diff=6542 2008-02-21T18:56:27Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> <br /> '''Meeting changes'''<br /> *NOTE Switch from 2 and 4 back to 1 and 3 Thursdays.<br /> <br /> <br /> '''Scheduled meetings:'''<br /> *Next meeting March 6 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany<br /> *BIWEEKLY (every 1nd and 3th Thursday) starting March 6, 2008 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Schedule&diff=6541 2008-02-21T18:43:31Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> <br /> '''Meeting changes'''<br /> *NO CALL on Thursday, December 27, 2007. Midwinter Holidays.<br /> <br /> <br /> '''Scheduled meetings:'''<br /> *Next meeting March 6 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany<br /> *BIWEEKLY (every 1nd and 3th Thursday) starting March 6, 2008 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Call-in_Information&diff=6540 2008-02-19T17:00:51Z

<p>Hkhagler: /* Alternate Dial In for UK (if above doesn't work) */</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> ==Conference Dial In Instructions (All Countries)==<br /> <br /> *1. Dial: 1.218.486.1600 (NOT Toll Free, Everyone pays long distance charges) This uses account with www.freeconference.com<br /> *2. Enter Entry Code: 831986 (followed by the # key)<br /> <br /> ==Conference Dial In Instructions for UK==<br /> <br /> *See previous section<br /> <br /> ==Alternate Dial In for UK (if above doesn't work)==<br /> *Presently no alternative available</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Call-in_Information&diff=6539 2008-02-19T17:00:20Z

<p>Hkhagler: /* Conference Dial In Instructions for UK */</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> ==Conference Dial In Instructions (All Countries)==<br /> <br /> *1. Dial: 1.218.486.1600 (NOT Toll Free, Everyone pays long distance charges) This uses account with www.freeconference.com<br /> *2. Enter Entry Code: 831986 (followed by the # key)<br /> <br /> ==Conference Dial In Instructions for UK==<br /> <br /> *See previous section<br /> <br /> ==Alternate Dial In for UK (if above doesn't work)==<br /> *1. Dial: 0-800-96-9130<br /> *2. Enter: 78076426<br /> *3. Enter Conference Entry Code: 53029 (followed by the # key)<br /> <br /> If you experience problems connecting, please call LINK Conference Service at 1.800.756.8280.<br /> If you will be calling in from somewhere outside of US, Canada or UK, please contact me to arrange for a toll-free dial in number.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Call-in_Information&diff=6538 2008-02-19T16:59:53Z

<p>Hkhagler: /* Conference Dial In Instructions (US/Canada) */</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> ==Conference Dial In Instructions (All Countries)==<br /> <br /> *1. Dial: 1.218.486.1600 (NOT Toll Free, Everyone pays long distance charges) This uses account with www.freeconference.com<br /> *2. Enter Entry Code: 831986 (followed by the # key)<br /> <br /> ==Conference Dial In Instructions for UK==<br /> <br /> *1. Dial: 00-800-000-32468<br /> *2. Enter: 488.893.204.601<br /> *3. Enter Conference Entry Code: 53029 (followed by the # key)<br /> <br /> ==Alternate Dial In for UK (if above doesn't work)==<br /> *1. Dial: 0-800-96-9130<br /> *2. Enter: 78076426<br /> *3. Enter Conference Entry Code: 53029 (followed by the # key)<br /> <br /> If you experience problems connecting, please call LINK Conference Service at 1.800.756.8280.<br /> If you will be calling in from somewhere outside of US, Canada or UK, please contact me to arrange for a toll-free dial in number.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Call-in_Information&diff=6537 2008-02-19T16:59:26Z

<p>Hkhagler: /* Conference Dial In Instructions (US/Canada) */</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> ==Conference Dial In Instructions (US/Canada)==<br /> <br /> *1. Dial: 1.218.486.1600 (NOT Toll Free, Everyone pays long distance charges) This uses account with www.freeconference.com<br /> *2. Enter Entry Code: 831986 (followed by the # key)<br /> <br /> ==Conference Dial In Instructions for UK==<br /> <br /> *1. Dial: 00-800-000-32468<br /> *2. Enter: 488.893.204.601<br /> *3. Enter Conference Entry Code: 53029 (followed by the # key)<br /> <br /> ==Alternate Dial In for UK (if above doesn't work)==<br /> *1. Dial: 0-800-96-9130<br /> *2. Enter: 78076426<br /> *3. Enter Conference Entry Code: 53029 (followed by the # key)<br /> <br /> If you experience problems connecting, please call LINK Conference Service at 1.800.756.8280.<br /> If you will be calling in from somewhere outside of US, Canada or UK, please contact me to arrange for a toll-free dial in number.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Agendas&diff=6421 2008-01-10T16:42:32Z

<p>Hkhagler: /* Conference Call Agendas */</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> = Conference Call Agendas =<br /> <br /> ==January 25, 2008==<br /> *Review Terms in Google Docs<br /> *Discuss Use Cases that are needed to match with the terms<br /> *Next Steps<br /> <br /> ==November 29==<br /> *Continue working on Google Docs Terms and Definitions&lt;br&gt;<br /> <br /> ==August 10==<br /> 1. Overview of the BRIDG project by Doug Fridsma&lt;br&gt;<br /> <br /> <br /> ==August 2==<br /> 1. Overview of the CDISC Terminology project by Bron Kisler&lt;br&gt;<br /> 2. Brief review of Jim Zhengs text mining approach for identifying clinical terms from clinical protocols&lt;br&gt;<br /> <br /> ==May 10==<br /> 1. Review the recent work that several people have added&lt;br&gt;<br /> 2. Review the goals and organization of the workshop&lt;br&gt;<br /> 3. Discuss how we think the CTO could be useful (use cases)&lt;br&gt;<br /> <br /> ==May 3==<br /> *Discussion of High-Level BFO-OBI Structure<br /> *Discussion of new added terms<br /> *Plans for CTO Workshop<br /> *Action items for the coming week<br /> <br /> ==April 19==<br /> '''1. Ontology of Biomedical Investigation'''<br /> *a. Overview of OBI core (Fostel, tentative)<br /> '''2. CTO development approach (with deadlines and milestones)'''<br /> *a. Goals for completion by May16th<br /> *b. Status of proposed steps<br /> **term list assembly<br /> **term list merging<br /> **term positioning into branches<br /> **term CTO definition<br /> '''3. High-level concept branches'''<br /> <br /> '''4. Others'''<br /> <br /> ==April 12==<br /> '''1. CTO Working Group (WG) Organization'''<br /> *a. Are current assignments acceptable?<br /> *b. Need a secretary<br /> *c. Responsibilities<br /> *d. Schedule of calls<br /> '''2. Development and WG policies in general'''<br /> *a. Draft metadata and CTO check-out policies<br /> *b. CTO WG membership policy<br /> '''3. Ontology Organization'''<br /> *a. Relationship with the BFO<br /> *b. Relationship with the OBI<br /> '''4. CTO scope'''<br /> *a. Definition of the CTO domain<br /> *b. Relationship with other ontologies<br /> '''5. CTO development approach (with deadlines and milestones)'''<br /> *a. Proposed steps<br /> **term list assembly<br /> **term list merging<br /> **term positioning into branches<br /> **term CTO definition<br /> *b. Goals for completion by May 16th<br /> *c. Managing discussion threads<br /> '''6. Information objects as dependent continuants (if time)'''</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=OCI:Main_Page&diff=6420 2008-01-10T16:39:56Z

<p>Hkhagler: /* Conference Call Information */</p> <hr /> <div>=OCI - Ontology for Clinical Investigations=<br /> <br /> ==About OCI==<br /> <br /> The goal of the OCI Working Group is to foster the creation and dissemination of a reference ontology (high-quality controlled structured vocabulary) for the annotation of the results of clinical trials.<br /> <br /> ==Recent Developments==<br /> <br /> ==Conference Call Information==<br /> * '''Next OCI conference call: Thursday, January 25 at 10am CST, 17:00 Germany, 14:00 UCT(GMT).'''<br /> * [[Conference Call Schedule]]<br /> * [[Call-in Information]]<br /> * [[Conference Call Agendas]]<br /> * [[Conference Call Minutes]]<br /> * [[Action Items]]<br /> <br /> ==Meetings==<br /> * [[Upcoming Meetings]]<br /> * [[Meetings Attended]]<br /> <br /> ==Communities and Working Group (WG) Participants==<br /> * [[OCI WG Chairs]]<br /> * [[OCI Curators]]<br /> * [[Other members of OCI WG]]<br /> <br /> ==Draft version of OCI==<br /> <br /> ==Ontology Development Items==<br /> * [[Design Principles]]<br /> * [[Term Lists]]<br /> * [[High-level Concepts]]<br /> * [[High-level Concepts v0.2]]<br /> * [[Initial OCI-OBI Mapping]]<br /> * [[OCI Term Compilation (Jennifer)]]<br /> * [[OBI v0.6.6 Schematic]]<br /> <br /> ==OCI Development Policies==<br /> * [[Ontology Metadata Policy (from OBI)]]<br /> * [[OCI Check-out Procedure Policy]]<br /> * [[OCI Working Group Membership Policy]]<br /> <br /> ==Publications==<br /> <br /> OCI Google group: http://groups.google.com/group/OCInv<br /> <br /> OCI Google mailing list: mailto:OCInv@googlegroups.com<br /> <br /> OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)<br /> <br /> ==OCI Wiki information==</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Schedule&diff=6419 2008-01-10T16:38:51Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> <br /> '''Meeting changes'''<br /> *NO CALL on Thursday, December 27, 2007. Midwinter Holidays.<br /> <br /> <br /> '''Scheduled meetings:'''<br /> *Next meeting January 25 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany<br /> *BIWEEKLY (every 2nd and 4th Thursday) starting December 13, 2007 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_01/10/08_Conference_Call&diff=6417 2008-01-10T16:37:57Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Jim Zheng, Jennifer Fostel, Herb Hagler&lt;br&gt;<br /> <br /> 1. Discussed the next steps&lt;br&gt;<br /> 2. Need to develop some use cases with the terms that have been collected to date&lt;br&gt;<br /> 3. Jim will contact his clinical trials group on his campus to gauge the support for this effort&lt;br&gt;<br /> 4. Herb will get with Richard and the new CTSA group. It may be possible to use the use cases that are being used as part of our RFP for a clinical trials management system.&lt;br&gt;<br /> 5. Question for Richard - Would it be possible to use some of the use cases developed for Immport? This may not be relevant...&lt;br&gt;<br /> 6. Plan on going over more terms next time.&lt;br&gt;<br /> <br /> Next call scheduled for January 24th at regular time, 10 am Central, 11 am Eastern, 1700 Germany.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_01/10/08_Conference_Call&diff=6416 2008-01-10T16:37:15Z

<p>Hkhagler: New page: Go back to OCI:Main Page Present on the call: Jim Zheng, Jennifer Fostel, Herb Hagler&lt;br&gt; 1. Discussed the next steps 2. Need to develop some use cases with the terms that have been...</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Jim Zheng, Jennifer Fostel, Herb Hagler&lt;br&gt;<br /> <br /> 1. Discussed the next steps<br /> 2. Need to develop some use cases with the terms that have been collected to date<br /> 3. Jim will contact his clinical trials group on his campus to gauge the support for this effort<br /> 4. Herb will get with Richard and the new CTSA group. It may be possible to use the use cases that are being used as part of our RFP for a clinical trials management system.<br /> 5. Question for Richard - Would it be possible to use some of the use cases developed for Immport? This may not be relevant...<br /> 6. Plan on going over more terms next time.<br /> <br /> Next call scheduled for January 24th at regular time, 10 am Central, 11 am Eastern, 1700 Germany.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Minutes&diff=6415 2008-01-10T16:30:35Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> * [[Minutes from 01/10/08 Conference Call]]<br /> * [[Minutes from 10/11/07 Conference Call]]<br /> * [[Minutes from 08/30/07 Conference Call]]<br /> * [[Minutes from 08/10/07 Conference Call]]<br /> * [[Minutes from 08/02/07 Conference Call]]<br /> * [[Minutes from 07/19/07 Conference Call]]<br /> * [[Minutes from 06/28/07 Conference Call]]<br /> * [[Minutes from 05/10/07 Conference Call]]<br /> * [[Minutes from 05/03/07 Conference Call]]<br /> * [[Minutes from 04/19/07 Conference Call]]<br /> * [[Minutes from 04/12/07 Conference Call]]</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Agendas&diff=6323 2007-11-19T16:25:38Z

<p>Hkhagler: /* Conference Call Agendas */</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> = Conference Call Agendas =<br /> <br /> ==November 29==<br /> *Continue working on Google Docs Terms and Definitions&lt;br&gt;<br /> <br /> ==August 10==<br /> 1. Overview of the BRIDG project by Doug Fridsma&lt;br&gt;<br /> <br /> <br /> ==August 2==<br /> 1. Overview of the CDISC Terminology project by Bron Kisler&lt;br&gt;<br /> 2. Brief review of Jim Zhengs text mining approach for identifying clinical terms from clinical protocols&lt;br&gt;<br /> <br /> ==May 10==<br /> 1. Review the recent work that several people have added&lt;br&gt;<br /> 2. Review the goals and organization of the workshop&lt;br&gt;<br /> 3. Discuss how we think the CTO could be useful (use cases)&lt;br&gt;<br /> <br /> ==May 3==<br /> *Discussion of High-Level BFO-OBI Structure<br /> *Discussion of new added terms<br /> *Plans for CTO Workshop<br /> *Action items for the coming week<br /> <br /> ==April 19==<br /> '''1. Ontology of Biomedical Investigation'''<br /> *a. Overview of OBI core (Fostel, tentative)<br /> '''2. CTO development approach (with deadlines and milestones)'''<br /> *a. Goals for completion by May16th<br /> *b. Status of proposed steps<br /> **term list assembly<br /> **term list merging<br /> **term positioning into branches<br /> **term CTO definition<br /> '''3. High-level concept branches'''<br /> <br /> '''4. Others'''<br /> <br /> ==April 12==<br /> '''1. CTO Working Group (WG) Organization'''<br /> *a. Are current assignments acceptable?<br /> *b. Need a secretary<br /> *c. Responsibilities<br /> *d. Schedule of calls<br /> '''2. Development and WG policies in general'''<br /> *a. Draft metadata and CTO check-out policies<br /> *b. CTO WG membership policy<br /> '''3. Ontology Organization'''<br /> *a. Relationship with the BFO<br /> *b. Relationship with the OBI<br /> '''4. CTO scope'''<br /> *a. Definition of the CTO domain<br /> *b. Relationship with other ontologies<br /> '''5. CTO development approach (with deadlines and milestones)'''<br /> *a. Proposed steps<br /> **term list assembly<br /> **term list merging<br /> **term positioning into branches<br /> **term CTO definition<br /> *b. Goals for completion by May 16th<br /> *c. Managing discussion threads<br /> '''6. Information objects as dependent continuants (if time)'''</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Schedule&diff=6322 2007-11-19T15:49:17Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> <br /> '''Meeting changes'''<br /> *NO CALL on Thursday, December 27, 2007. Midwinter Holidays.<br /> <br /> <br /> '''Scheduled meetings:'''<br /> *Next meeting November 29 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany<br /> *BIWEEKLY (every 2nd and 4th Thursday) starting December 13, 2007 at 8:00am PST, 10:00am CST, 11:00am EST, 5:00pm Germany</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=OCI:Main_Page&diff=6321 2007-11-19T15:42:44Z

<p>Hkhagler: /* Conference Call Information */</p> <hr /> <div>=OCI - Ontology for Clinical Investigations=<br /> <br /> ==About OCI==<br /> <br /> The goal of the OCI Working Group is to foster the creation and dissemination of a reference ontology (high-quality controlled structured vocabulary) for the annotation of the results of clinical trials.<br /> <br /> ==Recent Developments==<br /> <br /> ==Conference Call Information==<br /> * '''Next OCI conference call: Thursday, November 29 at 10am CST, 17:00 Germany, 14:00 UCT(GMT).'''<br /> * [[Conference Call Schedule]]<br /> * [[Call-in Information]]<br /> * [[Conference Call Agendas]]<br /> * [[Conference Call Minutes]]<br /> * [[Action Items]]<br /> <br /> ==Meetings==<br /> * [[Upcoming Meetings]]<br /> * [[Meetings Attended]]<br /> <br /> ==Communities and Working Group (WG) Participants==<br /> * [[OCI WG Chairs]]<br /> * [[OCI Curators]]<br /> * [[Other members of OCI WG]]<br /> <br /> ==Draft version of OCI==<br /> <br /> ==Ontology Development Items==<br /> * [[Design Principles]]<br /> * [[Term Lists]]<br /> * [[High-level Concepts]]<br /> * [[High-level Concepts v0.2]]<br /> * [[Initial CTO-OBI Mapping]]<br /> * [[OCI Term Compilation (Jennifer)]]<br /> * [[OBI v0.6.6 Schematic]]<br /> <br /> ==OCI Development Policies==<br /> * [[Ontology Metadata Policy (from OBI)]]<br /> * [[OCI Check-out Procedure Policy]]<br /> * [[OCI Working Group Membership Policy]]<br /> <br /> ==Publications==<br /> <br /> OCI Google group: http://groups.google.com/group/OCInv<br /> <br /> OCI Google mailing list: mailto:OCInv@googlegroups.com<br /> <br /> OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)<br /> <br /> ==OCI Wiki information==</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=OCI:Main_Page&diff=6169 2007-10-19T15:53:27Z

