https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=RubinNCBO Wiki - User contributions [en]2026-06-05T09:14:51ZUser contributionsMediaWiki 1.35.9https://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6821NCBO Phenotype Workshop2008-04-23T06:30:24Z<p>Rubin: /* Participants */</p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''8:45 Introduction (Mark Musen)<br />
<br />
-- Welcome and workshop goals<br />
<br />
-- Participant self-introductions<br />
<br />
'''9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases''' XXX (Moderator) <br />
<br />
-- Phenotypes in model organisms (Suzi, Chris M)<br />
<br />
-- Phenotypes in neurobiology (Maryann)<br />
<br />
'''10:30am Coffee'''<br />
<br />
'''11:00am Session I (Part 2)'''<br />
<br />
-- Phenotypes in clinical research (Ida)<br />
<br />
-- Phenotypes in clinical medicine (Barry C)<br />
<br />
'''11:30am Session I (Part 3)'''<br />
<br />
-- Phenotypes in cognitive science (NDAR; Amar)<br />
<br />
-- Phenotypes in pharmacogenomics (Russ/Teri)<br />
<br />
'''12:30pm Lunch''' <br />
<br />
'''1:30pm Discussion: commonalities in phenotype descriptions'''<br />
<br />
'''2:30pm Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
-- PaTO and PhenoXML (Chris M)<br />
<br />
-- SWRL (Samson)<br />
<br />
-- Discussion<br />
<br />
3:30pm Coffee <br />
<br />
'''3:00pm Commonalities/differences in requirements for representing phenotypes'''<br />
<br />
4:30pm Summary and Next Steps<br />
<br />
== Participants ==<br />
<br />
Mark Musen (NCBO)<br />
<br />
Daniel Rubin (NCBO)<br />
<br />
Suzi Lewis (NCBO)<br />
<br />
Chris Mungall (NCBO)<br />
<br />
Nigam Shah (NCBO)<br />
<br />
Amar Das (Stanford)<br />
<br />
Samson Tu (Stanford)<br />
<br />
Mor Peleg (University of Haifa)<br />
<br />
Maryann Martone (BIRN)<br />
<br />
Russ Altman (PharmGKB)<br />
<br />
Teri Klein (PharmGKB)<br />
<br />
Barry Coller (Rockefeller CTSA)<br />
<br />
Jon Blumenfeld (Rockefeller CTSA)<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]<br />
<br />
----<br />
<br />
Availability:<br />
MA: NOT July 14-23 or Aug 13-15<br />
IS: NOT July 21-Aug 8<br />
JB: NOT last week in August before Labor Day</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6820NCBO Phenotype Workshop2008-04-23T06:29:27Z<p>Rubin: /* Participants */</p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''8:45 Introduction (Mark Musen)<br />
<br />
-- Welcome and workshop goals<br />
<br />
-- Participant self-introductions<br />
<br />
'''9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases''' XXX (Moderator) <br />
<br />
-- Phenotypes in model organisms (Suzi, Chris M)<br />
<br />
-- Phenotypes in neurobiology (Maryann)<br />
<br />
'''10:30am Coffee'''<br />
<br />
'''11:00am Session I (Part 2)'''<br />
<br />
-- Phenotypes in clinical research (Ida)<br />
<br />
-- Phenotypes in clinical medicine (Barry C)<br />
<br />
'''11:30am Session I (Part 3)'''<br />
<br />
-- Phenotypes in cognitive science (NDAR; Amar)<br />
<br />
-- Phenotypes in pharmacogenomics (Russ/Teri)<br />
<br />
'''12:30pm Lunch''' <br />
<br />
'''1:30pm Discussion: commonalities in phenotype descriptions'''<br />
<br />
'''2:30pm Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
-- PaTO and PhenoXML (Chris M)<br />
<br />
-- SWRL (Samson)<br />
<br />
-- Discussion<br />
<br />
3:30pm Coffee <br />
<br />
'''3:00pm Commonalities/differences in requirements for representing phenotypes'''<br />
<br />
4:30pm Summary and Next Steps<br />
<br />
== Participants ==<br />
<br />
Mark Musen (NCBO)<br />
<br />
Daniel Rubin (NCBO)<br />
<br />
Nigam Shah (NCBO)<br />
<br />
Amar Das (Stanford)<br />
<br />
Samson Tu (Stanford)<br />
<br />
Mor Peleg (University of Haifa)<br />
<br />
Maryann Martone (BIRN)<br />
<br />
Russ Altman (PharmGKB)<br />
<br />
Teri Klein (PharmGKB)<br />
<br />
Barry Coller (Rockefeller CTSA)<br />
<br />
Jon Blumenfeld (Rockefeller CTSA)<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]<br />
<br />
----<br />
<br />
Availability:<br />
MA: NOT July 14-23 or Aug 13-15<br />
IS: NOT July 21-Aug 8<br />
JB: NOT last week in August before Labor Day</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6652NCBO Phenotype Workshop2008-03-19T17:43:18Z<p>Rubin: /* Some Relevant Links */</p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''8:45 Introduction (Mark Musen)<br />
<br />
-- Welcome and workshop goals<br />
<br />
-- Participant self-introductions<br />
<br />
'''9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases''' XXX (Moderator) <br />
<br />
-- Phenotypes in model organisms (Suzi, Chris M)<br />
<br />
-- Phenotypes in neurobiology (Maryann)<br />
<br />
'''10:30am Coffee'''<br />
<br />
'''11:00am Session I (Part 2)'''<br />
<br />
-- Phenotypes in clinical research (Ida)<br />
<br />
-- Phenotypes in clinical medicine (Barry C)<br />
<br />
'''11:30am Session I (Part 3)'''<br />
<br />
-- Phenotypes in cognitive science (NDAR; Amar)<br />
<br />
-- Phenotypes in pharmacogenomics (Russ/Teri)<br />
<br />
'''12:30pm Lunch''' <br />
<br />
'''1:30pm Discussion: commonalities in phenotype descriptions'''<br />
<br />
'''2:30pm Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
-- PaTO and PhenoXML (Chris M)<br />
<br />
-- SWRL (Samson)<br />
<br />
-- Discussion<br />
<br />
3:30pm Coffee <br />
<br />
'''3:00pm Commonalities/differences in requirements for representing phenotypes'''<br />
<br />
4:30pm Summary and Next Steps<br />
<br />
== Participants ==<br />
<br />
Mark Musen (NCBO)<br />
<br />
Daniel Rubin (NCBO)<br />
<br />
Nigam Shah (NCBO)<br />
<br />
Amar Das (Stanford)<br />
<br />
Samson Tu (Stanford)<br />
<br />
Mor Peleg (University of Haifa)<br />
<br />
Maryann Martone (BIRN)<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]<br />
<br />
----<br />
<br />
Availability:<br />
MA: NOT July 14-23 or Aug 13-15<br />
IS: NOT July 21-Aug 8<br />
JB: NOT last week in August before Labor Day</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6614NCBO Phenotype Workshop2008-03-07T01:19:15Z<p>Rubin: </p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''8:45 Introduction (Mark Musen)<br />
<br />
-- Welcome and workshop goals<br />
<br />
-- Participant self-introductions<br />
<br />
'''9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases''' XXX (Moderator) <br />
<br />
-- Phenotypes in model organisms (Suzi, Chris M)<br />
<br />
-- Phenotypes in neurobiology (Maryann)<br />
<br />
'''10:30am Coffee'''<br />
<br />
'''11:00am Session I (Part 2)'''<br />
<br />
-- Phenotypes in clinical research (Ida)<br />
<br />
-- Phenotypes in clinical medicine (Barry C)<br />
<br />
'''11:30am Session I (Part 3)'''<br />
<br />
-- Phenotypes in cognitive science (NDAR; Amar)<br />
<br />
-- Phenotypes in pharmacogenomics (Russ/Teri)<br />
<br />
'''12:30pm Lunch''' <br />
<br />
'''1:30pm Discussion: commonalities in phenotype descriptions'''<br />
<br />
'''2:30pm Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
-- PaTO and PhenoXML (Chris M)<br />
<br />
-- SWRL (Samson)<br />
<br />
-- Discussion<br />
<br />
3:30pm Coffee <br />
<br />
'''3:00pm Commonalities/differences in requirements for representing phenotypes'''<br />
<br />
4:30pm Summary and Next Steps<br />
<br />
== Participants ==<br />
<br />
Mark Musen (NCBO)<br />
<br />
Daniel Rubin (NCBO)<br />
<br />
Nigam Shah (NCBO)<br />
<br />
Amar Das (Stanford)<br />
<br />
Samson Tu (Stanford)<br />
<br />
Mor Peleg (University of Haifa)<br />
<br />
Maryann Martone (BIRN)<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]<br />
<br />
----<br />
<br />
Availability:<br />
MA: NOT July 14-23 or Aug 13-15<br />
IS: NOT July 21-Aug 8</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6609NCBO Phenotype Workshop2008-03-06T16:58:35Z<p>Rubin: </p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''8:45 Introduction (Mark Musen)<br />
<br />
-- Welcome and workshop goals<br />
<br />
-- Participant self-introductions<br />
<br />
'''9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases''' XXX (Moderator) <br />
<br />
-- Phenotypes in model organisms (Suzi, Chris M)<br />
<br />
-- Phenotypes in neurobiology (Maryann)<br />
<br />
'''10:30am Coffee'''<br />
<br />
'''11:00am Session I (Part 2)'''<br />
<br />
-- Phenotypes in clinical research (Ida)<br />
<br />
-- Phenotypes in clinical medicine (Barry C)<br />
<br />
'''11:30am Session I (Part 3)'''<br />
<br />
-- Phenotypes in cognitive science (NDAR; Amar)<br />
<br />
'''12:00pm Lunch''' <br />
<br />
'''1:00pm Discussion: commonalities in phenotype descriptions'''<br />
<br />
'''2:00pm Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
-- PaTO and PhenoXML (Chris M)<br />
<br />
-- SWRL (Samson)<br />
<br />
-- Discussion<br />
<br />
3:30pm Coffee <br />
<br />
'''3:00pm Commonalities/differences in requirements for representing phenotypes'''<br />
<br />
4:30pm Summary and Next Steps<br />
<br />
== Participants ==<br />
<br />
Mark Musen (NCBO)<br />
<br />
Daniel Rubin (NCBO)<br />
<br />
Nigam Shah (NCBO)<br />
<br />
Amar Das (Stanford)<br />
<br />
Samson Tu (Stanford)<br />
<br />
Mor Peleg (University of Haifa)<br />
<br />
Maryann Martone (BIRN)<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]<br />
<br />
----<br />
<br />
Availability:<br />
MA: NOT July 14-23 or Aug 13-15<br />
IS: NOT July 21-Aug 8</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6608NCBO Phenotype Workshop2008-03-06T15:36:06Z<p>Rubin: </p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''8:45 Introduction (Mark Musen)<br />
<br />
-- Welcome and workshop goals<br />
<br />
-- Participant self-introductions<br />
<br />
'''9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases''' XXX (Moderator) <br />
<br />
-- Phenotypes in model organisms (Suzi, Chris M)<br />
<br />
-- Phenotypes in neurobiology (Maryann)<br />
<br />
'''10:30am Coffee'''<br />
<br />
'''11:00am Session I (Part 2)'''<br />
<br />
-- Phenotypes in clinical research (Ida)<br />
<br />
-- Phenotypes in clinical medicine (Barry C)<br />
<br />
'''11:30am Session I (Part 3)'''<br />
<br />
-- Phenotypes in cognitive science (NDAR; Amar)<br />
<br />
'''12:00pm Lunch''' <br />
<br />
'''1:00pm Discussion: commonalities in phenotype descriptions'''<br />
<br />
'''2:00pm Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
-- PaTO and PhenoXML (Chris M)<br />
<br />
-- SWRL (Samson)<br />
<br />
-- Discussion<br />
<br />
3:30pm Coffee <br />
<br />
'''3:00pm Commonalities/differences in requirements for representing phenotypes'''<br />
<br />
4:30pm Summary and Next Steps<br />
<br />
== Participants ==<br />
<br />
Mark Musen (NCBO)<br />
<br />
Daniel Rubin (NCBO)<br />
<br />
Nigam Shah (NCBO)<br />
<br />
Amar Das (Stanford)<br />
<br />
Samson Tu (Stanford)<br />
<br />
Mor Peleg (University of Haifa)<br />
<br />
Maryann Martone (BIRN)<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]<br />
<br />
----<br />
<br />
Availability:<br />
MA: NOT July 14-23 or Aug 13-15</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6585NCBO Phenotype Workshop2008-03-04T22:47:40Z<p>Rubin: </p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''8:45 Introduction (Mark Musen)<br />
<br />
-- Welcome and workshop goals<br />
<br />
-- Participant self-introductions<br />
<br />
'''9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases''' XXX (Moderator) <br />
<br />
-- Phenotypes in model organisms (Suzi, Chris M)<br />
<br />
-- Phenotypes in neurobiology (Maryann)<br />
<br />
'''10:30am Coffee'''<br />
<br />
'''11:00am Session I (Part 2)'''<br />
<br />
-- Phenotypes in clinical research (Ida)<br />
<br />
-- Phenotypes in clinical medicine (Barry C)<br />
<br />
'''11:30am Session I (Part 3)'''<br />
<br />
-- Phenotypes in cognitive science (NDAR; Amar)<br />
<br />
'''12:00pm Lunch''' <br />
<br />
'''1:00pm Discussion: commonalities in phenotype descriptions'''<br />
<br />
'''2:00pm Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
-- PaTO and PhenoXML (Chris M)<br />
<br />
-- SWRL (Samson)<br />
<br />
-- Discussion<br />
<br />
3:30pm Coffee <br />
<br />
'''3:00pm Commonalities/differences in requirements for representing phenotypes'''<br />
<br />
4:30pm Summary and Next Steps<br />
<br />
== Participants ==<br />
<br />
Mark Musen (NCBO)<br />
<br />
Daniel Rubin (NCBO)<br />
<br />
Nigam Shah (NCBO)<br />
<br />
Amar Das (Stanford)<br />
<br />
Samson Tu (Stanford)<br />
<br />
Mor Peleg (University of Haifa)<br />
<br />
Maryann Martone (BIRN)<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]<br />
<br />
----<br />
<br />
Availability:<br />
Ida Sim: June 5, 6, 13, 19, 20 and 27</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6567NCBO Phenotype Workshop2008-02-26T16:58:58Z<p>Rubin: /* Agenda */</p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''8:45 Introduction (Mark Musen)<br />
<br />
-- Welcome and workshop goals<br />
<br />
-- Participant self-introductions<br />
<br />
'''9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases''' XXX (Moderator) <br />
<br />
-- Phenotypes in model organisms (Suzi, Chris M)<br />
<br />
-- Phenotypes in neurobiology (Maryann)<br />
<br />
'''10:30am Coffee'''<br />
<br />
'''11:00am Session I (Part 2)'''<br />
<br />
-- Phenotypes in clinical research (Ida)<br />
<br />
-- Phenotypes in clinical medicine (Barry C)<br />
<br />