<p>Hkhagler: /* Conference Call Information */</p> <hr /> <div>=OCI - Ontology for Clinical Investigations=<br /> <br /> ==About OCI==<br /> <br /> The goal of the OCI Working Group is to foster the creation and dissemination of a reference ontology (high-quality controlled structured vocabulary) for the annotation of the results of clinical trials.<br /> <br /> ==Recent Developments==<br /> <br /> ==Conference Call Information==<br /> * '''Next OCI conference call: Thursday, November 1 at 10am CDT, 15:00 UCT(GMT).'''<br /> * [[Conference Call Schedule]]<br /> * [[Call-in Information]]<br /> * [[Conference Call Agendas]]<br /> * [[Conference Call Minutes]]<br /> * [[Action Items]]<br /> <br /> ==Meetings==<br /> * [[Upcoming Meetings]]<br /> * [[Meetings Attended]]<br /> <br /> ==Communities and Working Group (WG) Participants==<br /> * [[OCI WG Chairs]]<br /> * [[OCI Curators]]<br /> * [[Other members of OCI WG]]<br /> <br /> ==Draft version of OCI==<br /> <br /> ==Ontology Development Items==<br /> * [[Design Principles]]<br /> * [[Term Lists]]<br /> * [[High-level Concepts]]<br /> * [[High-level Concepts v0.2]]<br /> * [[Initial CTO-OBI Mapping]]<br /> * [[OCI Term Compilation (Jennifer)]]<br /> * [[OBI v0.6.6 Schematic]]<br /> <br /> ==OCI Development Policies==<br /> * [[Ontology Metadata Policy (from OBI)]]<br /> * [[OCI Check-out Procedure Policy]]<br /> * [[OCI Working Group Membership Policy]]<br /> <br /> ==Publications==<br /> <br /> OCI Google group: http://groups.google.com/group/OCInv<br /> <br /> OCI Google mailing list: mailto:OCInv@googlegroups.com<br /> <br /> OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)<br /> <br /> ==OCI Wiki information==</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Action_items_from_10/11/07_call&diff=6151 2007-10-12T20:31:28Z

<p>Hkhagler: New page: Go back to OCI:Main Page '''Action Items to be completed for next Telecon 10-18-2007''' * Jennifer post spreadsheet on Google Docs combining her terms with Jim's algorithm processed t...</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> '''Action Items to be completed for next Telecon 10-18-2007'''<br /> * Jennifer post spreadsheet on Google Docs combining her terms with Jim's algorithm processed terms<br /> * Each group member pick a column 1-6, place their initials, and assign OBI branches</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Action_Items&diff=6150 2007-10-12T20:29:03Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> <br /> *[[Action items from 10/11/07 call]]<br /> *[[Action items from 05/10/07 call]]<br /> *[[Action items from 05/03/07 call]]<br /> *[[Action items from 04/19/07 call]]</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_10/11/07_Conference_Call&diff=6149 2007-10-12T20:27:45Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Jim Zheng, Christian Cocos, Jennifer Fostel, Richard Scheuermann, Herb Hagler&lt;br&gt;<br /> <br /> 1. Discussion of merging Jennifer's term list with Jim's algorithm. Prioritize by CDISC then STDM terms. Jennifer has posted on google docs a spreadsheet with Jim's terms alligned with Jennifer's. Everyone should edit the google doc online, place their initials in the column 1-6 and indicate the OBI branch that best represents each term's placement. Try to complete this before next week's meeting.&lt;br&gt;<br /> 2. Richard's report -&lt;br&gt;<br /> I wanted to give you all a quick summary of two recent meetings that I attended that are relevant to the OCI project.<br /> <br /> A. A week ago Friday I attended a clinical research data standards workshop hosted by Chris Chute at Mayo for the CTSA informatics groups. There were several presentations related to existing and emerging data standards of interest to the clinical and translational research communities, including HL7RIM, CDISC, caBIG, OCRe, NCI EVS, and BRIDG. The Ontology of Clinical Research (OCRe) is a completing effort being lead by Ida Sim to represent the clinical research domain. Toward the end of the meeting, the group discussed the possibility of working together on a well-defined data standards project that would be potentially valuable in support of data interoperability. We decided to try to work on the structuring of clinical trial registry data as it relates to the WHO CONSORT checklist (see attachment). Ida will be leading the effort, but I will also be actively involved. I'd like to discuss this further during our call this week.<br /> <br /> B. Last week I presented OCI at the CDISC International Interchange Workshop (also attached). Although the content was quite a bit more abstract in comparison with the other presentations, I think that it generated a fair amount of interest in the audience since several speakers mentioned the talk in their presentations and ontologies as the future direction for their terminology standards. I think we may be able to leverage the work that we might do on the CONSORT checklist as a mechanism for collaboration with the CDISC Terminology community. Again, another topic for discussion on Thursday.&lt;br&gt;<br /> <br /> 3. Discussed Item A. above and everyone agreed that working on the Clinical Trial Registry Data would be a good place to start completing the term list annotation.&lt;br&gt;<br /> 4. Discussed Item B. above and will wait for Ida's white paper regarding CONSORT checklist.&lt;br&gt;<br /> 5. Jim's algorithm <br /> <br /> Next call scheduled for October 18th at regular time.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_10/11/07_Conference_Call&diff=6148 2007-10-12T20:25:26Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Jim Zheng, Christian Cocos, Jennifer Fostel, Richard Scheuermann, Herb Hagler&lt;br&gt;<br /> <br /> 1. Discussion of merging Jennifer's term list with Jim's algorythm. Prioritize by CDISC then STDM terms. Jennifer has posted on google docs a spreadsheet with Jim's terms alligned with Jennifer's. Everyone should edit the google doc online, place their initials in the column 1-6 and indicate the OBI branch that best represents each term's placement. Try to complete this before next week's meeting.&lt;br&gt;<br /> 2. Richard's report -&lt;br&gt;<br /> I wanted to give you all a quick summary of two recent meetings that I attended that are relevant to the OCI project.<br /> <br /> A. A week ago Friday I attended a clinical research data standards workshop hosted by Chris Chute at Mayo for the CTSA informatics groups. There were several presentations related to existing and emerging data standards of interest to the clinical and translational research communities, including HL7RIM, CDISC, caBIG, OCRe, NCI EVS, and BRIDG. The Ontology of Clinical Research (OCRe) is a completing effort being lead by Ida Sim to represent the clinical research domain. Toward the end of the meeting, the group discussed the possibility of working together on a well-defined data standards project that would be potentially valuable in support of data interoperability. We decided to try to work on the structuring of clinical trial registry data as it relates to the WHO CONSORT checklist (see attachment). Ida will be leading the effort, but I will also be actively involved. I'd like to discuss this further during our call this week.<br /> <br /> B. Last week I presented OCI at the CDISC International Interchange Workshop (also attached). Although the content was quite a bit more abstract in comparison with the other presentations, I think that it generated a fair amount of interest in the audience since several speakers mentioned the talk in their presentations and ontologies as the future direction for their terminology standards. I think we may be able to leverage the work that we might do on the CONSORT checklist as a mechanism for collaboration with the CDISC Terminology community. Again, another topic for discussion on Thursday.&lt;br&gt;<br /> <br /> 3. Discussed Item A. above and everyone agreed that working on the Clinical Trial Registry Data would be a good place to start completing the term list annotation.<br /> Next call scheduled for October 18th at regular time.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_10/11/07_Conference_Call&diff=6147 2007-10-12T20:21:56Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Jim Zheng, Christian Cocos, Jennifer Fostel, Richard Scheuermann, Herb Hagler&lt;br&gt;<br /> <br /> 1. Discussion of merging Jennifer's term list with Jim's algorythm. Prioritize by CDISC then STDM terms. Jennifer has posted on google docs a spreadsheet with Jim's terms alligned with Jennifer's. Everyone should edit the google doc online, place their initials in the column 1-6 and indicate the OBI branch that best represents each term's placement.&lt;br&gt;<br /> 2. Richard's report -&lt;br&gt;<br /> I wanted to give you all a quick summary of two recent meetings that I attended that are relevant to the OCI project.<br /> <br /> 1. A week ago Friday I attended a clinical research data standards workshop hosted by Chris Chute at Mayo for the CTSA informatics groups. There were several presentations related to existing and emerging data standards of interest to the clinical and translational research communities, including HL7RIM, CDISC, caBIG, OCRe, NCI EVS, and BRIDG. The Ontology of Clinical Research (OCRe) is a completing effort being lead by Ida Sim to represent the clinical research domain. Toward the end of the meeting, the group discussed the possibility of working together on a well-defined data standards project that would be potentially valuable in support of data interoperability. We decided to try to work on the structuring of clinical trial registry data as it relates to the WHO CONSORT checklist (see attachment). Ida will be leading the effort, but I will also be actively involved. I'd like to discuss this further during our call this week.<br /> <br /> 2. Last week I presented OCI at the CDISC International Interchange Workshop (also attached). Although the content was quite a bit more abstract in comparison with the other presentations, I think that it generated a fair amount of interest in the audience since several speakers mentioned the talk in their presentations and ontologies as the future direction for their terminology standards. I think we may be able to leverage the work that we might do on the CONSORT checklist as a mechanism for collaboration with the CDISC Terminology community. Again, another topic for discussion on Thursday.<br /> <br /> Next call scheduled for October 18th.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_10/11/07_Conference_Call&diff=6146 2007-10-12T20:15:28Z

<p>Hkhagler: New page: Go back to OCI:Main Page Present on the call: Jim Zheng, Wenle Zhao, Jennifer Fostel, Richard Scheuermann&lt;br&gt; &lt;br&gt; Next call scheduled for October 18th.</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Jim Zheng, Wenle Zhao, Jennifer Fostel, Richard Scheuermann&lt;br&gt;<br /> <br /> &lt;br&gt;<br /> <br /> Next call scheduled for October 18th.</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Minutes&diff=6145 2007-10-12T20:13:41Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> * [[Minutes from 10/11/07 Conference Call]]<br /> * [[Minutes from 08/30/07 Conference Call]]<br /> * [[Minutes from 08/10/07 Conference Call]]<br /> * [[Minutes from 08/02/07 Conference Call]]<br /> * [[Minutes from 07/19/07 Conference Call]]<br /> * [[Minutes from 06/28/07 Conference Call]]<br /> * [[Minutes from 05/10/07 Conference Call]]<br /> * [[Minutes from 05/03/07 Conference Call]]<br /> * [[Minutes from 04/19/07 Conference Call]]<br /> * [[Minutes from 04/12/07 Conference Call]]</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Schedule&diff=6144 2007-10-12T20:12:46Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> <br /> '''Meeting changes'''<br /> *NO CALL on Thursday, April 26, 2007. Action items to be accomplished via wiki and email.<br /> *NO CALL on Thursday, July 12, 2007 (OBI meeting).<br /> *ADDED CALL on Friday, August 10, 2007 at 12:00 noon EDT. Doug Fridsma will be presenting an overview of BRIDG.<br /> <br /> <br /> '''Scheduled meetings:'''<br /> *BIWEEKLY (every other Thursday) starting August 2, 2007 at 9:00am PST, 11:00am CST, noon EST, 6:00pm Germany<br /> *BIWEEKLY (every other Thursday) starting November 1, 2007 at 8:00am PST, 10:00am CST, 11am EST, 5:00pm Germany (provided conference number is available)</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=OCI:Main_Page&diff=6143 2007-10-12T20:11:34Z