'''11:30am Session I (Part 3)'''<br />
<br />
-- Phenotypes in cognitive science (NDAR; Amar)<br />
<br />
'''12:00pm Lunch''' <br />
<br />
'''1:00pm Discussion: commonalities in phenotype descriptions'''<br />
<br />
'''2:00pm Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
-- PaTO and PhenoXML (Chris M)<br />
<br />
-- SWRL (Samson)<br />
<br />
-- Discussion<br />
<br />
3:30pm Coffee <br />
<br />
'''3:00pm Commonalities/differences in requirements for representing phenotypes'''<br />
<br />
4:30pm Summary and Next Steps<br />
<br />
== Participants ==<br />
<br />
Mark Musen (NCBO)<br />
<br />
Daniel Rubin (NCBO)<br />
<br />
Nigam Shah (NCBO)<br />
<br />
Amar Das (Stanford)<br />
<br />
Samson Tu (Stanford)<br />
<br />
Mor Peleg (University of Haifa)<br />
<br />
Maryann Martone (BIRN)<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6566NCBO Phenotype Workshop2008-02-26T16:57:27Z<p>Rubin: /* Participants */</p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''8:45 Introduction (Mark Musen)<br />
<br />
-- Welcome and workshop goals<br />
<br />
-- Participant self-introductions<br />
<br />
'''9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases''' XXX (Moderator) <br />
<br />
-- Phenotypes in model organisms (Suzi, Chris M)<br />
<br />
-- Phenotypes in neurobiology (Maryann)<br />
<br />
'''10:30am Coffee'''<br />
<br />
'''11:00am Session I (Part 2)'''<br />
<br />
-- Phenotypes in clinical research (Ida)<br />
<br />
-- Phenotypes in clinical medicine (Barry C)<br />
<br />
'''11:30am ession I (Part 3)'''<br />
<br />
-- Phenotypes in cognitive science (NDAR; Amar)<br />
<br />
'''12:00pm Lunch''' <br />
<br />
'''1:00pm Discussion: commonalities in phenotype descriptions'''<br />
<br />
'''2:00pm Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
-- PaTO and PhenoXML (Chris M)<br />
<br />
-- SWRL (Samson)<br />
<br />
-- Discussion<br />
<br />
3:30pm Coffee <br />
<br />
'''3:00pm Commonalities/differences in requirements for representing phenotypes'''<br />
<br />
4:30pm Summary and Next Steps<br />
<br />
== Participants ==<br />
<br />
Mark Musen (NCBO)<br />
<br />
Daniel Rubin (NCBO)<br />
<br />
Nigam Shah (NCBO)<br />
<br />
Amar Das (Stanford)<br />
<br />
Samson Tu (Stanford)<br />
<br />
Mor Peleg (University of Haifa)<br />
<br />
Maryann Martone (BIRN)<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6565NCBO Phenotype Workshop2008-02-26T16:55:22Z<p>Rubin: /* Agenda */</p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''8:45 Introduction (Mark Musen)<br />
<br />
-- Welcome and workshop goals<br />
<br />
-- Participant self-introductions<br />
<br />
'''9:00am Session I (Part 1): The spectrum of phenotypes: a review of use cases''' XXX (Moderator) <br />
<br />
-- Phenotypes in model organisms (Suzi, Chris M)<br />
<br />
-- Phenotypes in neurobiology (Maryann)<br />
<br />
'''10:30am Coffee'''<br />
<br />
'''11:00am Session I (Part 2)'''<br />
<br />
-- Phenotypes in clinical research (Ida)<br />
<br />
-- Phenotypes in clinical medicine (Barry C)<br />
<br />
'''11:30am ession I (Part 3)'''<br />
<br />
-- Phenotypes in cognitive science (NDAR; Amar)<br />
<br />
'''12:00pm Lunch''' <br />
<br />
'''1:00pm Discussion: commonalities in phenotype descriptions'''<br />
<br />
'''2:00pm Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
-- PaTO and PhenoXML (Chris M)<br />
<br />
-- SWRL (Samson)<br />
<br />
-- Discussion<br />
<br />
3:30pm Coffee <br />
<br />
'''3:00pm Commonalities/differences in requirements for representing phenotypes'''<br />
<br />
4:30pm Summary and Next Steps<br />
<br />
== Participants ==<br />
<br />
Maryann Martone (BIRN)<br />
<br />
Nigam Shah (Stanford)<br />
<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6564NCBO Phenotype Workshop2008-02-26T16:41:13Z<p>Rubin: /* Agenda */</p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''9:00 Welcome and workshop goals (Mark Musen)<br />
<br />
-- Participant self-introductions<br />
<br />
'''9:30am Session I: The spectrum of phenotypes''' XXX (Moderator) <br />
<br />
-- Phenotypes in model organisms <br />
<br />
-- The OBO Foundry Project <br />
<br />
-- The OBO Relation Ontology <br />
<br />
11:00am Coffee <br />
<br />
11:00am Discussion <br />
<br />
12:30pm Lunch <br />
<br />
'''Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
1:30pm <br />
<br />
2:00pm Ontologies and Terminologies in Radiology and Biological Imaging <br />
<br />
-- Curt Langlotz: RadLex <br />
<br />
-- Maryann Martone: BIRNLex <br />
<br />
-- Anand Kumar: DICOM <br />
<br />
3:30pm Coffee <br />
<br />
4:00pm Relations and Reasoning in Image Ontologies <br />
<br />
-- Dirk Marwede: Relations in Image Ontologies and Anatomy Ontologies <br />
<br />
-- Mariana Casella dos Santos: Bootstrapping an Image Ontology <br />
<br />
-- Helen Chen: Building Real-World Applications and Reasoning in Radiology <br />
<br />
'''Session III: Image Ontologies''' <br />
Suzanna Lewis (Moderatrix) <br />
<br />
9:00am Examples <br />
<br />
-- Matthew Fielding: From RadLex to RadiO <br />
<br />
-- C. Forbes Dewey: Experibase <br />
<br />
10:30am Coffee <br />
<br />
11:00am Reasoning with Image Ontologies <br />
<br />
-- W. Lorensen: Engineering Beyond Pixels <br />
<br />
-- William Bug: BIRN's Image Ontology Requirements <br />
<br />
-- Louis Goldberg: On Reasoning with Images <br />
<br />
12:30pm Lunch <br />
<br />
'''Session IV: Imaging Tools and Data''' <br />
Ivo Dinov and Barry Smith (Moderators) <br />
<br />
1:30pm Towards an Ontology of Imaging Tools and Data <br />
<br />
-- David Kennedy: The Internet Analysis Tools Registry <br />
<br />
-- Barry Smith: What Should an Ontology of Tools and Data Look Like? <br />
<br />
-- Ontology vs. Yellow Pages: Concluding Debate between Ivo Dinov, Peter Lyster, Suzanna Lewis and Bill Lorensen<br />
<br />
3:30pm Coffee <br />
<br />
-- Strategy Session: How to Build an Image Ontology<br />
<br />
== Participants ==<br />
<br />
Maryann Martone (BIRN)<br />
<br />
Nigam Shah (Stanford)<br />
<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6563NCBO Phenotype Workshop2008-02-26T16:40:12Z<p>Rubin: /* Agenda */</p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
9:00<br />
<br />
-- Welcome and workshop goals (Mark Musen)<br />
<br />
-- Participant self-introductions<br />
<br />
9:30am '''Session I: The spectrum of phenotypes''' XXX (Moderator) <br />
<br />
<br />
-- Phenotypes in model organisms <br />
<br />
-- The OBO Foundry Project <br />
<br />
-- The OBO Relation Ontology <br />
<br />
11:00am Coffee <br />
<br />
11:00am Discussion <br />
<br />
12:30pm Lunch <br />
<br />
'''Session II: Methods for Representing Phenotypes''' XXX (Moderator) <br />
<br />
1:30pm <br />
<br />
2:00pm Ontologies and Terminologies in Radiology and Biological Imaging <br />
<br />
-- Curt Langlotz: RadLex <br />
<br />
-- Maryann Martone: BIRNLex <br />
<br />
-- Anand Kumar: DICOM <br />
<br />
3:30pm Coffee <br />
<br />
4:00pm Relations and Reasoning in Image Ontologies <br />
<br />
-- Dirk Marwede: Relations in Image Ontologies and Anatomy Ontologies <br />
<br />
-- Mariana Casella dos Santos: Bootstrapping an Image Ontology <br />
<br />
-- Helen Chen: Building Real-World Applications and Reasoning in Radiology <br />
<br />
'''Session III: Image Ontologies''' <br />
Suzanna Lewis (Moderatrix) <br />
<br />
9:00am Examples <br />
<br />
-- Matthew Fielding: From RadLex to RadiO <br />
<br />
-- C. Forbes Dewey: Experibase <br />
<br />
10:30am Coffee <br />
<br />
11:00am Reasoning with Image Ontologies <br />
<br />
-- W. Lorensen: Engineering Beyond Pixels <br />
<br />
-- William Bug: BIRN's Image Ontology Requirements <br />
<br />
-- Louis Goldberg: On Reasoning with Images <br />
<br />
12:30pm Lunch <br />
<br />
'''Session IV: Imaging Tools and Data''' <br />
Ivo Dinov and Barry Smith (Moderators) <br />
<br />
1:30pm Towards an Ontology of Imaging Tools and Data <br />
<br />
-- David Kennedy: The Internet Analysis Tools Registry <br />
<br />
-- Barry Smith: What Should an Ontology of Tools and Data Look Like? <br />
<br />
-- Ontology vs. Yellow Pages: Concluding Debate between Ivo Dinov, Peter Lyster, Suzanna Lewis and Bill Lorensen<br />
<br />
3:30pm Coffee <br />
<br />
-- Strategy Session: How to Build an Image Ontology<br />
<br />
== Participants ==<br />
<br />
Maryann Martone (BIRN)<br />
<br />
Nigam Shah (Stanford)<br />
<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6562NCBO Phenotype Workshop2008-02-26T16:33:04Z<p>Rubin: </p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Working Groups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.bioontology.org/wiki/index.php/NCBO_Phenotype_Workshop). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''Session I: The spectrum of phenotypes''' XXX (Moderator) <br />
<br />
9:00am <br />
<br />
-- Phenotypes in model organisms <br />
<br />
-- The OBO Foundry Project <br />
<br />
-- The OBO Relation Ontology <br />
<br />
10:30am Coffee <br />
<br />
11:00am Methods for representing phenotypes <br />
<br />
-- PaTO<br />
<br />
-- SWRL <br />
<br />
12:30pm Lunch <br />
<br />
'''Session II: Imaging Terms and Relations''' <br />
Daniel Rubin (Moderator) <br />
<br />
1:30pm Participant self-introductions <br />
<br />
2:00pm Ontologies and Terminologies in Radiology and Biological Imaging <br />
<br />
-- Curt Langlotz: RadLex <br />
<br />
-- Maryann Martone: BIRNLex <br />
<br />
-- Anand Kumar: DICOM <br />
<br />
3:30pm Coffee <br />
<br />
4:00pm Relations and Reasoning in Image Ontologies <br />
<br />
-- Dirk Marwede: Relations in Image Ontologies and Anatomy Ontologies <br />
<br />
-- Mariana Casella dos Santos: Bootstrapping an Image Ontology <br />
<br />
-- Helen Chen: Building Real-World Applications and Reasoning in Radiology <br />
<br />
'''Session III: Image Ontologies''' <br />
Suzanna Lewis (Moderatrix) <br />
<br />
9:00am Examples <br />
<br />
-- Matthew Fielding: From RadLex to RadiO <br />
<br />
-- C. Forbes Dewey: Experibase <br />
<br />
10:30am Coffee <br />
<br />
11:00am Reasoning with Image Ontologies <br />
<br />
-- W. Lorensen: Engineering Beyond Pixels <br />
<br />
-- William Bug: BIRN's Image Ontology Requirements <br />
<br />
-- Louis Goldberg: On Reasoning with Images <br />
<br />
12:30pm Lunch <br />
<br />
'''Session IV: Imaging Tools and Data''' <br />
Ivo Dinov and Barry Smith (Moderators) <br />
<br />
1:30pm Towards an Ontology of Imaging Tools and Data <br />
<br />
-- David Kennedy: The Internet Analysis Tools Registry <br />
<br />
-- Barry Smith: What Should an Ontology of Tools and Data Look Like? <br />
<br />
-- Ontology vs. Yellow Pages: Concluding Debate between Ivo Dinov, Peter Lyster, Suzanna Lewis and Bill Lorensen<br />
<br />
3:30pm Coffee <br />
<br />
-- Strategy Session: How to Build an Image Ontology<br />
<br />
== Participants ==<br />
<br />
Maryann Martone (BIRN)<br />
<br />
Nigam Shah (Stanford)<br />
<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6561NCBO Phenotype Workshop2008-02-26T16:29:39Z<p>Rubin: </p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on defining the requirements for representing biomedical phenotypes using ontologies. The workshop will take place on April XX-XX, 2008 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to collect the requirements for representing phenotypes by surveying the breadth of use cases for using ontologies to represent them. The workshop will be the first step in coordinating efforts to represent phenotypes in a breadth of biomedical domains. An additional goal is to explore possibility in attaining a representation ("annotation model") for ontology-based representation of phenotypes. <br />
<br />
The workshop will include in-depth studies of use cases for representing phenotypes in a spectrum of current large initiatives spanning the biomedical spectrum, including BIRN, CVRG, the CTSA program, and the model organism community. <br />
<br />
The following topics will be addressed:<br />
<br />
- definition of "phenotype" (and related notions, such as eligibility criteria)<br />
<br />
- ontologies needed to represent clinical phenotypes<br />
<br />
- spectrum of use cases for describing phenotypes across breadth of biomedical community (molecular, cellular, biological, and clinical)<br />
<br />
- requirements for modeling phenotypes, comparing EAV/EV models and richer representations (e.g., SWRL)<br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]) in grammars<br />
<br />
- tool support for creating phenotype descriptions ("annotations") and storing them<br />
<br />
The workshop is designed to be of value to researchers, resource developers, and clinicians interested in describing phenotypes in computationally-accessible formats. <br />
<br />
This workshop is being funded by the National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. <br />
<br />
Additional support is being provided by <br />
<br />
== Workgroups and Mailing List ==<br />
<br />
At the conclusion of the workshop, if participants are interested in continuing the discussions and undertaking the work related to representing phenotypes, a mailing list for these discussions will be set up.<br />
<br />
In addition, a Wiki to host materials related to the workshop has been created (http://www.neuroinformatics.org:8080/xwiki/bin/view/ImageOntology/Main). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