<p>Hkhagler: /* Conference Call Information */</p> <hr /> <div>=OCI - Ontology for Clinical Investigations=<br /> <br /> ==About OCI==<br /> <br /> The goal of the OCI Working Group is to foster the creation and dissemination of a reference ontology (high-quality controlled structured vocabulary) for the annotation of the results of clinical trials.<br /> <br /> ==Recent Developments==<br /> <br /> ==Conference Call Information==<br /> * '''Next OCI conference call: Thursday, October 18 at 11am CDT.'''<br /> * [[Conference Call Schedule]]<br /> * [[Call-in Information]]<br /> * [[Conference Call Agendas]]<br /> * [[Conference Call Minutes]]<br /> * [[Action Items]]<br /> <br /> ==Meetings==<br /> * [[Upcoming Meetings]]<br /> * [[Meetings Attended]]<br /> <br /> ==Communities and Working Group (WG) Participants==<br /> * [[OCI WG Chairs]]<br /> * [[OCI Curators]]<br /> * [[Other members of OCI WG]]<br /> <br /> ==Draft version of OCI==<br /> <br /> ==Ontology Development Items==<br /> * [[Design Principles]]<br /> * [[Term Lists]]<br /> * [[High-level Concepts]]<br /> * [[High-level Concepts v0.2]]<br /> * [[Initial CTO-OBI Mapping]]<br /> * [[OCI Term Compilation (Jennifer)]]<br /> * [[OBI v0.6.6 Schematic]]<br /> <br /> ==OCI Development Policies==<br /> * [[Ontology Metadata Policy (from OBI)]]<br /> * [[OCI Check-out Procedure Policy]]<br /> * [[OCI Working Group Membership Policy]]<br /> <br /> ==Publications==<br /> <br /> OCI Google group: http://groups.google.com/group/OCInv<br /> <br /> OCI Google mailing list: mailto:OCInv@googlegroups.com<br /> <br /> OCI SVN repository: http://cto.googlecode.com/svn/trunk/CTO.owl (save as CTO.owl)<br /> <br /> ==OCI Wiki information==</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_08/10/07_Conference_Call&diff=5909 2007-08-17T21:19:54Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Bron Kisler, Jim Zheng, Jennifer Fostel, Richard Scheuermann, Herb Hagler and Richard's Lab<br /> <br /> OCI Conference Call with Doug Fridsma M.D., Ph.D.<br /> <br /> Presenting: BRIDG: A Model to support interoperability in Clinical Research<br /> <br /> Doug Fridsma's presentation can be Downloaded here: http://pathcuric1.swmed.edu/Research/haglerdocs/Fridsma2007-08-OCI-Presentation-v2.ppt<br /> <br /> --------The following notes were compiled by several people present during the presentation<br /> ---------<br /> <br /> “ You can’t build a skyscraper by nailing together 10,000 dog houses.” Grady Booch<br /> <br /> There is a need for a blueprint to support clinical research.<br /> <br /> Agenda<br /> *Why do we need BRIDG?<br /> *Why is BRIDG?<br /> *What are the lessons learned<br /> *Does it work?<br /> *Current Status<br /> <br /> Clinical and Translational research is complex systems of organizations. You must know the definition of data and the process of care. All Clinical Trials must work in a single enterprise. But Clinical and translational data must be able to interoperate with the larger research enterprise. Standardization and the ability to hand off the data are critical to innovation. Ultimately to be successful information must pass not only with in organizations but also between organizations<br /> <br /> What are we trying to do?<br /> *To define implementation-independent domain semantics (define the what and the how of clinical research)<br /> *To uncover the myriad of semantic ambiguities present in the complex domain of clinical research<br /> *To build a foundation for achieving computable semantic interoperability<br /> <br /> BRIDG supports the syntactic with links to the semantics.<br /> *The ability of multiple systems to exchange information and to be able to use the information that has been exchanged.<br /> <br /> What is BRIDG?<br /> Biomedical Research Integrated Domain Group<br /> <br /> *A model of the shared semantics of regulated clinical research<br /> *A communication bridge between<br /> *Clinical research domain experts and technical experts<br /> *Different models of clinical research information (EPOCH-BRIDG)<br /> *An open community of stakeholders interested in developing standards for exchanging information about clinical research<br /> *HL7, NCI, CDISC, FDA, ITN<br /> *The semantic foundation for application and message development in HL7, caBIG, and CDISC<br /> *A foundation for research in knowledge representation and semantic interoperability<br /> <br /> How is BRDIG funded? Thru caBIG and NCI and some pharma companies.<br /> <br /> Two important streams of development that have been brought together into a collaborative framework<br /> *CDISC – 2003, started constructing an analysis model to map ODM standards to HL7<br /> *NCI – 2004, started caBIG initiative to construct a structured protocol representation and interoperability among clinical research in cancer<br /> <br /> Desiderata<br /> *Did not want to construct “Yet another standard…”<br /> *The good thing about standards is there are so many to choose from…<br /> *Open-source<br /> *Modeled processes and organization after other successful open-source projects Mozilla, Firefox, Linux, etc<br /> *Model is small groups (Technical Harmonization Committee), vet in large groups (Advisory Board)<br /> *Provide a mechanism to scale the development work<br /> *Parallelize the development<br /> *Prevent collaborators from “colliding” with each other<br /> <br /> Allow us do the modeling in the open<br /> <br /> In the BRIDG project, we have tried to operationalize the collaborative models required for roadmap initiatives <br /> <br /> Current classes of core elements- Conceptual Domains<br /> <br /> *Noun things - Organization, People<br /> *Role things - PIs<br /> *Do things - Participate <br /> *Happening things - Milestones<br /> *Measurement things - Things you measure<br /> *Interpretation things - Low Blood Count<br /> *Documentation things - Consent…<br /> <br /> This is conceptual to HL7 RIM as well.<br /> <br /> The Communications conundrum<br /> *Experts know about the how to do clinical research but don’t understand how to build software<br /> <br /> *Technologists understand how to build software but don’t understand the intricacies of the clinical environments and clinical research<br /> *Any implementation (i.e. solution) is a compromise of the original problem statement<br /> *Compromises must be chosen wisely<br /> *Should be based on a deep understanding of the problem and a dialogue between Problem Space and Solution Space Experts<br /> <br /> The Communication Pyramid<br /> This is formal Specification of requirements. It must be bi-directional Semantic traceability before they can be balloted.<br /> <br /> Current Collaborators<br /> *HL7<br /> Official domain analysis model for the HL7 RCRIM technical committee<br /> *All HL7 messages must be able to demonstrate “bi-directional semantic traceability” before they can be balloted<br /> <br /> *CDISC<br /> The integrative model for all current CDISC standards<br /> *FDA<br /> Developing an HL7 message based on CDISC SDTM in with the RFA requires capturing the semantics in BRIDG<br /> Regulated Product Submission (RPS) is the next HL7/FDA message to use BRIDG<br /> *Immune Tolerance Network (ITN)<br /> *Using BRIDG to integrate open-source caBIG tools with existing MDA applications<br /> caBIG<br /> *Utilized as framework for NCI’s caBIG™ (standard within CTMS WS)<br /> *Additional non-CTMS semantics (e.g. FireBird, CDUS, etc.) being incorporated<br /> <br /> <br /> BRIDG uses a complex process to harmonize. Using the STDM Implementation Guide and Model. They look at definitions level and fold into BRIDG. This may create two classes. The outcome is a mapping spreadsheet. Then they add things not present. Then they ask, “Here is A and B, describe how they are different”. <br /> <br /> We look at CDISC Terminology and look at the NCI definitions in terms of BRIDG and you may of may not have to create definitions and you may or may not have to harmonize for CDISC or NCI<br /> <br /> OBI has a similar process. OBI looked at having two definitions for the same term and quickly decided that was a recipe for disaster.<br /> <br /> Pilot Study mapping BRIDG to EPOCH<br /> This looked at the semantic alignment. They had to overcome both language and choice mismatch.<br /> BRIDG<br /> HL7, caBIG, CDISC stakeholders<br /> Developed collaboratively with stakeholders<br /> Shared domain model for protocol-driven clinical research<br /> Comprehensive<br /> Consensus-based<br /> Abstract and context neutral<br /> EPOCH<br /> Immune Tolerance Network (ITN)<br /> International collaborative research effort that sponsors clinical trials and mechanistic assays on immune tolerance<br /> EPOCH clinical trial model<br /> Developed at Stanford Medical Informatics<br /> Designed to provide semantic foundation for management of clinical trials<br /> Approach taken<br /> Semantic alignment<br /> Use Excel spreadsheet to systematically review and document possible mappings<br /> Define necessary preconditions for mapping<br /> Overcoming representation language mismatch <br /> Overcoming representation choice mismatches<br /> <br /> We had to understand the definitions to harmonize<br /> Subclass of Larger class must be careful to not get into trouble. Can do this in one direction, but can’t always do in the other which is problematic.<br /> <br /> Semantic Alignment: Restrictions on EPOCH<br /> *Mapping from EPOCH to BRIDG =&gt; Place restrictions on EPOCH<br /> *Only one schedule of activities<br /> *Period has no subperiods<br /> *Limited temporal annotations<br /> <br /> The EPOCH representation is in OWL, the BRIDG representation in UML.<br /> There is a representation of BRIDG in OWL for EPOCH. There may be some circumstances to use this version.<br /> <br /> This pilot demonstrated that we could overcome these mismatches.<br /> The BRIDG –EPOCH model has a notion of period that map as screening in EPOCH.<br /> <br /> SWRL rules were used to write formal rules. The Herold Protocol in EPOCH successfully used EPOCH in a Clinical Trial <br /> <br /> Successfully used an EPOCH clinical trial to configure BRIDG Patient Study Calendar application<br /> Automated mappings except for one relationship<br /> Because of OWL/SWRL’s open-world assumption, First epoch cannot be derived as an epoch that has no predecessor <br /> <br /> Pilot Conclusion<br /> Semantic interoperability requires<br /> Harmonization of subsets of ontologies/models<br /> Overcoming mismatches in representation languages and representation choices<br /> OWL restrictions and SWRL rules help to overcome semantic and syntactic mismatches<br /> Possible future work<br /> Continued harmonization of BRIDG/EPOCH<br /> Scalability and (semi-)automation of method<br /> <br /> What lessons have we learned?<br /> 1. Scope – keep it clear and focused (i.e., solve a problem that exists) and standardize to the extend needed<br /> *Keep the model generic, faithful, free of implementation-specific formalisms, and supporting the requirements<br /> *Refine through experience, and not endless discussions<br /> <br /> The domain of the regulated clinical research information management technical committee in HL7:<br /> Protocol-Driven Research with human, animal or device subjects, plus appropriate associated regulatory documentation.<br /> <br /> *Analysis-level semantics<br /> *Business processes<br /> *Static structures<br /> <br /> Use-case driven <br /> *n-scope and out-of-scope determined by the use-case <br /> <br /> Does not include vocabulary or terminology choices<br /> BRIDGCodedConcept Datatype links to other “places” where domain semantics can be represented<br /> Area of active research in understanding how ontologies and information models “link” to vocabularies and terminologies<br /> 2. Understand the difference between consensus, abstraction, and harmonization<br /> Consensus:<br /> *Consensus statements often achieve agreement through being ambiguous<br /> United Nations, guideline consensus statements<br /> <br /> Abstraction:<br /> *generalized models that are useful for a broad range of different domains (HL7 RIM)<br /> *definitions are abstract, domain independent (although specific to an implementation) and more helpful for implementation than they are for domain experts<br /> <br /> Harmonization:<br /> *Creating definitions that all experts agree on, creating distinctions between concepts to clarify the semantics when they don’t agree, and imbedding those semantics in the business processes<br /> *Harmonize concepts not words<br /> <br /> 3.Models are only a piece of the puzzle<br /> *Datatypes, vocabularies and terminologies provide additional clarification of the semantics<br /> 4.Use a larger development framework to organize, iterate, and trace the semantics<br /> Provides a mechanism to integrate multiple projects, manage change<br /> <br /> 5. Translational research is a cycle.<br /> <br /> In BRIDG: Process Matters<br /> Modeled on open-source software development initiatives<br /> Scalable processes to support coordination and collaboration across multiple modeling groups<br /> Organizational structure with stakeholder representation<br /> Focus on semantics, not representation or implementation allows for variation around a common model<br /> <br /> 6.The importance of capturing dynamic semantics (activities) of clinical trials research<br /> Clarifies the data and concept definitions<br /> Provides the context for use of the data structures<br /> Sets the stage for a service-oriented architecture<br /> <br /> Recent Experience With BRIDG:<br /> The CTMS WS Interoperability Project (1)<br /> Goal: In 9 weeks (including Holidays), build interoperable support for three Use Cases across five applications in the Clinical Trial Management System (CTMS) Work Space<br /> Use Cases to be defined by group of SMEs as ‘pain points’<br /> Applications include:<br /> *Patient Study Calendar<br /> *Static model has been harmonized with BRIDG<br /> *Lab Hub<br /> *Static model has been harmonized with BRIDG<br /> *Adverse Event Reporting System<br /> *Application development began concurrent with Interoperability Project<br /> *Early analysis work already done and compliant with BRIDG<br /> *Patient/Clinical Trial Registry<br /> *Repository of links between patients and trials<br /> *COT CTDMS (Oracle Clinical)<br /> *Trial repository – export capability only<br /> <br /> The CTMS WS Interoperability Project (2)<br /> Process: Iterative/Incremental SEP utilizing BRIDG as DAM<br /> *Two one-month iterations<br /> *Limited ability to change existing code base<br /> *Process began with Business Modeling<br /> *Activity Diagrams for each Use Case mapped to BRIDG<br /> *“BRIDG Extract” generated based on AD → BRIDG mapping<br /> *BRIDG Extract → XMI → analysis-level XSD → implementation-level XSM (“common wire format”)<br /> – short time-line → no ‘formal’ messaging structures (V3 messages will be developed at a future date)<br /> <br /> The Conclusion: The project could not have succeed without the use of a DAM<br /> The previous harmonization/common application of BRIDG by 3/5 of the applications (and the ability of the other 2 applications to map appropriate static structures to BRIDG) enabled the project to succeed<br /> <br /> Current Status<br /> *BRIDG is no longer a modeling exercise, but a robust model used by <br /> the National Cancer Institute for all application development<br /> *Commercial clinical trials software developers<br /> *CDISC to unify their existing models<br /> *HL7 for all HL7 messages related to clinical trials research<br /> *FDA for electronic data submission standards<br /> *Other collaborators (immune tolerance network) to integrate applications and clinical trials work processes<br /> BRIDG release V1 – June, 2007 Download: http://gforge.nci.nih.gov/frs/?group_id=342<br /> <br /> In the process we have <br /> *Developed generalizable scaleable processes to support collaboration across organizations, models, and domains<br /> *Begun to understand how to overcoming semantic and representational differences between different ontologies and terminologies<br /> <br /> Value of analysis modeling for semantic interoperability<br /> If you understand<br /> *The processes (activities) that you do within your organization to support clinical and translational research<br /> *The information (data) that you use for these activities<br /> You can <br /> *Reduce redundancy in your organization<br /> *Redesign organizational processes <br /> *Know what to share (and what not to)<br /> *Integrate custom and commercial applications (you know where they fit in your organizational activities and data)<br /> *Create a shared understanding of the work of clinical trials research (facilitates “culture change”)<br /> <br /> This becomes critical for any program in which you want to <br /> *Exchange data between different disciplines (translational research)<br /> *Clinical trials and translational programs (CTSA)<br /> <br /> <br /> ==Action Items/Future Work identified during and after the teleconference:==<br /> <br /> #Application of BRIDG and evaluate the model and get a paper out<br /> #Subject Eligibility as a trial piece for the modeling exercise at UT Southwestern<br /> #CDISC vocabulary and Ontology<br /> #Concept Paper (Barry as a probable co-author) CDISC-BRIDG-Ontolgy integration</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_08/10/07_Conference_Call&diff=5908 2007-08-17T21:19:25Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Bron Kisler, Jim Zheng, Jennifer Fostel, Richard Scheuermann, Herb Hagler and Richard's Lab<br /> <br /> OCI Conference Call with Doug Fridsma M.D., Ph.D.<br /> <br /> Presenting: BRIDG: A Model to support interoperability in Clinical Research<br /> <br /> Doug Fridsma's presentation can be Downloaded here: http://pathcuric1.swmed.edu/Research/haglerdocs/Fridsma2007-08-OCI-Presentation-v2.ppt<br /> <br /> --------The following notes were compiled by several people present during the presentation<br /> ---------<br /> <br /> “ You can’t build a skyscraper by nailing together 10,000 dog houses.” Grady Booch<br /> <br /> There is a need for a blueprint to support clinical research.<br /> <br /> Agenda<br /> *Why do we need BRIDG?<br /> *Why is BRIDG?<br /> *What are the lessons learned<br /> *Does it work?<br /> *Current Status<br /> <br /> Clinical and Translational research is complex systems of organizations. You must know the definition of data and the process of care. All Clinical Trials must work in a single enterprise. But Clinical and translational data must be able to interoperate with the larger research enterprise. Standardization and the ability to hand off the data are critical to innovation. Ultimately to be successful information must pass not only with in organizations but also between organizations<br /> <br /> What are we trying to do?<br /> *To define implementation-independent domain semantics (define the what and the how of clinical research)<br /> *To uncover the myriad of semantic ambiguities present in the complex domain of clinical research<br /> *To build a foundation for achieving computable semantic interoperability<br /> <br /> BRIDG supports the syntactic with links to the semantics.<br /> *The ability of multiple systems to exchange information and to be able to use the information that has been exchanged.<br /> <br /> What is BRIDG?<br /> Biomedical Research Integrated Domain Group<br /> <br /> *A model of the shared semantics of regulated clinical research<br /> *A communication bridge between<br /> *Clinical research domain experts and technical experts<br /> *Different models of clinical research information (EPOCH-BRIDG)<br /> *An open community of stakeholders interested in developing standards for exchanging information about clinical research<br /> *HL7, NCI, CDISC, FDA, ITN<br /> *The semantic foundation for application and message development in HL7, caBIG, and CDISC<br /> *A foundation for research in knowledge representation and semantic interoperability<br /> <br /> How is BRDIG funded? Thru caBIG and NCI and some pharma companies.<br /> <br /> Two important streams of development that have been brought together into a collaborative framework<br /> *CDISC – 2003, started constructing an analysis model to map ODM standards to HL7<br /> *NCI – 2004, started caBIG initiative to construct a structured protocol representation and interoperability among clinical research in cancer<br /> <br /> Desiderata<br /> *Did not want to construct “Yet another standard…”<br /> *The good thing about standards is there are so many to choose from…<br /> *Open-source<br /> *Modeled processes and organization after other successful open-source projects Mozilla, Firefox, Linux, etc<br /> *Model is small groups (Technical Harmonization Committee), vet in large groups (Advisory Board)<br /> *Provide a mechanism to scale the development work<br /> *Parallelize the development<br /> *Prevent collaborators from “colliding” with each other<br /> <br /> Allow us do the modeling in the open<br /> <br /> In the BRIDG project, we have tried to operationalize the collaborative models required for roadmap initiatives <br /> <br /> Current classes of core elements- Conceptual Domains<br /> <br /> *Noun things Organization, People<br /> *Role things PIs<br /> *Do things Participate <br /> *Happening things Milestones<br /> *Measurement things Things you measure<br /> *Interpretation things Low Blood Count<br /> *Documentation things Consent…<br /> <br /> This is conceptual to HL7 RIM as well.<br /> <br /> The Communications conundrum<br /> *Experts know about the how to do clinical research but don’t understand how to build software<br /> <br /> *Technologists understand how to build software but don’t understand the intricacies of the clinical environments and clinical research<br /> *Any implementation (i.e. solution) is a compromise of the original problem statement<br /> *Compromises must be chosen wisely<br /> *Should be based on a deep understanding of the problem and a dialogue between Problem Space and Solution Space Experts<br /> <br /> The Communication Pyramid<br /> This is formal Specification of requirements. It must be bi-directional Semantic traceability before they can be balloted.<br /> <br /> Current Collaborators<br /> *HL7<br /> Official domain analysis model for the HL7 RCRIM technical committee<br /> *All HL7 messages must be able to demonstrate “bi-directional semantic traceability” before they can be balloted<br /> <br /> *CDISC<br /> The integrative model for all current CDISC standards<br /> *FDA<br /> Developing an HL7 message based on CDISC SDTM in with the RFA requires capturing the semantics in BRIDG<br /> Regulated Product Submission (RPS) is the next HL7/FDA message to use BRIDG<br /> *Immune Tolerance Network (ITN)<br /> *Using BRIDG to integrate open-source caBIG tools with existing MDA applications<br /> caBIG<br /> *Utilized as framework for NCI’s caBIG™ (standard within CTMS WS)<br /> *Additional non-CTMS semantics (e.g. FireBird, CDUS, etc.) being incorporated<br /> <br /> <br /> BRIDG uses a complex process to harmonize. Using the STDM Implementation Guide and Model. They look at definitions level and fold into BRIDG. This may create two classes. The outcome is a mapping spreadsheet. Then they add things not present. Then they ask, “Here is A and B, describe how they are different”. <br /> <br /> We look at CDISC Terminology and look at the NCI definitions in terms of BRIDG and you may of may not have to create definitions and you may or may not have to harmonize for CDISC or NCI<br /> <br /> OBI has a similar process. OBI looked at having two definitions for the same term and quickly decided that was a recipe for disaster.<br /> <br /> Pilot Study mapping BRIDG to EPOCH<br /> This looked at the semantic alignment. They had to overcome both language and choice mismatch.<br /> BRIDG<br /> HL7, caBIG, CDISC stakeholders<br /> Developed collaboratively with stakeholders<br /> Shared domain model for protocol-driven clinical research<br /> Comprehensive<br /> Consensus-based<br /> Abstract and context neutral<br /> EPOCH<br /> Immune Tolerance Network (ITN)<br /> International collaborative research effort that sponsors clinical trials and mechanistic assays on immune tolerance<br /> EPOCH clinical trial model<br /> Developed at Stanford Medical Informatics<br /> Designed to provide semantic foundation for management of clinical trials<br /> Approach taken<br /> Semantic alignment<br /> Use Excel spreadsheet to systematically review and document possible mappings<br /> Define necessary preconditions for mapping<br /> Overcoming representation language mismatch <br /> Overcoming representation choice mismatches<br /> <br /> We had to understand the definitions to harmonize<br /> Subclass of Larger class must be careful to not get into trouble. Can do this in one direction, but can’t always do in the other which is problematic.<br /> <br /> Semantic Alignment: Restrictions on EPOCH<br /> *Mapping from EPOCH to BRIDG =&gt; Place restrictions on EPOCH<br /> *Only one schedule of activities<br /> *Period has no subperiods<br /> *Limited temporal annotations<br /> <br /> The EPOCH representation is in OWL, the BRIDG representation in UML.<br /> There is a representation of BRIDG in OWL for EPOCH. There may be some circumstances to use this version.<br /> <br /> This pilot demonstrated that we could overcome these mismatches.<br /> The BRIDG –EPOCH model has a notion of period that map as screening in EPOCH.<br /> <br /> SWRL rules were used to write formal rules. The Herold Protocol in EPOCH successfully used EPOCH in a Clinical Trial <br /> <br /> Successfully used an EPOCH clinical trial to configure BRIDG Patient Study Calendar application<br /> Automated mappings except for one relationship<br /> Because of OWL/SWRL’s open-world assumption, First epoch cannot be derived as an epoch that has no predecessor <br /> <br /> Pilot Conclusion<br /> Semantic interoperability requires<br /> Harmonization of subsets of ontologies/models<br /> Overcoming mismatches in representation languages and representation choices<br /> OWL restrictions and SWRL rules help to overcome semantic and syntactic mismatches<br /> Possible future work<br /> Continued harmonization of BRIDG/EPOCH<br /> Scalability and (semi-)automation of method<br /> <br /> What lessons have we learned?<br /> 1. Scope – keep it clear and focused (i.e., solve a problem that exists) and standardize to the extend needed<br /> *Keep the model generic, faithful, free of implementation-specific formalisms, and supporting the requirements<br /> *Refine through experience, and not endless discussions<br /> <br /> The domain of the regulated clinical research information management technical committee in HL7:<br /> Protocol-Driven Research with human, animal or device subjects, plus appropriate associated regulatory documentation.<br /> <br /> *Analysis-level semantics<br /> *Business processes<br /> *Static structures<br /> <br /> Use-case driven <br /> *n-scope and out-of-scope determined by the use-case <br /> <br /> Does not include vocabulary or terminology choices<br /> BRIDGCodedConcept Datatype links to other “places” where domain semantics can be represented<br /> Area of active research in understanding how ontologies and information models “link” to vocabularies and terminologies<br /> 2. Understand the difference between consensus, abstraction, and harmonization<br /> Consensus:<br /> *Consensus statements often achieve agreement through being ambiguous<br /> United Nations, guideline consensus statements<br /> <br /> Abstraction:<br /> *generalized models that are useful for a broad range of different domains (HL7 RIM)<br /> *definitions are abstract, domain independent (although specific to an implementation) and more helpful for implementation than they are for domain experts<br /> <br /> Harmonization:<br /> *Creating definitions that all experts agree on, creating distinctions between concepts to clarify the semantics when they don’t agree, and imbedding those semantics in the business processes<br /> *Harmonize concepts not words<br /> <br /> 3.Models are only a piece of the puzzle<br /> *Datatypes, vocabularies and terminologies provide additional clarification of the semantics<br /> 4.Use a larger development framework to organize, iterate, and trace the semantics<br /> Provides a mechanism to integrate multiple projects, manage change<br /> <br /> 5. Translational research is a cycle.