(See [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast] for videos of all sessions.)<br />
<br />
'''Session I: How to Build an Ontology''' Barry Smith (Moderator) <br />
<br />
9:00am Introduction <br />
<br />
-- What this Meeting is For <br />
<br />
-- Basic Principles of Ontology Design <br />
<br />
-- The OBO Foundry Project <br />
<br />
-- The OBO Relation Ontology <br />
<br />
10:30am Coffee <br />
<br />
11:00am Towards an Ontology for the Imaging Domain <br />
<br />
-- BIRNLex and RadLex Case Studies <br />
<br />
12:15pm Kaustubh Supekar: An Overview of the Groups Represented at this Meeting <br />
<br />
12:30pm Lunch <br />
<br />
'''Session II: Imaging Terms and Relations''' <br />
Daniel Rubin (Moderator) <br />
<br />
1:30pm Participant self-introductions <br />
<br />
2:00pm Ontologies and Terminologies in Radiology and Biological Imaging <br />
<br />
-- Curt Langlotz: RadLex <br />
<br />
-- Maryann Martone: BIRNLex <br />
<br />
-- Anand Kumar: DICOM <br />
<br />
3:30pm Coffee <br />
<br />
4:00pm Relations and Reasoning in Image Ontologies <br />
<br />
-- Dirk Marwede: Relations in Image Ontologies and Anatomy Ontologies <br />
<br />
-- Mariana Casella dos Santos: Bootstrapping an Image Ontology <br />
<br />
-- Helen Chen: Building Real-World Applications and Reasoning in Radiology <br />
<br />
'''Session III: Image Ontologies''' <br />
Suzanna Lewis (Moderatrix) <br />
<br />
9:00am Examples <br />
<br />
-- Matthew Fielding: From RadLex to RadiO <br />
<br />
-- C. Forbes Dewey: Experibase <br />
<br />
10:30am Coffee <br />
<br />
11:00am Reasoning with Image Ontologies <br />
<br />
-- W. Lorensen: Engineering Beyond Pixels <br />
<br />
-- William Bug: BIRN's Image Ontology Requirements <br />
<br />
-- Louis Goldberg: On Reasoning with Images <br />
<br />
12:30pm Lunch <br />
<br />
'''Session IV: Imaging Tools and Data''' <br />
Ivo Dinov and Barry Smith (Moderators) <br />
<br />
1:30pm Towards an Ontology of Imaging Tools and Data <br />
<br />
-- David Kennedy: The Internet Analysis Tools Registry <br />
<br />
-- Barry Smith: What Should an Ontology of Tools and Data Look Like? <br />
<br />
-- Ontology vs. Yellow Pages: Concluding Debate between Ivo Dinov, Peter Lyster, Suzanna Lewis and Bill Lorensen<br />
<br />
3:30pm Coffee <br />
<br />
-- Strategy Session: How to Build an Image Ontology<br />
<br />
== Participants ==<br />
<br />
Maryann Martone (BIRN)<br />
<br />
Nigam Shah (Stanford)<br />
<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6560NCBO Phenotype Workshop2008-02-26T16:11:29Z<p>Rubin: </p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of (biomedical) images and imaging. The workshop will take place on March 24-25, 2006 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to promote interoperability of biomedical image and imaging ontologies through the application of principles of sound ontology construction and through the coordination of current ontology development efforts in the imaging domain. One subsidiary goal is to ensure compatibility of image ontologies with ontologies of those biomedical entities which images represent. The workshop will include hands-on experiments directed towards building a biomedical image ontology on the basis of sample ontologies submitted by participants in advance.<br />
<br />
The following topics will be addressed:<br />
<br />
- coordination and integration of ontologies in the imaging domain<br />
<br />
- ontologies for classification of images, image features, interpretations, <br />
<br />
- the role of a reference ontology such as the [http://sig.biostr.washington.edu/projects/fm/AboutFM.html FMA] <br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]), including relations among images, features, interpretations, and the underlying reality<br />
<br />
- use of ontologies in reasoning<br />
<br />
- building an ontology of imaging tools and data, including issues related to the classification of imaging algorithms and to the potential uses of a tools ontology in supporting interoperability of bioinformatics software (in conjunction with the [http://na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group Software and Data Integration Working Group] of the NIH Roadmap National Centers for Biomedical Computing).<br />
<br />
The workshop is designed to be of value to all those involved in biocomputing in the imaging domain, including representatives of those NCBCs who use or develop imaging technologies. <br />
<br />
This workshop was funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. Additional support has been provided by GlaxoSmithKline (GSK), Language & Computing (L&C) and Agfa.<br />
<br />
== Workgroups and Mailing List ==<br />
<br />
At the conclusion of the workshop, many participants expressed interest in continuing the discussions and undertaking the work related to imaging ontology. A mailing list for these discussions was set up (https://www.neuroinformatics.org/mailman/listinfo/image-ontology)<br />
<br />
In addition, a Wiki to host materials related to a working group in imaging ontology was created (http://www.neuroinformatics.org:8080/xwiki/bin/view/ImageOntology/Main). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
(See [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast] for videos of all sessions.)<br />
<br />
'''Session I: How to Build an Ontology''' Barry Smith (Moderator) <br />
<br />
9:00am Introduction <br />
<br />
-- What this Meeting is For <br />
<br />
-- Basic Principles of Ontology Design <br />
<br />
-- The OBO Foundry Project <br />
<br />
-- The OBO Relation Ontology <br />
<br />
10:30am Coffee <br />
<br />
11:00am Towards an Ontology for the Imaging Domain <br />
<br />
-- BIRNLex and RadLex Case Studies <br />
<br />
12:15pm Kaustubh Supekar: An Overview of the Groups Represented at this Meeting <br />
<br />
12:30pm Lunch <br />
<br />
'''Session II: Imaging Terms and Relations''' <br />
Daniel Rubin (Moderator) <br />
<br />
1:30pm Participant self-introductions <br />
<br />
2:00pm Ontologies and Terminologies in Radiology and Biological Imaging <br />
<br />
-- Curt Langlotz: RadLex <br />
<br />
-- Maryann Martone: BIRNLex <br />
<br />
-- Anand Kumar: DICOM <br />
<br />
3:30pm Coffee <br />
<br />
4:00pm Relations and Reasoning in Image Ontologies <br />
<br />
-- Dirk Marwede: Relations in Image Ontologies and Anatomy Ontologies <br />
<br />
-- Mariana Casella dos Santos: Bootstrapping an Image Ontology <br />
<br />
-- Helen Chen: Building Real-World Applications and Reasoning in Radiology <br />
<br />
'''Session III: Image Ontologies''' <br />
Suzanna Lewis (Moderatrix) <br />
<br />
9:00am Examples <br />
<br />
-- Matthew Fielding: From RadLex to RadiO <br />
<br />
-- C. Forbes Dewey: Experibase <br />
<br />
10:30am Coffee <br />
<br />
11:00am Reasoning with Image Ontologies <br />
<br />
-- W. Lorensen: Engineering Beyond Pixels <br />
<br />
-- William Bug: BIRN's Image Ontology Requirements <br />
<br />
-- Louis Goldberg: On Reasoning with Images <br />
<br />
12:30pm Lunch <br />
<br />
'''Session IV: Imaging Tools and Data''' <br />
Ivo Dinov and Barry Smith (Moderators) <br />
<br />
1:30pm Towards an Ontology of Imaging Tools and Data <br />
<br />
-- David Kennedy: The Internet Analysis Tools Registry <br />
<br />
-- Barry Smith: What Should an Ontology of Tools and Data Look Like? <br />
<br />
-- Ontology vs. Yellow Pages: Concluding Debate between Ivo Dinov, Peter Lyster, Suzanna Lewis and Bill Lorensen<br />
<br />
3:30pm Coffee <br />
<br />
-- Strategy Session: How to Build an Image Ontology<br />
<br />
== Participants ==<br />
<br />
Maryann Martone (BIRN)<br />
<br />
Nigam Shah (Stanford)<br />
<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_Phenotype_Workshop&diff=6559NCBO Phenotype Workshop2008-02-26T16:08:23Z<p>Rubin: New page: Some Relevant Links == Background == The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of (biome...</p>
<hr />
<div>[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of (biomedical) images and imaging. The workshop will take place on March 24-25, 2006 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to promote interoperability of biomedical image and imaging ontologies through the application of principles of sound ontology construction and through the coordination of current ontology development efforts in the imaging domain. One subsidiary goal is to ensure compatibility of image ontologies with ontologies of those biomedical entities which images represent. The workshop will include hands-on experiments directed towards building a biomedical image ontology on the basis of sample ontologies submitted by participants in advance.<br />
<br />
The following topics will be addressed:<br />
<br />
- coordination and integration of ontologies in the imaging domain<br />
<br />
- ontologies for classification of images, image features, interpretations, <br />
<br />
- the role of a reference ontology such as the [http://sig.biostr.washington.edu/projects/fm/AboutFM.html FMA] <br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology]), including relations among images, features, interpretations, and the underlying reality<br />
<br />
- use of ontologies in reasoning<br />
<br />
- building an ontology of imaging tools and data, including issues related to the classification of imaging algorithms and to the potential uses of a tools ontology in supporting interoperability of bioinformatics software (in conjunction with the [http://na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group Software and Data Integration Working Group] of the NIH Roadmap National Centers for Biomedical Computing).<br />
<br />
The workshop is designed to be of value to all those involved in biocomputing in the imaging domain, including representatives of those NCBCs who use or develop imaging technologies. <br />
<br />
This workshop was funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. Additional support has been provided by GlaxoSmithKline (GSK), Language & Computing (L&C) and Agfa.<br />
<br />
== Workgroups and Mailing List ==<br />
<br />
At the conclusion of the workshop, many participants expressed interest in continuing the discussions and undertaking the work related to imaging ontology. A mailing list for these discussions was set up (https://www.neuroinformatics.org/mailman/listinfo/image-ontology)<br />
<br />
In addition, a Wiki to host materials related to a working group in imaging ontology was created (http://www.neuroinformatics.org:8080/xwiki/bin/view/ImageOntology/Main). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
(See [http://www.bioontology.org/wiki/index.php/Workshop_on_Ontology_of_Images#Webcast Webcast] for videos of all sessions.)<br />
<br />
'''Session I: How to Build an Ontology''' Barry Smith (Moderator) <br />
<br />
9:00am Introduction <br />
<br />
-- What this Meeting is For <br />
<br />
-- Basic Principles of Ontology Design <br />
<br />
-- The OBO Foundry Project <br />
<br />
-- The OBO Relation Ontology <br />
<br />
10:30am Coffee <br />
<br />
11:00am Towards an Ontology for the Imaging Domain <br />
<br />
-- BIRNLex and RadLex Case Studies <br />
<br />
12:15pm Kaustubh Supekar: An Overview of the Groups Represented at this Meeting <br />
<br />
12:30pm Lunch <br />
<br />
'''Session II: Imaging Terms and Relations''' <br />
Daniel Rubin (Moderator) <br />
<br />
1:30pm Participant self-introductions <br />
<br />
2:00pm Ontologies and Terminologies in Radiology and Biological Imaging <br />
<br />
-- Curt Langlotz: RadLex <br />
<br />
-- Maryann Martone: BIRNLex <br />
<br />
-- Anand Kumar: DICOM <br />
<br />
3:30pm Coffee <br />
<br />
4:00pm Relations and Reasoning in Image Ontologies <br />
<br />
-- Dirk Marwede: Relations in Image Ontologies and Anatomy Ontologies <br />
<br />
-- Mariana Casella dos Santos: Bootstrapping an Image Ontology <br />
<br />
-- Helen Chen: Building Real-World Applications and Reasoning in Radiology <br />
<br />
'''Session III: Image Ontologies''' <br />
Suzanna Lewis (Moderatrix) <br />
<br />
9:00am Examples <br />
<br />
-- Matthew Fielding: From RadLex to RadiO <br />
<br />
-- C. Forbes Dewey: Experibase <br />
<br />
10:30am Coffee <br />
<br />
11:00am Reasoning with Image Ontologies <br />
<br />
-- W. Lorensen: Engineering Beyond Pixels <br />
<br />
-- William Bug: BIRN's Image Ontology Requirements <br />
<br />
-- Louis Goldberg: On Reasoning with Images <br />
<br />
12:30pm Lunch <br />
<br />
'''Session IV: Imaging Tools and Data''' <br />
Ivo Dinov and Barry Smith (Moderators) <br />
<br />
1:30pm Towards an Ontology of Imaging Tools and Data <br />
<br />
-- David Kennedy: The Internet Analysis Tools Registry <br />
<br />
-- Barry Smith: What Should an Ontology of Tools and Data Look Like? <br />
<br />
-- Ontology vs. Yellow Pages: Concluding Debate between Ivo Dinov, Peter Lyster, Suzanna Lewis and Bill Lorensen<br />
<br />
3:30pm Coffee <br />
<br />
-- Strategy Session: How to Build an Image Ontology<br />
<br />
== Participants ==<br />
<br />
Yasser alSafadi (Philips Research)<br />
<br />
Carol Bean (NCRR)<br />
<br />
Bruce Bray (Utah) <br />
<br />
William Bug (BIRN)<br />
<br />
James A Butler (GlaxoSmithKline)<br />
<br />
David Channin (NMH)<br />
<br />
Helen Chen (Agfa)<br />