<br /> <br /> In BRIDG: Process Matters<br /> Modeled on open-source software development initiatives<br /> Scalable processes to support coordination and collaboration across multiple modeling groups<br /> Organizational structure with stakeholder representation<br /> Focus on semantics, not representation or implementation allows for variation around a common model<br /> <br /> 6.The importance of capturing dynamic semantics (activities) of clinical trials research<br /> Clarifies the data and concept definitions<br /> Provides the context for use of the data structures<br /> Sets the stage for a service-oriented architecture<br /> <br /> Recent Experience With BRIDG:<br /> The CTMS WS Interoperability Project (1)<br /> Goal: In 9 weeks (including Holidays), build interoperable support for three Use Cases across five applications in the Clinical Trial Management System (CTMS) Work Space<br /> Use Cases to be defined by group of SMEs as ‘pain points’<br /> Applications include:<br /> *Patient Study Calendar<br /> *Static model has been harmonized with BRIDG<br /> *Lab Hub<br /> *Static model has been harmonized with BRIDG<br /> *Adverse Event Reporting System<br /> *Application development began concurrent with Interoperability Project<br /> *Early analysis work already done and compliant with BRIDG<br /> *Patient/Clinical Trial Registry<br /> *Repository of links between patients and trials<br /> *COT CTDMS (Oracle Clinical)<br /> *Trial repository – export capability only<br /> <br /> The CTMS WS Interoperability Project (2)<br /> Process: Iterative/Incremental SEP utilizing BRIDG as DAM<br /> *Two one-month iterations<br /> *Limited ability to change existing code base<br /> *Process began with Business Modeling<br /> *Activity Diagrams for each Use Case mapped to BRIDG<br /> *“BRIDG Extract” generated based on AD → BRIDG mapping<br /> *BRIDG Extract → XMI → analysis-level XSD → implementation-level XSM (“common wire format”)<br /> – short time-line → no ‘formal’ messaging structures (V3 messages will be developed at a future date)<br /> <br /> The Conclusion: The project could not have succeed without the use of a DAM<br /> The previous harmonization/common application of BRIDG by 3/5 of the applications (and the ability of the other 2 applications to map appropriate static structures to BRIDG) enabled the project to succeed<br /> <br /> Current Status<br /> *BRIDG is no longer a modeling exercise, but a robust model used by <br /> the National Cancer Institute for all application development<br /> *Commercial clinical trials software developers<br /> *CDISC to unify their existing models<br /> *HL7 for all HL7 messages related to clinical trials research<br /> *FDA for electronic data submission standards<br /> *Other collaborators (immune tolerance network) to integrate applications and clinical trials work processes<br /> BRIDG release V1 – June, 2007 Download: http://gforge.nci.nih.gov/frs/?group_id=342<br /> <br /> In the process we have <br /> *Developed generalizable scaleable processes to support collaboration across organizations, models, and domains<br /> *Begun to understand how to overcoming semantic and representational differences between different ontologies and terminologies<br /> <br /> Value of analysis modeling for semantic interoperability<br /> If you understand<br /> *The processes (activities) that you do within your organization to support clinical and translational research<br /> *The information (data) that you use for these activities<br /> You can <br /> *Reduce redundancy in your organization<br /> *Redesign organizational processes <br /> *Know what to share (and what not to)<br /> *Integrate custom and commercial applications (you know where they fit in your organizational activities and data)<br /> *Create a shared understanding of the work of clinical trials research (facilitates “culture change”)<br /> <br /> This becomes critical for any program in which you want to <br /> *Exchange data between different disciplines (translational research)<br /> *Clinical trials and translational programs (CTSA)<br /> <br /> <br /> ==Action Items/Future Work identified during and after the teleconference:==<br /> <br /> #Application of BRIDG and evaluate the model and get a paper out<br /> #Subject Eligibility as a trial piece for the modeling exercise at UT Southwestern<br /> #CDISC vocabulary and Ontology<br /> #Concept Paper (Barry as a probable co-author) CDISC-BRIDG-Ontolgy integration</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_08/10/07_Conference_Call&diff=5907 2007-08-17T21:18:57Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Bron Kisler, Jim Zheng, Jennifer Fostel, Richard Scheuermann, Herb Hagler and Richard's Lab<br /> <br /> OCI Conference Call with Doug Fridsma M.D., Ph.D.<br /> <br /> Presenting: BRIDG: A Model to support interoperability in Clinical Research<br /> <br /> Doug Fridsma's presentation can be Downloaded here: http://pathcuric1.swmed.edu/Research/haglerdocs/Fridsma2007-08-OCI-Presentation-v2.ppt<br /> <br /> --------The following notes were compiled by several people present during the presentation<br /> ---------<br /> <br /> “ You can’t build a skyscraper by nailing together 10,000 dog houses.” Grady Booch<br /> <br /> There is a need for a blueprint to support clinical research.<br /> <br /> Agenda<br /> *Why do we need BRIDG?<br /> *Why is BRIDG?<br /> *What are the lessons learned<br /> *Does it work?<br /> *Current Status<br /> <br /> Clinical and Translational research is complex systems of organizations. You must know the definition of data and the process of care. All Clinical Trials must work in a single enterprise. But Clinical and translational data must be able to interoperate with the larger research enterprise. Standardization and the ability to hand off the data are critical to innovation. Ultimately to be successful information must pass not only with in organizations but also between organizations<br /> <br /> What are we trying to do?<br /> *To define implementation-independent domain semantics (define the what and the how of clinical research)<br /> *To uncover the myriad of semantic ambiguities present in the complex domain of clinical research<br /> *To build a foundation for achieving computable semantic interoperability<br /> <br /> BRIDG supports the syntactic with links to the semantics.<br /> *The ability of multiple systems to exchange information and to be able to use the information that has been exchanged.<br /> <br /> What is BRIDG?<br /> Biomedical Research Integrated Domain Group<br /> <br /> *A model of the shared semantics of regulated clinical research<br /> *A communication bridge between<br /> *Clinical research domain experts and technical experts<br /> *Different models of clinical research information (EPOCH-BRIDG)<br /> *An open community of stakeholders interested in developing standards for exchanging information about clinical research<br /> *HL7, NCI, CDISC, FDA, ITN<br /> *The semantic foundation for application and message development in HL7, caBIG, and CDISC<br /> *A foundation for research in knowledge representation and semantic interoperability<br /> <br /> How is BRDIG funded? Thru caBIG and NCI and some pharma companies.<br /> <br /> Two important streams of development that have been brought together into a collaborative framework<br /> *CDISC – 2003, started constructing an analysis model to map ODM standards to HL7<br /> *NCI – 2004, started caBIG initiative to construct a structured protocol representation and interoperability among clinical research in cancer<br /> <br /> Desiderata<br /> *Did not want to construct “Yet another standard…”<br /> *The good thing about standards is there are so many to choose from…<br /> *Open-source<br /> *Modeled processes and organization after other successful open-source projects Mozilla, Firefox, Linux, etc<br /> *Model is small groups (Technical Harmonization Committee), vet in large groups (Advisory Board)<br /> *Provide a mechanism to scale the development work<br /> *Parallelize the development<br /> *Prevent collaborators from “colliding” with each other<br /> <br /> Allow us do the modeling in the open<br /> <br /> In the BRIDG project, we have tried to operationalize the collaborative models required for roadmap initiatives <br /> <br /> Current classes of core elements- Conceptual Domains<br /> <br /> *Noun things Organization, People<br /> *Role things PIs<br /> *Do things Participate <br /> *Happening things Milestones<br /> *Measurement things Things you measure<br /> I*nterpretation things Low Blood Count<br /> *Documentation things Consent…<br /> <br /> This is conceptual to HL7 RIM as well.<br /> <br /> The Communications conundrum<br /> *Experts know about the how to do clinical research but don’t understand how to build software<br /> <br /> *Technologists understand how to build software but don’t understand the intricacies of the clinical environments and clinical research<br /> *Any implementation (i.e. solution) is a compromise of the original problem statement<br /> *Compromises must be chosen wisely<br /> *Should be based on a deep understanding of the problem and a dialogue between Problem Space and Solution Space Experts<br /> <br /> The Communication Pyramid<br /> This is formal Specification of requirements. It must be bi-directional Semantic traceability before they can be balloted.<br /> <br /> Current Collaborators<br /> *HL7<br /> Official domain analysis model for the HL7 RCRIM technical committee<br /> *All HL7 messages must be able to demonstrate “bi-directional semantic traceability” before they can be balloted<br /> <br /> *CDISC<br /> The integrative model for all current CDISC standards<br /> *FDA<br /> Developing an HL7 message based on CDISC SDTM in with the RFA requires capturing the semantics in BRIDG<br /> Regulated Product Submission (RPS) is the next HL7/FDA message to use BRIDG<br /> *Immune Tolerance Network (ITN)<br /> *Using BRIDG to integrate open-source caBIG tools with existing MDA applications<br /> caBIG<br /> *Utilized as framework for NCI’s caBIG™ (standard within CTMS WS)<br /> *Additional non-CTMS semantics (e.g. FireBird, CDUS, etc.) being incorporated<br /> <br /> <br /> BRIDG uses a complex process to harmonize. Using the STDM Implementation Guide and Model. They look at definitions level and fold into BRIDG. This may create two classes. The outcome is a mapping spreadsheet. Then they add things not present. Then they ask, “Here is A and B, describe how they are different”. <br /> <br /> We look at CDISC Terminology and look at the NCI definitions in terms of BRIDG and you may of may not have to create definitions and you may or may not have to harmonize for CDISC or NCI<br /> <br /> OBI has a similar process. OBI looked at having two definitions for the same term and quickly decided that was a recipe for disaster.<br /> <br /> Pilot Study mapping BRIDG to EPOCH<br /> This looked at the semantic alignment. They had to overcome both language and choice mismatch.<br /> BRIDG<br /> HL7, caBIG, CDISC stakeholders<br /> Developed collaboratively with stakeholders<br /> Shared domain model for protocol-driven clinical research<br /> Comprehensive<br /> Consensus-based<br /> Abstract and context neutral<br /> EPOCH<br /> Immune Tolerance Network (ITN)<br /> International collaborative research effort that sponsors clinical trials and mechanistic assays on immune tolerance<br /> EPOCH clinical trial model<br /> Developed at Stanford Medical Informatics<br /> Designed to provide semantic foundation for management of clinical trials<br /> Approach taken<br /> Semantic alignment<br /> Use Excel spreadsheet to systematically review and document possible mappings<br /> Define necessary preconditions for mapping<br /> Overcoming representation language mismatch <br /> Overcoming representation choice mismatches<br /> <br /> We had to understand the definitions to harmonize<br /> Subclass of Larger class must be careful to not get into trouble. Can do this in one direction, but can’t always do in the other which is problematic.<br /> <br /> Semantic Alignment: Restrictions on EPOCH<br /> *Mapping from EPOCH to BRIDG =&gt; Place restrictions on EPOCH<br /> *Only one schedule of activities<br /> *Period has no subperiods<br /> *Limited temporal annotations<br /> <br /> The EPOCH representation is in OWL, the BRIDG representation in UML.<br /> There is a representation of BRIDG in OWL for EPOCH. There may be some circumstances to use this version.<br /> <br /> This pilot demonstrated that we could overcome these mismatches.<br /> The BRIDG –EPOCH model has a notion of period that map as screening in EPOCH.<br /> <br /> SWRL rules were used to write formal rules. The Herold Protocol in EPOCH successfully used EPOCH in a Clinical Trial <br /> <br /> Successfully used an EPOCH clinical trial to configure BRIDG Patient Study Calendar application<br /> Automated mappings except for one relationship<br /> Because of OWL/SWRL’s open-world assumption, First epoch cannot be derived as an epoch that has no predecessor <br /> <br /> Pilot Conclusion<br /> Semantic interoperability requires<br /> Harmonization of subsets of ontologies/models<br /> Overcoming mismatches in representation languages and representation choices<br /> OWL restrictions and SWRL rules help to overcome semantic and syntactic mismatches<br /> Possible future work<br /> Continued harmonization of BRIDG/EPOCH<br /> Scalability and (semi-)automation of method<br /> <br /> What lessons have we learned?<br /> 1. Scope – keep it clear and focused (i.e., solve a problem that exists) and standardize to the extend needed<br /> *Keep the model generic, faithful, free of implementation-specific formalisms, and supporting the requirements<br /> *Refine through experience, and not endless discussions<br /> <br /> The domain of the regulated clinical research information management technical committee in HL7:<br /> Protocol-Driven Research with human, animal or device subjects, plus appropriate associated regulatory documentation.<br /> <br /> *Analysis-level semantics<br /> *Business processes<br /> *Static structures<br /> <br /> Use-case driven <br /> *n-scope and out-of-scope determined by the use-case <br /> <br /> Does not include vocabulary or terminology choices<br /> BRIDGCodedConcept Datatype links to other “places” where domain semantics can be represented<br /> Area of active research in understanding how ontologies and information models “link” to vocabularies and terminologies<br /> 2. Understand the difference between consensus, abstraction, and harmonization<br /> Consensus:<br /> *Consensus statements often achieve agreement through being ambiguous<br /> United Nations, guideline consensus statements<br /> <br /> Abstraction:<br /> *generalized models that are useful for a broad range of different domains (HL7 RIM)<br /> *definitions are abstract, domain independent (although specific to an implementation) and more helpful for implementation than they are for domain experts<br /> <br /> Harmonization:<br /> *Creating definitions that all experts agree on, creating distinctions between concepts to clarify the semantics when they don’t agree, and imbedding those semantics in the business processes<br /> *Harmonize concepts not words<br /> <br /> 3.Models are only a piece of the puzzle<br /> *Datatypes, vocabularies and terminologies provide additional clarification of the semantics<br /> 4.Use a larger development framework to organize, iterate, and trace the semantics<br /> Provides a mechanism to integrate multiple projects, manage change<br /> <br /> 5. Translational research is a cycle.<br /> <br /> In BRIDG: Process Matters<br /> Modeled on open-source software development initiatives<br /> Scalable processes to support coordination and collaboration across multiple modeling groups<br /> Organizational structure with stakeholder representation<br /> Focus on semantics, not representation or implementation allows for variation around a common model<br /> <br /> 6.The importance of capturing dynamic semantics (activities) of clinical trials research<br /> Clarifies the data and concept definitions<br /> Provides the context for use of the data structures<br /> Sets the stage for a service-oriented architecture<br /> <br /> Recent Experience With BRIDG:<br /> The CTMS WS Interoperability Project (1)<br /> Goal: In 9 weeks (including Holidays), build interoperable support for three Use Cases across five applications in the Clinical Trial Management System (CTMS) Work Space<br /> Use Cases to be defined by group of SMEs as ‘pain points’<br /> Applications include:<br /> *Patient Study Calendar<br /> *Static model has been harmonized with BRIDG<br /> *Lab Hub<br /> *Static model has been harmonized with BRIDG<br /> *Adverse Event Reporting System<br /> *Application development began concurrent with Interoperability Project<br /> *Early analysis work already done and compliant with BRIDG<br /> *Patient/Clinical Trial Registry<br /> *Repository of links between patients and trials<br /> *COT CTDMS (Oracle Clinical)<br /> *Trial repository – export capability only<br /> <br /> The CTMS WS Interoperability Project (2)<br /> Process: Iterative/Incremental SEP utilizing BRIDG as DAM<br /> *Two one-month iterations<br /> *Limited ability to change existing code base<br /> *Process began with Business Modeling<br /> *Activity Diagrams for each Use Case mapped to BRIDG<br /> *“BRIDG Extract” generated based on AD → BRIDG mapping<br /> *BRIDG Extract → XMI → analysis-level XSD → implementation-level XSM (“common wire format”)<br /> – short time-line → no ‘formal’ messaging structures (V3 messages will be developed at a future date)<br /> <br /> The Conclusion: The project could not have succeed without the use of a DAM<br /> The previous harmonization/common application of BRIDG by 3/5 of the applications (and the ability of the other 2 applications to map appropriate static structures to BRIDG) enabled the project to succeed<br /> <br /> Current Status<br /> *BRIDG is no longer a modeling exercise, but a robust model used by <br /> the National Cancer Institute for all application development<br /> *Commercial clinical trials software developers<br /> *CDISC to unify their existing models<br /> *HL7 for all HL7 messages related to clinical trials research<br /> *FDA for electronic data submission standards<br /> *Other collaborators (immune tolerance network) to integrate applications and clinical trials work processes<br /> BRIDG release V1 – June, 2007 Download: http://gforge.nci.nih.gov/frs/?group_id=342<br /> <br /> In the process we have <br /> *Developed generalizable scaleable processes to support collaboration across organizations, models, and domains<br /> *Begun to understand how to overcoming semantic and representational differences between different ontologies and terminologies<br /> <br /> Value of analysis modeling for semantic interoperability<br /> If you understand<br /> *The processes (activities) that you do within your organization to support clinical and translational research<br /> *The information (data) that you use for these activities<br /> You can <br /> *Reduce redundancy in your organization<br /> *Redesign organizational processes <br /> *Know what to share (and what not to)<br /> *Integrate custom and commercial applications (you know where they fit in your organizational activities and data)<br /> *Create a shared understanding of the work of clinical trials research (facilitates “culture change”)<br /> <br /> This becomes critical for any program in which you want to <br /> *Exchange data between different disciplines (translational research)<br /> *Clinical trials and translational programs (CTSA)<br /> <br /> <br /> ==Action Items/Future Work identified during and after the teleconference:==<br /> <br /> #Application of BRIDG and evaluate the model and get a paper out<br /> #Subject Eligibility as a trial piece for the modeling exercise at UT Southwestern<br /> #CDISC vocabulary and Ontology<br /> #Concept Paper (Barry as a probable co-author) CDISC-BRIDG-Ontolgy integration</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_08/10/07_Conference_Call&diff=5906 2007-08-17T20:58:25Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Bron Kisler, Jim Zheng, Jennifer Fostel, Richard Scheuermann, Herb Hagler and Richard's Lab<br /> <br /> OCI Conference Call with Doug Fridsma M.D., Ph.D.<br /> <br /> Presenting: BRIDG: A Model to support interoperability in Clinical Research<br /> <br /> Doug Fridsma's presentation can be Downloaded here: http://pathcuric1.swmed.edu/Research/haglerdocs/Fridsma2007-08-OCI-Presentation-v2.ppt<br /> <br /> --------The following notes were compiled by several people present during the presentation<br /> ---------<br /> <br /> “ You can’t build a skyscraper by nailing together 10,000 dog houses.” Grady Booch<br /> <br /> There is a need for a blueprint to support clinical research.<br /> <br /> Agenda<br /> Why do we need BRIDG?<br /> Why is BRIDG?<br /> What are the lessons learned<br /> Does it work?<br /> Current Status<br /> <br /> Clinical and Translational research is complex systems of organizations. You must know the definition of data and the process of care. All Clinical Trials must work in a single enterprise. But Clinical and translational data must be able to interoperate with the larger research enterprise. Standardization and the ability to hand off the data are critical to innovation. Ultimately to be successful information must pass not only with in organizations but also between organizations<br /> <br /> What are we trying to do?<br /> To define implementation-independent domain semantics (define the what and the how of clinical research)<br /> To uncover the myriad of semantic ambiguities present in the complex domain of clinical research<br /> To build a foundation for achieving computable semantic interoperability<br /> <br /> BRIDG supports the syntactic with links to the semantics.<br /> The ability of multiple systems to exchange information and to be able to use the information that has been exchanged.<br /> <br /> What is BRIDG?<br /> Biomedical Research Integrated Domain Group<br /> <br /> A model of the shared semantics of regulated clinical research<br /> A communication bridge between<br /> Clinical research domain experts and technical experts<br /> Different models of clinical research information (EPOCH-BRIDG)<br /> An open community of stakeholders interested in developing standards for exchanging information about clinical research<br /> HL7, NCI, CDISC, FDA, ITN<br /> The semantic foundation for application and message development in HL7, caBIG, and CDISC<br /> A foundation for research in knowledge representation and semantic interoperability<br /> <br /> How is BRDIG funded? Thru caBIG and NCI and some pharma companies.<br /> <br /> Two important streams of development that have been brought together into a collaborative framework<br /> CDISC – 2003, started constructing an analysis model to map ODM standards to HL7<br /> NCI – 2004, started caBIG initiative to construct a structured protocol representation and interoperability among clinical research in cancer<br /> <br /> Desiderata<br /> Did not want to construct “Yet another standard…”<br /> The good thing about standards is there are so many to choose from…<br /> Open-source<br /> Modeled processes and organization after other successful open-source projects<br /> Mozilla, Firefox, Linux, etc<br /> Model is small groups (Technical Harmonization Committee), vet in large groups (Advisory Board)<br /> Provide a mechanism to scale the development work<br /> Parallelize the development<br /> Prevent collaborators from “colliding” with each other<br /> <br /> Allow us do the modeling in the open<br /> <br /> In the BRIDG project, we have tried to operationalize the collaborative models required for roadmap initiatives <br /> <br /> Current classes of core elements- Conceptual Domains<br /> <br /> Noun things Organization, People<br /> Role things PIs<br /> Do things Participate <br /> Happening things Milestones<br /> Measurement things Things you measure<br /> Interpretation things Low Blood Count<br /> Documentation things Consent…<br /> <br /> This is conceptual to HL7 RIM as well.<br /> <br /> The Communications conundrum<br /> Experts know about the how to do clinical research but don’t understand how to build software<br /> <br /> Technologists understand how to build software but don’t understand the intricacies of the clinical environments and clinical research<br /> Any implementation (i.e. solution) is a compromise of the original problem statement<br /> Compromises must be chosen wisely<br /> Should be based on a deep understanding of the problem and a dialogue between Problem Space and Solution Space Experts<br /> <br /> The Communication Pyramid<br /> This is formal Specification of requirements. It must be bi-directional Semantic traceability before they can be balloted.<br /> <br /> Current Collaborators<br /> HL7<br /> Official domain analysis model for the HL7 RCRIM technical committee<br /> All HL7 messages must be able to demonstrate “bi-directional semantic traceability” before they can be balloted<br /> <br /> CDISC<br /> The integrative model for all current CDISC standards<br /> FDA<br /> Developing an HL7 message based on CDISC SDTM in with the RFA requires capturing the semantics in BRIDG<br /> Regulated Product Submission (RPS) is the next HL7/FDA message to use BRIDG<br /> Immune Tolerance Network (ITN)<br /> Using BRIDG to integrate open-source caBIG tools with existing MDA applications<br /> caBIG<br /> Utilized as framework for NCI’s caBIG™ (standard within CTMS WS)<br /> Additional non-CTMS semantics (e.g. FireBird, CDUS, etc.) being incorporated<br /> <br /> <br /> BRIDG uses a complex process to harmonize. Using the STDM Implementation Guide and Model. They look at definitions level and fold into BRIDG. This may create two classes. The outcome is a mapping spreadsheet. Then they add things not present. Then they ask, “Here is A and B, describe how they are different”. <br /> <br /> We look at CDISC Terminology and look at the NCI definitions in terms of BRIDG and you may of may not have to create definitions and you may or may not have to harmonize for CDISC or NCI<br /> <br /> OBI has a similar process. OBI looked at having two definitions for the same term and quickly decided that was a recipe for disaster.<br /> <br /> Pilot Study mapping BRIDG to EPOCH<br /> This looked at the semantic alignment. They had to overcome both language and choice mismatch.<br /> BRIDG<br /> HL7, caBIG, CDISC stakeholders<br /> Developed collaboratively with stakeholders<br /> Shared domain model for protocol-driven clinical research<br /> Comprehensive<br /> Consensus-based<br /> Abstract and context neutral<br /> EPOCH<br /> Immune Tolerance Network (ITN)<br /> International collaborative research effort that sponsors clinical trials and mechanistic assays on immune tolerance<br /> EPOCH clinical trial model<br /> Developed at Stanford Medical Informatics<br /> Designed to provide semantic foundation for management of clinical trials<br /> Approach taken<br /> Semantic alignment<br /> Use Excel spreadsheet to systematically review and document possible mappings<br /> Define necessary preconditions for mapping<br /> Overcoming representation language mismatch <br /> Overcoming representation choice mismatches<br /> <br /> We had to understand the definitions to harmonize<br /> Subclass of Larger class must be careful to not get into trouble. Can do this in one direction, but can’t always do in the other which is problematic.<br /> <br /> Semantic Alignment: Restrictions on EPOCH<br /> Mapping from EPOCH to BRIDG =&gt; Place restrictions on EPOCH<br /> Only one schedule of activities<br /> Period has no subperiods<br /> Limited temporal annotations<br /> <br /> The EPOCH representation is in OWL, the BRIDG representation in UML.<br /> There is a representation of BRIDG in OWL for EPOCH. There may be some circumstances to use this version.<br /> <br /> This pilot demonstrated that we could overcome these mismatches.<br /> The BRIDG –EPOCH model has a notion of period that map as screening in EPOCH.<br /> <br /> SWRL rules were used to write formal rules. The Herold Protocol in EPOCH successfully used EPOCH in a Clinical Trial <br /> <br /> Successfully used an EPOCH clinical trial to configure BRIDG Patient Study Calendar application<br /> Automated mappings except for one relationship<br /> Because of OWL/SWRL’s open-world assumption, First epoch cannot be derived as an epoch that has no predecessor <br /> <br /> Pilot Conclusion<br /> Semantic interoperability requires<br /> Harmonization of subsets of ontologies/models<br /> Overcoming mismatches in representation languages and representation choices<br /> OWL restrictions and SWRL rules help to overcome semantic and syntactic mismatches<br /> Possible future work<br /> Continued harmonization of BRIDG/EPOCH<br /> Scalability and (semi-)automation of method<br /> <br /> What lessons have we learned?<br /> 1.Scope – keep it clear and focused (i.e., solve a problem that exists) and standardize to the extend needed<br /> Keep the model generic, faithful, free of implementation-specific formalisms, and supporting the requirements<br /> Refine through experience, and not endless discussions<br /> <br /> The domain of the regulated clinical research information management technical committee in HL7:<br /> Protocol-Driven Research with human, animal or device subjects, plus appropriate associated regulatory documentation.<br /> <br /> Analysis-level semantics<br /> Business processes<br /> Static structures<br /> <br /> Use-case driven <br /> in-scope and out-of-scope determined by the use-case <br /> <br /> Does not include vocabulary or terminology choices<br /> BRIDGCodedConcept Datatype links to other “places” where domain semantics can be represented<br /> Area of active research in understanding how ontologies and information models “link” to vocabularies and terminologies<br /> 2. Understand the difference between consensus, abstraction, and harmonization<br /> Consensus:<br /> Consensus statements often achieve agreement through being ambiguous<br /> United Nations, guideline consensus statements<br /> <br /> Abstraction:<br /> generalized models that are useful for a broad range of different domains (HL7 RIM)<br /> definitions are abstract, domain independent (although specific to an implementation) and more helpful for implementation than they are for domain experts<br /> <br /> Harmonization:<br /> Creating definitions that all experts agree on, creating distinctions between concepts to clarify the semantics when they don’t agree, and imbedding those semantics in the business processes<br /> Harmonize concepts not words<br /> 3.Models are only a piece of the puzzle<br /> Datatypes, vocabularies and terminologies provide additional clarification of the semantics<br /> 4.Use a larger development framework to organize, iterate, and trace the semantics<br /> Provides a mechanism to integrate multiple projects, manage change<br /> 5. Translational research is a cycle.<br /> <br /> In BRIDG: Process Matters<br /> Modeled on open-source software development initiatives<br /> Scalable processes to support coordination and collaboration across multiple modeling groups<br /> Organizational structure with stakeholder representation<br /> Focus on semantics, not representation or implementation allows for variation around a common model<br /> 6.The importance of capturing dynamic semantics (activities) of clinical trials research<br /> Clarifies the data and concept definitions<br /> Provides the context for use of the data structures<br /> Sets the stage for a service-oriented architecture<br /> <br /> Recent Experience With BRIDG:<br /> The CTMS WS Interoperability Project (1)<br /> Goal: In 9 weeks (including Holidays), build interoperable support for three Use Cases across five applications in the Clinical Trial Management System (CTMS) Work Space<br /> Use Cases to be defined by group of SMEs as ‘pain points’<br /> Applications include:<br /> Patient Study Calendar<br /> Static model has been harmonized with BRIDG<br /> Lab Hub<br /> Static model has been harmonized with BRIDG<br /> Adverse Event Reporting System<br /> Application development began concurrent with Interoperability Project<br /> Early analysis work already done and compliant with BRIDG<br /> Patient/Clinical Trial Registry<br /> Repository of links between patients and trials<br /> COT CTDMS (Oracle Clinical)<br /> Trial repository – export capability only<br /> <br /> The CTMS WS Interoperability Project (2)<br /> Process: Iterative/Incremental SEP utilizing BRIDG as DAM<br /> Two one-month iterations<br /> Limited ability to change existing code base<br /> Process began with Business Modeling<br /> Activity Diagrams for each Use Case mapped to BRIDG<br /> “BRIDG Extract” generated based on AD → BRIDG mapping<br /> BRIDG Extract → XMI → analysis-level XSD → implementation-level XSM (“common wire format”)<br /> – short time-line → no ‘formal’ messaging structures (V3 messages will be developed at a future date)<br /> <br /> The Conclusion: The project could not have succeed without the use of a DAM<br /> The previous harmonization/common application of BRIDG by 3/5 of the applications (and the ability of the other 2 applications to map appropriate static structures to BRIDG) enabled the project to succeed<br /> <br /> Current Status<br /> BRIDG is no longer a modeling exercise, but a robust model used by <br /> the National Cancer Institute for all application development<br /> Commercial clinical trials software developers<br /> CDISC to unify their existing models<br /> HL7 for all HL7 messages related to clinical trials research<br /> FDA for electronic data submission standards<br /> Other collaborators (immune tolerance network) to integrate applications and clinical trials work processes<br /> BRIDG release V1 – June, 2007 Download: http://gforge.nci.nih.gov/frs/?group_id=342<br /> In the process we have <br /> Developed generalizable scaleable processes to support collaboration across organizations, models, and domains<br /> Begun to understand how to overcoming semantic and representational differences between different ontologies and terminologies<br /> <br /> Value of analysis modeling for semantic interoperability<br /> If you understand<br /> The processes (activities) that you do within your organization to support clinical and translational research<br /> The information (data) that you use for these activities<br /> You can <br /> Reduce redundancy in your organization<br /> Redesign organizational processes <br /> Know what to share (and what not to)<br /> Integrate custom and commercial applications (you know where they fit in your organizational activities and data)<br /> Create a shared understanding of the work of clinical trials research (facilitates “culture change”)<br /> <br /> This becomes critical for any program in which you want to <br /> Exchange data between different disciplines (translational research)<br /> Clinical trials and translational programs (CTSA)<br /> <br /> <br /> Action Items/Future Work identified during and after the teleconference:<br /> <br /> #Application of BRIDG and evaluate the model and get a paper out<br /> #Subject Eligibility as a trial piece for the modeling exercise at UT Southwestern<br /> #CDISC vocabulary and Ontology<br /> #Concept Paper (Barry as a probable co-author) CDISC-BRIDG-Ontolgy integration</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_08/10/07_Conference_Call&diff=5905 2007-08-17T20:55:30Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Bron Kisler, Jim Zheng, Jennifer Fostel, Richard Scheuermann, Herb Hagler and Richard's Lab<br /> <br /> OCI Conference Call with Doug Fridsma M.D., Ph.D.<br /> <br /> Presenting: BRIDG: A Model to support interoperability in Clinical Research<br /> <br /> Doug Fridsma's presentation can be Downloaded here: http://pathcuric1.swmed.edu/Research/haglerdocs/Fridsma2007-08-OCI-Presentation-v2.ppt<br /> <br /> --------The following notes were compiled by several people present during the presentation<br /> ---------<br /> <br /> “ You can’t build a skyscraper by nailing together 10,000 dog houses.” Grady Booch<br /> <br /> There is a need for a blueprint to support clinical research.<br /> <br /> Agenda<br /> Why do we need BRIDG?<br /> Why is BRIDG?<br /> What are the lessons learned<br /> Does it work?<br /> Current Status<br /> <br /> Clinical and Translational research is complex systems of organizations. You must know the definition of data and the process of care. All Clinical Trials must work in a single enterprise. But Clinical and translational data must be able to interoperate with the larger research enterprise. Standardization and the ability to hand off the data are critical to innovation. Ultimately to be successful information must pass not only with in organizations but also between organizations<br /> <br /> What are we trying to do?<br /> To define implementation-independent domain semantics (define the what and the how of clinical research)<br /> To uncover the myriad of semantic ambiguities present in the complex domain of clinical research<br /> To build a foundation for achieving computable semantic interoperability<br /> <br /> BRIDG supports the syntactic with links to the semantics.<br /> The ability of multiple systems to exchange information and to be able to use the information that has been exchanged.<br /> <br /> What is BRIDG?<br /> Biomedical Research Integrated Domain Group<br /> <br /> A model of the shared semantics of regulated clinical research<br /> A communication bridge between<br /> Clinical research domain experts and technical experts<br /> Different models of clinical research information (EPOCH-BRIDG)<br /> An open community of stakeholders interested in developing standards for exchanging information about clinical research<br /> HL7, NCI, CDISC, FDA, ITN<br /> The semantic foundation for application and message development in HL7, caBIG, and CDISC<br /> A foundation for research in knowledge representation and semantic interoperability<br /> <br /> How is BRDIG funded? Thru caBIG and NCI and some pharma companies.<br /> <br /> Two important streams of development that have been brought together into a collaborative framework<br /> CDISC – 2003, started constructing an analysis model to map ODM standards to HL7<br /> NCI – 2004, started caBIG initiative to construct a structured protocol representation and interoperability among clinical research in cancer<br /> <br /> Desiderata<br /> Did not want to construct “Yet another standard…”<br /> The good thing about standards is there are so many to choose from…<br /> Open-source<br /> Modeled processes and organization after other successful open-source projects<br /> Mozilla, Firefox, Linux, etc<br /> Model is small groups (Technical Harmonization Committee), vet in large groups (Advisory Board)<br /> Provide a mechanism to scale the development work<br /> Parallelize the development<br /> Prevent collaborators from “colliding” with each other<br /> <br /> Allow us do the modeling in the open<br /> <br /> In the BRIDG project, we have tried to operationalize the collaborative models required for roadmap initiatives <br /> <br /> Current classes of core elements- Conceptual Domains<br /> <br /> Noun things Organization, People<br /> Role things PIs<br /> Do things Participate <br /> Happening things Milestones<br /> Measurement things Things you measure<br /> Interpretation things Low Blood Count<br /> Documentation things Consent…<br /> <br /> This is conceptual to HL7 RIM as well.<br /> <br /> The Communications conundrum<br /> Experts know about the how to do clinical research but don’t understand how to build software<br /> <br /> Technologists understand how to build software but don’t understand the intricacies of the clinical environments and clinical research<br /> Any implementation (i.e. solution) is a compromise of the original problem statement<br /> Compromises must be chosen wisely<br /> Should be based on a deep understanding of the problem and a dialogue between Problem Space and Solution Space Experts<br /> <br /> The Communication Pyramid<br /> This is formal Specification of requirements. It must be bi-directional Semantic traceability before they can be balloted.<br /> <br /> Current Collaborators<br /> HL7<br /> Official domain analysis model for the HL7 RCRIM technical committee<br /> All HL7 messages must be able to demonstrate “bi-directional semantic traceability” before they can be balloted<br /> <br /> CDISC<br /> The integrative model for all current CDISC standards<br /> FDA<br /> Developing an HL7 message based on CDISC SDTM in with the RFA requires capturing the semantics in BRIDG<br /> Regulated Product Submission (RPS) is the next HL7/FDA message to use BRIDG<br /> Immune Tolerance Network (ITN)<br /> Using BRIDG to integrate open-source caBIG tools with existing MDA applications<br /> caBIG<br /> Utilized as framework for NCI’s caBIG™ (standard within CTMS WS)<br /> Additional non-CTMS semantics (e.g. FireBird, CDUS, etc.) being incorporated<br /> <br /> <br /> BRIDG uses a complex process to harmonize. Using the STDM Implementation Guide and Model. They look at definitions level and fold into BRIDG. This may create two classes. The outcome is a mapping spreadsheet. Then they add things not present. Then they ask, “Here is A and B, describe how they are different”. <br /> <br /> We look at CDISC Terminology and look at the NCI definitions in terms of BRIDG and you may of may not have to create definitions and you may or may not have to harmonize for CDISC or NCI<br /> <br /> OBI has a similar process. OBI looked at having two definitions for the same term and quickly decided that was a recipe for disaster.<br /> <br /> Pilot Study mapping BRIDG to EPOCH<br /> This looked at the semantic alignment. They had to overcome both language and choice mismatch.<br /> BRIDG<br /> HL7, caBIG, CDISC stakeholders<br /> Developed collaboratively with stakeholders<br /> Shared domain model for protocol-driven clinical research<br /> Comprehensive<br /> Consensus-based<br /> Abstract and context neutral<br /> EPOCH<br /> Immune Tolerance Network (ITN)<br /> International collaborative research effort that sponsors clinical trials and mechanistic assays on immune tolerance<br /> EPOCH clinical trial model<br /> Developed at Stanford Medical Informatics<br /> Designed to provide semantic foundation for management of clinical trials<br /> Approach taken<br /> Semantic alignment<br /> Use Excel spreadsheet to systematically review and document possible mappings<br /> Define necessary preconditions for mapping<br /> Overcoming representation language mismatch <br /> Overcoming representation choice mismatches<br /> <br /> We had to understand the definitions to harmonize<br /> Subclass of Larger class must be careful to not get into trouble. Can do this in one direction, but can’t always do in the other which is problematic.<br /> <br /> Semantic Alignment: Restrictions on EPOCH<br /> Mapping from EPOCH to BRIDG =&gt; Place restrictions on EPOCH<br /> Only one schedule of activities<br /> Period has no subperiods<br /> Limited temporal annotations<br /> <br /> The EPOCH representation is in OWL, the BRIDG representation in UML.<br /> There is a representation of BRIDG in OWL for EPOCH. There may be some circumstances to use this version.<br /> <br /> This pilot demonstrated that we could overcome these mismatches.<br /> The BRIDG –EPOCH model has a notion of period that map as screening in EPOCH.<br /> <br /> SWRL rules were used to write formal rules. The Herold Protocol in EPOCH successfully used EPOCH in a Clinical Trial <br /> <br /> Successfully used an EPOCH clinical trial to configure BRIDG Patient Study Calendar application<br /> Automated mappings except for one relationship<br /> Because of OWL/SWRL’s open-world assumption, First epoch cannot be derived as an epoch that has no predecessor <br /> <br /> Pilot Conclusion<br /> Semantic interoperability requires<br /> Harmonization of subsets of ontologies/models<br /> Overcoming mismatches in representation languages and representation choices<br /> OWL restrictions and SWRL rules help to overcome semantic and syntactic mismatches<br /> Possible future work<br /> Continued harmonization of BRIDG/EPOCH<br /> Scalability and (semi-)automation of method<br /> <br /> What lessons have we learned?<br /> 1.Scope – keep it clear and focused (i.e., solve a problem that exists) and standardize to the extend needed<br /> Keep the model generic, faithful, free of implementation-specific formalisms, and supporting the requirements<br /> Refine through experience, and not endless discussions<br /> <br /> The domain of the regulated clinical research information management technical committee in HL7:<br /> Protocol-Driven Research with human, animal or device subjects, plus appropriate associated regulatory documentation.<br /> <br /> Analysis-level semantics<br /> Business processes<br /> Static structures<br /> <br /> Use-case driven <br /> in-scope and out-of-scope determined by the use-case <br /> <br /> Does not include vocabulary or terminology choices<br /> BRIDGCodedConcept Datatype links to other “places” where domain semantics can be represented<br /> Area of active research in understanding how ontologies and information models “link” to vocabularies and terminologies<br /> 2. Understand the difference between consensus, abstraction, and harmonization<br /> Consensus:<br /> Consensus statements often achieve agreement through being ambiguous<br /> United Nations, guideline consensus statements<br /> <br /> Abstraction:<br /> generalized models that are useful for a broad range of different domains (HL7 RIM)<br /> definitions are abstract, domain independent (although specific to an implementation) and more helpful for implementation than they are for domain experts<br /> <br /> Harmonization:<br /> Creating definitions that all experts agree on, creating distinctions between concepts to clarify the semantics when they don’t agree, and imbedding those semantics in the business processes<br /> Harmonize concepts not words<br /> 3.Models are only a piece of the puzzle<br /> Datatypes, vocabularies and terminologies provide additional clarification of the semantics<br /> 4.Use a larger development framework to organize, iterate, and trace the semantics<br /> Provides a mechanism to integrate multiple projects, manage change<br /> 5. Translational research is a cycle.<br /> <br /> In BRIDG: Process Matters<br /> Modeled on open-source software development initiatives<br /> Scalable processes to support coordination and collaboration across multiple modeling groups<br /> Organizational structure with stakeholder representation<br /> Focus on semantics, not representation or implementation allows for variation around a common model<br /> 6.The importance of capturing dynamic semantics (activities) of clinical trials research<br /> Clarifies the data and concept definitions<br /> Provides the context for use of the data structures<br /> Sets the stage for a service-oriented architecture<br /> <br /> Recent Experience With BRIDG:<br /> The CTMS WS Interoperability Project (1)<br /> Goal: In 9 weeks (including Holidays), build interoperable support for three Use Cases across five applications in the Clinical Trial Management System (CTMS) Work Space<br /> Use Cases to be defined by group of SMEs as ‘pain points’<br /> Applications include:<br /> Patient Study Calendar<br /> Static model has been harmonized with BRIDG<br /> Lab Hub<br /> Static model has been harmonized with BRIDG<br /> Adverse Event Reporting System<br /> Application development began concurrent with Interoperability Project<br /> Early analysis work already done and compliant with BRIDG<br /> Patient/Clinical Trial Registry<br /> Repository of links between patients and trials<br /> COT CTDMS (Oracle Clinical)<br /> Trial repository – export capability only<br /> <br /> The CTMS WS Interoperability Project (2)<br /> Process: Iterative/Incremental SEP utilizing BRIDG as DAM<br /> Two one-month iterations<br /> Limited ability to change existing code base<br /> Process began with Business Modeling<br /> Activity Diagrams for each Use Case mapped to BRIDG<br /> “BRIDG Extract” generated based on AD → BRIDG mapping<br /> BRIDG Extract → XMI → analysis-level XSD → implementation-level XSM (“common wire format”)<br /> – short time-line → no ‘formal’ messaging structures (V3 messages will be developed at a future date)<br /> <br /> The Conclusion: The project could not have succeed without the use of a DAM<br /> The previous harmonization/common application of BRIDG by 3/5 of the applications (and the ability of the other 2 applications to map appropriate static structures to BRIDG) enabled the project to succeed<br /> <br /> Current Status<br /> BRIDG is no longer a modeling exercise, but a robust model used by <br /> the National Cancer Institute for all application development<br /> Commercial clinical trials software developers<br /> CDISC to unify their existing models<br /> HL7 for all HL7 messages related to clinical trials research<br /> FDA for electronic data submission standards<br /> Other collaborators (immune tolerance network) to integrate applications and clinical trials work processes<br /> BRIDG release V1 – June, 2007<br /> In the process we have <br /> Developed generalizable scaleable processes to support collaboration across organizations, models, and domains<br /> Begun to understand how to overcoming semantic and representational differences between different ontologies and terminologies<br /> <br /> Value of analysis modeling for semantic interoperability<br /> If you understand<br /> The processes (activities) that you do within your organization to support clinical and translational research<br /> The information (data) that you use for these activities<br /> You can <br /> Reduce redundancy in your organization<br /> Redesign organizational processes <br /> Know what to share (and what not to)<br /> Integrate custom and commercial applications (you know where they fit in your organizational activities and data)<br /> Create a shared understanding of the work of clinical trials research (facilitates “culture change”)<br /> <br /> This becomes critical for any program in which you want to <br /> Exchange data between different disciplines (translational research)<br /> Clinical trials and translational programs (CTSA)<br /> <br /> <br /> Action Items/Future Work identified during and after the teleconference:<br /> <br /> #Application of BRIDG and evaluate the model and get a paper out<br /> #Subject Eligibility as a trial piece for the modeling exercise at UT Southwestern<br /> #CDISC vocabulary and Ontology<br /> #Concept Paper (Barry as a probable co-author) CDISC-BRIDG-Ontolgy integration</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_08/10/07_Conference_Call&diff=5904 2007-08-17T20:54:12Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Bron Kisler, Jim Zheng, Jennifer Fostel, Richard Scheuermann, Herb Hagler and Richard's Lab<br /> <br /> OCI Conference Call with Doug Fridsma M.D., Ph.D.<br /> <br /> Presenting: BRIDG: A Model to support interoperability in Clinical Research<br /> <br /> Doug Fridsma's presentation can be Downloaded here: http://pathcuric1.swmed.edu/Research/haglerdocs/Fridsma2007-08-OCI-Presentation-v2.ppt<br /> <br /> --------The following notes were compiled by several people present during the presentation<br /> ---------<br /> <br /> “ You can’t build a skyscraper by nailing together 10,000 dog houses.” Grady Booch<br /> <br /> There is a need to a blueprint to support clinical research.<br /> <br /> Agenda<br /> Why do we need BRIDG?<br /> Why is BRIDG?<br /> What are the lessons learned<br /> Does it work?<br /> Current Status<br /> <br /> Clinical and Translational research is complex systems of organizations. You must know the definition of data and the process of care. All Clinical Trials must work in a single enterprise. But Clinical and translational data must be able to interoperate with the larger research enterprise. Standardization and the ability to hand off the data are critical to innovation. Ultimately to be successful information must pass not only with in organizations but also between organizations<br /> <br /> What are we trying to do?<br /> To define implementation-independent domain semantics (define the what and the how of clinical research)<br /> To uncover the myriad of semantic ambiguities present in the complex domain of clinical research<br /> To build a foundation for achieving computable semantic interoperability<br /> <br /> BRIDG supports the syntactic with links to the semantics.<br /> The ability of multiple systems to exchange information and to be able to use the information that has been exchanged.<br /> <br /> What is BRIDG?<br /> Biomedical Research Integrated Domain Group<br /> <br /> A model of the shared semantics of regulated clinical research<br /> A communication bridge between<br /> Clinical research domain experts and technical experts<br /> Different models of clinical research information (EPOCH-BRIDG)<br /> An open community of stakeholders interested in developing standards for exchanging information about clinical research<br /> HL7, NCI, CDISC, FDA, ITN<br /> The semantic foundation for application and message development in HL7, caBIG, and CDISC<br /> A foundation for research in knowledge representation and semantic interoperability<br /> <br /> How is BRDIG funded? Thru caBIG and NCI and some pharma companies.<br /> <br /> Two important streams of development that have been brought together into a collaborative framework<br /> CDISC – 2003, started constructing an analysis model to map ODM standards to HL7<br /> NCI – 2004, started caBIG initiative to construct a structured protocol representation and interoperability among clinical research in cancer<br /> <br /> Desiderata<br /> Did not want to construct “Yet another standard…”<br /> The good thing about standards is there are so many to choose from…<br /> Open-source<br /> Modeled processes and organization after other successful open-source projects<br /> Mozilla, Firefox, Linux, etc<br /> Model is small groups (Technical Harmonization Committee), vet in large groups (Advisory Board)<br /> Provide a mechanism to scale the development work<br /> Parallelize the development<br /> Prevent collaborators from “colliding” with each other<br /> <br /> Allow us do the modeling in the open<br /> <br /> In the BRIDG project, we have tried to operationalize the collaborative models required for roadmap initiatives <br /> <br /> Current classes of core elements- Conceptual Domains<br /> <br /> Noun things Organization, People<br /> Role things PIs<br /> Do things Participate <br /> Happening things Milestones<br /> Measurement things Things you measure<br /> Interpretation things Low Blood Count<br /> Documentation things Consent…<br /> <br /> This is conceptual to HL7 RIM as well.