<br />
Beverly Collins (Radlex) <br />
<br />
Sherri de Coronado (NCI)<br />
<br />
C. Forbes Dewey (MIT)<br />
<br />
Ivo Dinov (UCLA)<br />
<br />
Keith Dreyer (Harvard)<br />
<br />
Matthew Fielding (IFOMIS)<br />
<br />
Daniel Gardner (Cornell)<br />
<br />
Christine Golbreich (Rennes)<br />
<br />
Louis Goldberg (Buffalo)<br />
<br />
Jeff Grethe (BIRN)<br />
<br />
Ammar Halawa (FujiFilm Medical Systems)<br />
<br />
Donald Harrington (NIBIB)<br />
<br />
David Hellman (L&C) <br />
<br />
Peter Hunter (Aukland)<br />
<br />
David Kennedy (Harvard)<br />
<br />
Richard I. Kitney (Imperial College, London)<br />
<br />
Anand Kumar (IFOMIS)<br />
<br />
Curtis Langlotz (University of Pennsylvania)<br />
<br />
Suzanna Lewis (Berkeley)<br />
<br />
William Lorensen (General Electric)<br />
<br />
Peter F. Lyster (NIH/NIGMS)<br />
<br />
Maryann Martone (BIRN)<br />
<br />
Dirk Marwede (IFOMIS / Department of Radiology, University of Leipzig)<br />
<br />
Jose L. Mejino, Jr. (Foundational Model of Anatomy)<br />
<br />
John Michon (Duke)<br />
<br />
Chris Mungall (Berkeley)<br />
<br />
Robert Murphy (CMU)<br />
<br />
Mark Musen (Stanford)<br />
<br />
Dianne Reeves (NCI)<br />
<br />
Jens Rittscher (GE)<br />
<br />
Daniel Rubin (Stanford)<br />
<br />
Mariana Casella Dos Santos (L&C, Belgium)<br />
<br />
Nigam Shah (Stanford)<br />
<br />
Ken Shastri (FujiMed)<br />
<br />
Barry Smith (Buffalo)<br />
<br />
Kaushtubh Supekar (Stanford)<br />
<br />
== Webcast ==<br />
<br />
Session I<br />
Barry Smith (Moderator)<br />
<br />
'''How to Build an Ontology''' <br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram<br />
<br />
'''Towards an Ontology for the Imaging Domain'''<br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram<br />
<br />
<br />
Session II <br />
Daniel Rubin (Moderator)<br />
<br />
'''Imaging Terms and Relations''' <br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-1330.ram<br />
<br />
'''Relations and Reasoning in Image Ontologies'''<br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-1600.ram<br />
<br />
<br />
Session III <br />
Suzanna Lewis (Moderatrix)<br />
<br />
'''Image Ontologies''' <br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-09.ram<br />
<br />
'''Reasoning with Image Ontologies'''<br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-11.ram<br />
<br />
<br />
Session IV <br />
Ivo Dinov and Barry Smith (Moderatores)<br />
<br />
'''Imaging Tools and Data''' <br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-1330.ram<br />
<br />
'''Ontology vs. Yellow Pages'''<br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-1600.ram<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://genomebiology.com/2005/6/5/R47 The Open Microscopy Environment (OME) Data Model]<br />
<br />
[http://obo.sourceforge.net/cgi-bin/detail.cgi?image OBO Biological Imaging Methods]<br />
<br />
[http://www.rsna.org/Radlex/index.cfm RadLex: A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources]<br />
<br />
[http://medical.nema.org/ DICOM]<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
[http://www.dclunie.com/ David Clunie's Medical Image Format Site]<br />
<br />
[http://www.library.uthscsa.edu/internet/ImageDatabases.cfm Medical Image Databases]<br />
<br />
[http://www.pathbase.net/Pathbase/ Mutant Mouse Images]<br />
<br />
[http://sig.biostr.washington.edu/projects/fm/AboutFM.html Foundational Model of Anatomy]<br />
<br />
[http://www.structuredreporting.com/ Structured Reporting]<br />
<br />
[http://murphylab.web.cmu.edu/services/ Murphy Lab Image Services]<br />
<br />
[https://cabig.nci.nih.gov/workspaces/Imaging In Vivo Imaging]<br />
<br />
[http://www.cl.cam.ac.uk/%7Eafb21/publications/TwD98.html A Taxonomy of Diagram Taxonomies]<br />
<br />
[http://www.bioimage.org/ Bioimage Database]<br />
<br />
[http://www.brainmap.org/ BrainMap:A Functional Neuroimaging Database]<br />
<br />
<br />
== Tool Registries ==<br />
<br />
[http://www.cma.mgh.harvard.edu/iatr/ Registry of Image Analysis Tools]<br />
<br />
[http://www.brc-central.org/tdb/prok_manatee/brc-central/software.shtml BRC Central Bioinformatics Resource Center]<br />
<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_News&diff=6558NCBO News2008-02-26T16:05:06Z<p>Rubin: </p>
<hr />
<div>==Press Releases==<br />
[http://med.stanford.edu/research/spotlight/archive/biocomp_center.html cBiO helps structure data]<br />
==Announcements==<br />
[[NCBO_Phenotype_Workshop | NCBO Workshop on Requirements for Describing Phenotypes]]'''</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=NCBO_News&diff=6557NCBO News2008-02-26T16:03:48Z<p>Rubin: </p>
<hr />
<div>==Press Releases==<br />
[http://med.stanford.edu/research/spotlight/archive/biocomp_center.html cBiO helps structure data]<br />
==Announcements==<br />
[NCBO_Announcements]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Public_Requirements_Redirect&diff=4990Public Requirements Redirect2007-02-16T13:45:24Z<p>Rubin: </p>
<hr />
<div>(We have completed our requirements gathering phase for BioPortal 2.0. Current requirements are in the RDD document at https://ncboprojects.updatelog.com/projects/879071/file/4526432/OBO-RDD+R2+v1.doc)</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=4989Main Page2007-02-16T13:43:42Z<p>Rubin: </p>
<hr />
<div>Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, <br><br />
dissemination events conducted by the NCBO and publically shared materials from the NCBO.<br />
<br />
<br />
=== NCBO Links ===<br />
*[http://www.bioontology.org/ NCBO Home page]<br />
*[http://www.bioontology.org/wiki/index.php/CBio_FAQ NCBO FAQ]<br />
*[[Meetings and Events]]<br />
<br />
=== Shared Materials===<br />
<br />
*[[Public Requirements Redirect|Public Requirements]]<br />
<br />
*[[Shared Materials]]<br />
<br />
*[[Evaluation Activities]]<br />
<br />
=== Other NCBC Links ===<br />
<br />
*[http://www.bisti.nih.gov/ncbc/ NCBC Home page]<br />
<br />
*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]<br />
<br />
=== Ontology Development Area ===<br />
<br />
Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki<br />
<br />
*[[PATO:Main_Page]] - An ontology of phenotypic qualities<br />
<br />
*[[RO:Main_Page]] - OBO Relations ontology<br />
<br />
*[[CARO:Main_Page]] - Reference anatomical ontology<br />
<br />
*[[CL:Main_Page]] - OBO Cell ontology<br />
<br />
*[[SO:Main_Page]] - Sequence Ontology<br />
<br />
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders<br />
<br />
Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.<br />
<br />
*[[OboInOwl:Main_Page]] - Mapping between Obo and OWL</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=4988Main Page2007-02-16T13:43:16Z<p>Rubin: </p>