<br /> <br /> The Communications conundrum<br /> Experts know about the how to do clinical research but don’t understand how to build software<br /> <br /> Technologists understand how to build software but don’t understand the intricacies of the clinical environments and clinical research<br /> Any implementation (i.e. solution) is a compromise of the original problem statement<br /> Compromises must be chosen wisely<br /> Should be based on a deep understanding of the problem and a dialogue between Problem Space and Solution Space Experts<br /> <br /> The Communication Pyramid<br /> This is formal Specification of requirements. It must be bi-directional Semantic traceability before they can be balloted.<br /> <br /> Current Collaborators<br /> HL7<br /> Official domain analysis model for the HL7 RCRIM technical committee<br /> All HL7 messages must be able to demonstrate “bi-directional semantic traceability” before they can be balloted<br /> <br /> CDISC<br /> The integrative model for all current CDISC standards<br /> FDA<br /> Developing an HL7 message based on CDISC SDTM in with the RFA requires capturing the semantics in BRIDG<br /> Regulated Product Submission (RPS) is the next HL7/FDA message to use BRIDG<br /> Immune Tolerance Network (ITN)<br /> Using BRIDG to integrate open-source caBIG tools with existing MDA applications<br /> caBIG<br /> Utilized as framework for NCI’s caBIG™ (standard within CTMS WS)<br /> Additional non-CTMS semantics (e.g. FireBird, CDUS, etc.) being incorporated<br /> <br /> <br /> BRIDG uses a complex process to harmonize. Using the STDM Implementation Guide and Model. They look at definitions level and fold into BRIDG. This may create two classes. The outcome is a mapping spreadsheet. Then they add things not present. Then they ask, “Here is A and B, describe how they are different”. <br /> <br /> We look at CDISC Terminology and look at the NCI definitions in terms of BRIDG and you may of may not have to create definitions and you may or may not have to harmonize for CDISC or NCI<br /> <br /> OBI has a similar process. OBI looked at having two definitions for the same term and quickly decided that was a recipe for disaster.<br /> <br /> Pilot Study mapping BRIDG to EPOCH<br /> This looked at the semantic alignment. They had to overcome both language and choice mismatch.<br /> BRIDG<br /> HL7, caBIG, CDISC stakeholders<br /> Developed collaboratively with stakeholders<br /> Shared domain model for protocol-driven clinical research<br /> Comprehensive<br /> Consensus-based<br /> Abstract and context neutral<br /> EPOCH<br /> Immune Tolerance Network (ITN)<br /> International collaborative research effort that sponsors clinical trials and mechanistic assays on immune tolerance<br /> EPOCH clinical trial model<br /> Developed at Stanford Medical Informatics<br /> Designed to provide semantic foundation for management of clinical trials<br /> Approach taken<br /> Semantic alignment<br /> Use Excel spreadsheet to systematically review and document possible mappings<br /> Define necessary preconditions for mapping<br /> Overcoming representation language mismatch <br /> Overcoming representation choice mismatches<br /> <br /> We had to understand the definitions to harmonize<br /> Subclass of Larger class must be careful to not get into trouble. Can do this in one direction, but can’t always do in the other which is problematic.<br /> <br /> Semantic Alignment: Restrictions on EPOCH<br /> Mapping from EPOCH to BRIDG =&gt; Place restrictions on EPOCH<br /> Only one schedule of activities<br /> Period has no subperiods<br /> Limited temporal annotations<br /> <br /> The EPOCH representation is in OWL, the BRIDG representation in UML.<br /> There is a representation of BRIDG in OWL for EPOCH. There may be some circumstances to use this version.<br /> <br /> This pilot demonstrated that we could overcome these mismatches.<br /> The BRIDG –EPOCH model has a notion of period that map as screening in EPOCH.<br /> <br /> SWRL rules were used to write formal rules. The Herold Protocol in EPOCH successfully used EPOCH in a Clinical Trial <br /> <br /> Successfully used an EPOCH clinical trial to configure BRIDG Patient Study Calendar application<br /> Automated mappings except for one relationship<br /> Because of OWL/SWRL’s open-world assumption, First epoch cannot be derived as an epoch that has no predecessor <br /> <br /> Pilot Conclusion<br /> Semantic interoperability requires<br /> Harmonization of subsets of ontologies/models<br /> Overcoming mismatches in representation languages and representation choices<br /> OWL restrictions and SWRL rules help to overcome semantic and syntactic mismatches<br /> Possible future work<br /> Continued harmonization of BRIDG/EPOCH<br /> Scalability and (semi-)automation of method<br /> <br /> What lessons have we learned?<br /> 1.Scope – keep it clear and focused (i.e., solve a problem that exists) and standardize to the extend needed<br /> Keep the model generic, faithful, free of implementation-specific formalisms, and supporting the requirements<br /> Refine through experience, and not endless discussions<br /> <br /> The domain of the regulated clinical research information management technical committee in HL7:<br /> Protocol-Driven Research with human, animal or device subjects, plus appropriate associated regulatory documentation.<br /> <br /> Analysis-level semantics<br /> Business processes<br /> Static structures<br /> <br /> Use-case driven <br /> in-scope and out-of-scope determined by the use-case <br /> <br /> Does not include vocabulary or terminology choices<br /> BRIDGCodedConcept Datatype links to other “places” where domain semantics can be represented<br /> Area of active research in understanding how ontologies and information models “link” to vocabularies and terminologies<br /> 2. Understand the difference between consensus, abstraction, and harmonization<br /> Consensus:<br /> Consensus statements often achieve agreement through being ambiguous<br /> United Nations, guideline consensus statements<br /> <br /> Abstraction:<br /> generalized models that are useful for a broad range of different domains (HL7 RIM)<br /> definitions are abstract, domain independent (although specific to an implementation) and more helpful for implementation than they are for domain experts<br /> <br /> Harmonization:<br /> Creating definitions that all experts agree on, creating distinctions between concepts to clarify the semantics when they don’t agree, and imbedding those semantics in the business processes<br /> Harmonize concepts not words<br /> 3.Models are only a piece of the puzzle<br /> Datatypes, vocabularies and terminologies provide additional clarification of the semantics<br /> 4.Use a larger development framework to organize, iterate, and trace the semantics<br /> Provides a mechanism to integrate multiple projects, manage change<br /> 5. Translational research is a cycle.<br /> <br /> In BRIDG: Process Matters<br /> Modeled on open-source software development initiatives<br /> Scalable processes to support coordination and collaboration across multiple modeling groups<br /> Organizational structure with stakeholder representation<br /> Focus on semantics, not representation or implementation allows for variation around a common model<br /> 6.The importance of capturing dynamic semantics (activities) of clinical trials research<br /> Clarifies the data and concept definitions<br /> Provides the context for use of the data structures<br /> Sets the stage for a service-oriented architecture<br /> <br /> Recent Experience With BRIDG:<br /> The CTMS WS Interoperability Project (1)<br /> Goal: In 9 weeks (including Holidays), build interoperable support for three Use Cases across five applications in the Clinical Trial Management System (CTMS) Work Space<br /> Use Cases to be defined by group of SMEs as ‘pain points’<br /> Applications include:<br /> Patient Study Calendar<br /> Static model has been harmonized with BRIDG<br /> Lab Hub<br /> Static model has been harmonized with BRIDG<br /> Adverse Event Reporting System<br /> Application development began concurrent with Interoperability Project<br /> Early analysis work already done and compliant with BRIDG<br /> Patient/Clinical Trial Registry<br /> Repository of links between patients and trials<br /> COT CTDMS (Oracle Clinical)<br /> Trial repository – export capability only<br /> <br /> The CTMS WS Interoperability Project (2)<br /> Process: Iterative/Incremental SEP utilizing BRIDG as DAM<br /> Two one-month iterations<br /> Limited ability to change existing code base<br /> Process began with Business Modeling<br /> Activity Diagrams for each Use Case mapped to BRIDG<br /> “BRIDG Extract” generated based on AD → BRIDG mapping<br /> BRIDG Extract → XMI → analysis-level XSD → implementation-level XSM (“common wire format”)<br /> – short time-line → no ‘formal’ messaging structures (V3 messages will be developed at a future date)<br /> <br /> The Conclusion: The project could not have succeed without the use of a DAM<br /> The previous harmonization/common application of BRIDG by 3/5 of the applications (and the ability of the other 2 applications to map appropriate static structures to BRIDG) enabled the project to succeed<br /> <br /> Current Status<br /> BRIDG is no longer a modeling exercise, but a robust model used by <br /> the National Cancer Institute for all application development<br /> Commercial clinical trials software developers<br /> CDISC to unify their existing models<br /> HL7 for all HL7 messages related to clinical trials research<br /> FDA for electronic data submission standards<br /> Other collaborators (immune tolerance network) to integrate applications and clinical trials work processes<br /> BRIDG release V1 – June, 2007<br /> In the process we have <br /> Developed generalizable scaleable processes to support collaboration across organizations, models, and domains<br /> Begun to understand how to overcoming semantic and representational differences between different ontologies and terminologies<br /> <br /> Value of analysis modeling for semantic interoperability<br /> If you understand<br /> The processes (activities) that you do within your organization to support clinical and translational research<br /> The information (data) that you use for these activities<br /> You can <br /> Reduce redundancy in your organization<br /> Redesign organizational processes <br /> Know what to share (and what not to)<br /> Integrate custom and commercial applications (you know where they fit in your organizational activities and data)<br /> Create a shared understanding of the work of clinical trials research (facilitates “culture change”)<br /> <br /> This becomes critical for any program in which you want to <br /> Exchange data between different disciplines (translational research)<br /> Clinical trials and translational programs (CTSA)<br /> <br /> <br /> Action Items/Future Work identified during and after the teleconference:<br /> <br /> #Application of BRIDG and evaluate the model and get a paper out<br /> #Subject Eligibility as a trial piece for the modeling exercise at UT Southwestern<br /> #CDISC vocabulary and Ontology<br /> #Concept Paper (Barry as a probable co-author) CDISC-BRIDG-Ontolgy integration</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_08/10/07_Conference_Call&diff=5903 2007-08-17T20:53:55Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Bron Kisler, Jim Zheng, Jennifer Fostel, Richard Scheuermann, Herb Hagler and Richard's Lab<br /> <br /> OCI Conference Call with Doug Fridsma M.D., Ph.D.<br /> <br /> Presenting: BRIDG: A Model to support interoperability in Clinical Research<br /> <br /> Doug Fridsma's presentation can be Downloaded here: http://pathcuric1.swmed.edu/Research/haglerdocs/Fridsma2007-08-OCI-Presentation-v2.ppt<br /> <br /> --------The following notes were compiled by several people present during the presentation---------<br /> <br /> “ You can’t build a skyscraper by nailing together 10,000 dog houses.” Grady Booch<br /> <br /> There is a need to a blueprint to support clinical research.<br /> <br /> Agenda<br /> Why do we need BRIDG?<br /> Why is BRIDG?<br /> What are the lessons learned<br /> Does it work?<br /> Current Status<br /> <br /> Clinical and Translational research is complex systems of organizations. You must know the definition of data and the process of care. All Clinical Trials must work in a single enterprise. But Clinical and translational data must be able to interoperate with the larger research enterprise. Standardization and the ability to hand off the data are critical to innovation. Ultimately to be successful information must pass not only with in organizations but also between organizations<br /> <br /> What are we trying to do?<br /> To define implementation-independent domain semantics (define the what and the how of clinical research)<br /> To uncover the myriad of semantic ambiguities present in the complex domain of clinical research<br /> To build a foundation for achieving computable semantic interoperability<br /> <br /> BRIDG supports the syntactic with links to the semantics.<br /> The ability of multiple systems to exchange information and to be able to use the information that has been exchanged.<br /> <br /> What is BRIDG?<br /> Biomedical Research Integrated Domain Group<br /> <br /> A model of the shared semantics of regulated clinical research<br /> A communication bridge between<br /> Clinical research domain experts and technical experts<br /> Different models of clinical research information (EPOCH-BRIDG)<br /> An open community of stakeholders interested in developing standards for exchanging information about clinical research<br /> HL7, NCI, CDISC, FDA, ITN<br /> The semantic foundation for application and message development in HL7, caBIG, and CDISC<br /> A foundation for research in knowledge representation and semantic interoperability<br /> <br /> How is BRDIG funded? Thru caBIG and NCI and some pharma companies.<br /> <br /> Two important streams of development that have been brought together into a collaborative framework<br /> CDISC – 2003, started constructing an analysis model to map ODM standards to HL7<br /> NCI – 2004, started caBIG initiative to construct a structured protocol representation and interoperability among clinical research in cancer<br /> <br /> Desiderata<br /> Did not want to construct “Yet another standard…”<br /> The good thing about standards is there are so many to choose from…<br /> Open-source<br /> Modeled processes and organization after other successful open-source projects<br /> Mozilla, Firefox, Linux, etc<br /> Model is small groups (Technical Harmonization Committee), vet in large groups (Advisory Board)<br /> Provide a mechanism to scale the development work<br /> Parallelize the development<br /> Prevent collaborators from “colliding” with each other<br /> <br /> Allow us do the modeling in the open<br /> <br /> In the BRIDG project, we have tried to operationalize the collaborative models required for roadmap initiatives <br /> <br /> Current classes of core elements- Conceptual Domains<br /> <br /> Noun things Organization, People<br /> Role things PIs<br /> Do things Participate <br /> Happening things Milestones<br /> Measurement things Things you measure<br /> Interpretation things Low Blood Count<br /> Documentation things Consent…<br /> <br /> This is conceptual to HL7 RIM as well.<br /> <br /> The Communications conundrum<br /> Experts know about the how to do clinical research but don’t understand how to build software<br /> <br /> Technologists understand how to build software but don’t understand the intricacies of the clinical environments and clinical research<br /> Any implementation (i.e. solution) is a compromise of the original problem statement<br /> Compromises must be chosen wisely<br /> Should be based on a deep understanding of the problem and a dialogue between Problem Space and Solution Space Experts<br /> <br /> The Communication Pyramid<br /> This is formal Specification of requirements. It must be bi-directional Semantic traceability before they can be balloted.<br /> <br /> Current Collaborators<br /> HL7<br /> Official domain analysis model for the HL7 RCRIM technical committee<br /> All HL7 messages must be able to demonstrate “bi-directional semantic traceability” before they can be balloted<br /> <br /> CDISC<br /> The integrative model for all current CDISC standards<br /> FDA<br /> Developing an HL7 message based on CDISC SDTM in with the RFA requires capturing the semantics in BRIDG<br /> Regulated Product Submission (RPS) is the next HL7/FDA message to use BRIDG<br /> Immune Tolerance Network (ITN)<br /> Using BRIDG to integrate open-source caBIG tools with existing MDA applications<br /> caBIG<br /> Utilized as framework for NCI’s caBIG™ (standard within CTMS WS)<br /> Additional non-CTMS semantics (e.g. FireBird, CDUS, etc.) being incorporated<br /> <br /> <br /> BRIDG uses a complex process to harmonize. Using the STDM Implementation Guide and Model. They look at definitions level and fold into BRIDG. This may create two classes. The outcome is a mapping spreadsheet. Then they add things not present. Then they ask, “Here is A and B, describe how they are different”. <br /> <br /> We look at CDISC Terminology and look at the NCI definitions in terms of BRIDG and you may of may not have to create definitions and you may or may not have to harmonize for CDISC or NCI<br /> <br /> OBI has a similar process. OBI looked at having two definitions for the same term and quickly decided that was a recipe for disaster.<br /> <br /> Pilot Study mapping BRIDG to EPOCH<br /> This looked at the semantic alignment. They had to overcome both language and choice mismatch.<br /> BRIDG<br /> HL7, caBIG, CDISC stakeholders<br /> Developed collaboratively with stakeholders<br /> Shared domain model for protocol-driven clinical research<br /> Comprehensive<br /> Consensus-based<br /> Abstract and context neutral<br /> EPOCH<br /> Immune Tolerance Network (ITN)<br /> International collaborative research effort that sponsors clinical trials and mechanistic assays on immune tolerance<br /> EPOCH clinical trial model<br /> Developed at Stanford Medical Informatics<br /> Designed to provide semantic foundation for management of clinical trials<br /> Approach taken<br /> Semantic alignment<br /> Use Excel spreadsheet to systematically review and document possible mappings<br /> Define necessary preconditions for mapping<br /> Overcoming representation language mismatch <br /> Overcoming representation choice mismatches<br /> <br /> We had to understand the definitions to harmonize<br /> Subclass of Larger class must be careful to not get into trouble. Can do this in one direction, but can’t always do in the other which is problematic.<br /> <br /> Semantic Alignment: Restrictions on EPOCH<br /> Mapping from EPOCH to BRIDG =&gt; Place restrictions on EPOCH<br /> Only one schedule of activities<br /> Period has no subperiods<br /> Limited temporal annotations<br /> <br /> The EPOCH representation is in OWL, the BRIDG representation in UML.<br /> There is a representation of BRIDG in OWL for EPOCH. There may be some circumstances to use this version.<br /> <br /> This pilot demonstrated that we could overcome these mismatches.<br /> The BRIDG –EPOCH model has a notion of period that map as screening in EPOCH.<br /> <br /> SWRL rules were used to write formal rules. The Herold Protocol in EPOCH successfully used EPOCH in a Clinical Trial <br /> <br /> Successfully used an EPOCH clinical trial to configure BRIDG Patient Study Calendar application<br /> Automated mappings except for one relationship<br /> Because of OWL/SWRL’s open-world assumption, First epoch cannot be derived as an epoch that has no predecessor <br /> <br /> Pilot Conclusion<br /> Semantic interoperability requires<br /> Harmonization of subsets of ontologies/models<br /> Overcoming mismatches in representation languages and representation choices<br /> OWL restrictions and SWRL rules help to overcome semantic and syntactic mismatches<br /> Possible future work<br /> Continued harmonization of BRIDG/EPOCH<br /> Scalability and (semi-)automation of method<br /> <br /> What lessons have we learned?<br /> 1.Scope – keep it clear and focused (i.e., solve a problem that exists) and standardize to the extend needed<br /> Keep the model generic, faithful, free of implementation-specific formalisms, and supporting the requirements<br /> Refine through experience, and not endless discussions<br /> <br /> The domain of the regulated clinical research information management technical committee in HL7:<br /> Protocol-Driven Research with human, animal or device subjects, plus appropriate associated regulatory documentation.<br /> <br /> Analysis-level semantics<br /> Business processes<br /> Static structures<br /> <br /> Use-case driven <br /> in-scope and out-of-scope determined by the use-case <br /> <br /> Does not include vocabulary or terminology choices<br /> BRIDGCodedConcept Datatype links to other “places” where domain semantics can be represented<br /> Area of active research in understanding how ontologies and information models “link” to vocabularies and terminologies<br /> 2. Understand the difference between consensus, abstraction, and harmonization<br /> Consensus:<br /> Consensus statements often achieve agreement through being ambiguous<br /> United Nations, guideline consensus statements<br /> <br /> Abstraction:<br /> generalized models that are useful for a broad range of different domains (HL7 RIM)<br /> definitions are abstract, domain independent (although specific to an implementation) and more helpful for implementation than they are for domain experts<br /> <br /> Harmonization:<br /> Creating definitions that all experts agree on, creating distinctions between concepts to clarify the semantics when they don’t agree, and imbedding those semantics in the business processes<br /> Harmonize concepts not words<br /> 3.Models are only a piece of the puzzle<br /> Datatypes, vocabularies and terminologies provide additional clarification of the semantics<br /> 4.Use a larger development framework to organize, iterate, and trace the semantics<br /> Provides a mechanism to integrate multiple projects, manage change<br /> 5. Translational research is a cycle.<br /> <br /> In BRIDG: Process Matters<br /> Modeled on open-source software development initiatives<br /> Scalable processes to support coordination and collaboration across multiple modeling groups<br /> Organizational structure with stakeholder representation<br /> Focus on semantics, not representation or implementation allows for variation around a common model<br /> 6.The importance of capturing dynamic semantics (activities) of clinical trials research<br /> Clarifies the data and concept definitions<br /> Provides the context for use of the data structures<br /> Sets the stage for a service-oriented architecture<br /> <br /> Recent Experience With BRIDG:<br /> The CTMS WS Interoperability Project (1)<br /> Goal: In 9 weeks (including Holidays), build interoperable support for three Use Cases across five applications in the Clinical Trial Management System (CTMS) Work Space<br /> Use Cases to be defined by group of SMEs as ‘pain points’<br /> Applications include:<br /> Patient Study Calendar<br /> Static model has been harmonized with BRIDG<br /> Lab Hub<br /> Static model has been harmonized with BRIDG<br /> Adverse Event Reporting System<br /> Application development began concurrent with Interoperability Project<br /> Early analysis work already done and compliant with BRIDG<br /> Patient/Clinical Trial Registry<br /> Repository of links between patients and trials<br /> COT CTDMS (Oracle Clinical)<br /> Trial repository – export capability only<br /> <br /> The CTMS WS Interoperability Project (2)<br /> Process: Iterative/Incremental SEP utilizing BRIDG as DAM<br /> Two one-month iterations<br /> Limited ability to change existing code base<br /> Process began with Business Modeling<br /> Activity Diagrams for each Use Case mapped to BRIDG<br /> “BRIDG Extract” generated based on AD → BRIDG mapping<br /> BRIDG Extract → XMI → analysis-level XSD → implementation-level XSM (“common wire format”)<br /> – short time-line → no ‘formal’ messaging structures (V3 messages will be developed at a future date)<br /> <br /> The Conclusion: The project could not have succeed without the use of a DAM<br /> The previous harmonization/common application of BRIDG by 3/5 of the applications (and the ability of the other 2 applications to map appropriate static structures to BRIDG) enabled the project to succeed<br /> <br /> Current Status<br /> BRIDG is no longer a modeling exercise, but a robust model used by <br /> the National Cancer Institute for all application development<br /> Commercial clinical trials software developers<br /> CDISC to unify their existing models<br /> HL7 for all HL7 messages related to clinical trials research<br /> FDA for electronic data submission standards<br /> Other collaborators (immune tolerance network) to integrate applications and clinical trials work processes<br /> BRIDG release V1 – June, 2007<br /> In the process we have <br /> Developed generalizable scaleable processes to support collaboration across organizations, models, and domains<br /> Begun to understand how to overcoming semantic and representational differences between different ontologies and terminologies<br /> <br /> Value of analysis modeling for semantic interoperability<br /> If you understand<br /> The processes (activities) that you do within your organization to support clinical and translational research<br /> The information (data) that you use for these activities<br /> You can <br /> Reduce redundancy in your organization<br /> Redesign organizational processes <br /> Know what to share (and what not to)<br /> Integrate custom and commercial applications (you know where they fit in your organizational activities and data)<br /> Create a shared understanding of the work of clinical trials research (facilitates “culture change”)<br /> <br /> This becomes critical for any program in which you want to <br /> Exchange data between different disciplines (translational research)<br /> Clinical trials and translational programs (CTSA)<br /> <br /> <br /> Action Items/Future Work identified during and after the teleconference:<br /> <br /> #Application of BRIDG and evaluate the model and get a paper out<br /> #Subject Eligibility as a trial piece for the modeling exercise at UT Southwestern<br /> #CDISC vocabulary and Ontology<br /> #Concept Paper (Barry as a probable co-author) CDISC-BRIDG-Ontolgy integration</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_08/10/07_Conference_Call&diff=5899 2007-08-15T20:04:43Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Bron Kisler, Jim Zheng, Jennifer Fostel, Richard Scheuermann, Herb Hagler and Richard's Lab<br /> <br /> OCI Conference Call with Doug Fridsma M.D., Ph.D.<br /> <br /> Presenting: BRIDG: A Model to support interoperability in Clinical Research<br /> <br /> Doug Fridsma's presentation can be Downloaded here: http://pathcuric1.swmed.edu/Research/haglerdocs/Fridsma2007-08-OCI-Presentation-v2.ppt<br /> <br /> <br /> Action Items/Future Work identified during and after the teleconference:<br /> <br /> #Application of BRIDG and evaluate the model and get a paper out<br /> #Subject Eligibility as a trial piece for the modeling exercise at UT Southwestern<br /> #CDISC vocabulary and Ontology<br /> #Concept Paper (Barry as a probable co-author) CDISC-BRIDG-Ontolgy integration</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_08/10/07_Conference_Call&diff=5898 2007-08-15T20:03:19Z

<p>Hkhagler: New page: Go back to OCI:Main Page Present on the call: Bron Kisler, Jim Zheng, Jennifer Fostel, Richard Scheuermann, Herb Hagler and Richard's Lab OCI Conference Call with Doug Fridsma M.D., ...</p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Bron Kisler, Jim Zheng, Jennifer Fostel, Richard Scheuermann, Herb Hagler and Richard's Lab<br /> <br /> OCI Conference Call with Doug Fridsma M.D., Ph.D.<br /> <br /> Presenting: BRIDG: A Model to support interoperability in Clinical Research<br /> <br /> Doug Fridsma's presentation can be Downloaded here: http://pathcuric1.swmed.edu/Research/haglerdocs/Fridsma2007-08-OCI-Presentation-v2.ppt<br /> <br /> <br /> Action Items/Future Work identified during and after the teleconference:<br /> <br /> i Application of BRIDG and evaluate the model and get a paper out<br /> ii Subject Eligibility as a trial piece for the modeling exercise at UT Southwestern<br /> iii CDISC vocabulary and Ontology<br /> iv Concept Paper (Barry as a probable co-author) CDISC-BRIDG-Ontolgy integration</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Conference_Call_Minutes&diff=5897 2007-08-15T19:59:17Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> * [[Minutes from 08/10/07 Conference Call]]<br /> * [[Minutes from 08/02/07 Conference Call]]<br /> * [[Minutes from 07/19/07 Conference Call]]<br /> * [[Minutes from 06/28/07 Conference Call]]<br /> * [[Minutes from 05/10/07 Conference Call]]<br /> * [[Minutes from 05/03/07 Conference Call]]<br /> * [[Minutes from 04/19/07 Conference Call]]<br /> * [[Minutes from 04/12/07 Conference Call]]</div>

Hkhagler https://www.bioontology.org//mediawiki/index.php?title=Minutes_from_08/02/07_Conference_Call&diff=5870 2007-08-06T13:52:09Z

<p>Hkhagler: </p> <hr /> <div>Go back to [[OCI:Main Page]]<br /> <br /> Present on the call: Christian Cocos, Jim Zheng, Wenle Zhao, Herb Hagler, Jennifer Fostel, Matthias Samwald, Richard Scheuermann&lt;br&gt;<br /> <br /> ''Next TC will be the BRIDG presentation by Doug Fridsma'' <br /> <br /> <br /> <br /> *Aug 10 at 11 CDT Doug Fridsma will give a presentation about BRIDG and its relationship with the NCI Enterprise Vocabulary System (EVS)<br /> <br /> Bron Kisler's presentation can be downloaded here: http://pathcuric1.swmed.edu/Research/haglerdocs/Kisler_OCI_Work_Group_CDISC_Terminology_2Aug2007.ppt<br /> <br /> The following instructions were forwarded describing access to the SDTM Packages under development and the CDISC Glossary. <br /> <br /> Accessing the SDTM Package 2A Terminology set currently posted for public review through 17 August – (i) go to the CDISC website @ www.cdisc.org; (ii) go to the 3rd section posted under “What’s New” on the homepage for the Terminology Team; (iii) go to the “click here” link; and (iv) finally go to the links to download Terminology SDTM Package 2A and the Public Review comment spreadsheet. Once comments are made they can be posted onto the Discussion Forum. SDTM Package 2A represents a compilation of terminology code lists for specific fields in the CDISC Submission Model (SDTM) – ECG fields as well as Concomitant Meds, Drug Exposure and Substance Use.<br /> <br /> <br /> Accessing SDTM Package 1 and the 1st set of Labtest Terms currently in production within the NCI EVS environment – (i) follow steps i-iii above; (ii) click on the link http://www.cancer.gov/cancertopics/terminologyresources/ …this will take you to an environment where CDISC, FDA and other production terminology subsets can be downloaded; (iii) click on the “CDISC Terminology” link on the left side of the web page; and finally (iv) click on the “Excel” link at the bottom to download the CDISC spreadsheet with production terms. Once again, what you will see is a compilation of controlled terminology code list (drawn directly from NCI Thesaurus) associated with specific SDTM fields. We are currently working on a XML rendition of this information for improved system consumption.<br /> <br /> <br /> If anyone on the OCI team would like to ensure they receive the most up-to-date information regarding future public review cycles as well as production terminology releases, they should check “What’s New” on the homepage regularly and/or sign up to the CDISC mailing list. To do so…(i) click the “CDISC Mailing List” link on the homepage; and (ii) then go to “Join our e-mail list” The next set of 200 Labtest terms will be posted for public review this month and SDTM Package 2B this fall. Once a terminology set completes public review and comments are addressed, it is moved into production within the NCI EVS environment. Also, the CDISC Glossary will be posted on the NCI Terminology Resource site by September which will make it much easier for people to access and use.</div>

Hkhagler