<hr />
<div>Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, <br><br />
dissemination events conducted by the NCBO and publically shared materials from the NCBO.<br />
<br />
<br />
=== NCBO Links ===<br />
*[http://www.bioontology.org/ NCBO Home page]<br />
*[http://www.bioontology.org/wiki/index.php/CBio_FAQ NCBO FAQ]<br />
*[[Meetings and Events]]<br />
<br />
=== Shared Materials===<br />
<br />
*[[Public Requirements 1|Public Requirements]]<br />
<br />
*[[Shared Materials]]<br />
<br />
*[[Evaluation Activities]]<br />
<br />
=== Other NCBC Links ===<br />
<br />
*[http://www.bisti.nih.gov/ncbc/ NCBC Home page]<br />
<br />
*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]<br />
<br />
=== Ontology Development Area ===<br />
<br />
Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki<br />
<br />
*[[PATO:Main_Page]] - An ontology of phenotypic qualities<br />
<br />
*[[RO:Main_Page]] - OBO Relations ontology<br />
<br />
*[[CARO:Main_Page]] - Reference anatomical ontology<br />
<br />
*[[CL:Main_Page]] - OBO Cell ontology<br />
<br />
*[[SO:Main_Page]] - Sequence Ontology<br />
<br />
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders<br />
<br />
Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.<br />
<br />
*[[OboInOwl:Main_Page]] - Mapping between Obo and OWL</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=4987Main Page2007-02-16T13:42:43Z<p>Rubin: </p>
<hr />
<div>Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, <br><br />
dissemination events conducted by the NCBO and publically shared materials from the NCBO.<br />
<br />
<br />
=== NCBO Links ===<br />
*[http://www.bioontology.org/ NCBO Home page]<br />
*[http://www.bioontology.org/wiki/index.php/CBio_FAQ NCBO FAQ]<br />
*[[Meetings and Events]]<br />
<br />
=== Shared Materials===<br />
<br />
*[[Public Requirements|Public_Requirements_1]]<br />
<br />
*[[Shared Materials]]<br />
<br />
*[[Evaluation Activities]]<br />
<br />
=== Other NCBC Links ===<br />
<br />
*[http://www.bisti.nih.gov/ncbc/ NCBC Home page]<br />
<br />
*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]<br />
<br />
=== Ontology Development Area ===<br />
<br />
Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki<br />
<br />
*[[PATO:Main_Page]] - An ontology of phenotypic qualities<br />
<br />
*[[RO:Main_Page]] - OBO Relations ontology<br />
<br />
*[[CARO:Main_Page]] - Reference anatomical ontology<br />
<br />
*[[CL:Main_Page]] - OBO Cell ontology<br />
<br />
*[[SO:Main_Page]] - Sequence Ontology<br />
<br />
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders<br />
<br />
Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.<br />
<br />
*[[OboInOwl:Main_Page]] - Mapping between Obo and OWL</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=4981MediaWiki:Sidebar2007-02-10T21:08:27Z<p>Rubin: </p>
<hr />
<div>* navigation<br />
** mainpage|mainpage<br />
** CBio_News|NCBO News<br />
** CBio_FAQ|NCBO FAQ<br />
** Public_Requirements|Public RQs<br />
** Shared_Materials|Shared Materials<br />
** Glossary|Glossary<br />
** Dissemination_Wiki|Dissemination Wiki<br />
** Education|Education/NCBO Lab<br />
** Outreach_and_Dev|Outreach and Sci Dev<br />
** Meetings_and_Events|Meetings and Events<br />
** recentchanges-url|recentchanges<br />
** helppage|help</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Glossary&diff=4980Glossary2007-02-10T21:07:25Z<p>Rubin: /* Definitions */</p>
<hr />
<div>==About==<br />
<br />
This glossary is to help communication within the NCBO by standardizing the terms we use internally<br />
<br />
Many of the terms here are sourced from:<br />
[[Media:SmithCeusters.pdf]]<br />
<br />
== Meanings of terms used in NCBO ==<br />
<br />
'''Levels of Reality:'''<br />
<br />
1 - Physical Reality<br />
<br />
2 - Psychological Reality = our knowledge and beliefs about 1.<br />
<br />
3 - Propositions, Theories, Texts = formalizations of those ideas and beliefs<br />
<br />
== Definitions ==<br />
<br />
===Entity===<br />
<br />
anything which exists, including things and processes, functions and qualities, beliefs and actions, documents and software (Levels 1, 2 and 3)<br />
<br />
Note that sometimes in software engineering the term "entity" refers solely to a the digital representation itself rather than the thing being represented. Within NCBO we use "entity" to mean anything that exists, but typically for level 1 entities.<br />
<br />
===Domain===<br />
<br />
portion of reality that forms the subject-matter of a single science or technology or mode of study.<br />
<br />
===Representation===<br />
<br />
an image, idea, map, picture, name or description ... of some entity or entities.<br />
<br />
===Representational Units===<br />
<br />
terms, icons, alphanumeric identifiers ... which refer, or are intended to refer, to entities. <br />
<br />
===Ontology===<br />
<br />
a representational artifact whose representational units (which may be drawn from a natural or from some formalized language) are intended to represent types in reality and those relations between these types which obtain universally (universally = for all instances)<br />
<br />
====Application vs Reference Ontology====<br />
<br />
There is a good summary here:<br />
Reference Ontologies - Application Ontologies: Either/Or or Both/And?<br />
Christopher Menzel<br />
Texas AM University<br />
<br />
[[Media:MenzelOntology.pdf]]<br />
<br />
=== Mapping vs. Alignment ===<br />
Mapping = Refers to the process of creation of a relationship b/w<br />
terms in separate ontologies<br />
<br />
Alignment = Refers to the process of creation of a near-synonymy<br />
relation b/w terms in separate ontologies<br />
<br />
<br />
===Universal (type)===<br />
<br />
===Particular (instance)===<br />
<br />
===Aristotelian Definition===<br />
<br />
Also known as genus-differentia definition (but not limited to species taxonomies).<br />
<br />
http://en.wikipedia.org/wiki/Genus-differentia_definition</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=4979MediaWiki:Sidebar2007-02-09T14:38:56Z<p>Rubin: </p>
<hr />
<div>* navigation<br />
** mainpage|mainpage<br />
** CBio_News|NCBO News<br />
** CBio_FAQ|NCBO FAQ<br />
** Public_Requirements|Public RQs<br />
** Shared_Materials|Shared Materials<br />
** Dissemination_Wiki|Dissemination Wiki<br />
** Education|Education/NCBO Lab<br />
** Outreach_and_Dev|Outreach and Sci Dev<br />
** Meetings_and_Events|Meetings and Events<br />
** recentchanges-url|recentchanges<br />
** helppage|help</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=4978MediaWiki:Sidebar2007-02-09T14:38:22Z<p>Rubin: </p>
<hr />
<div>* navigation<br />
** mainpage|mainpage<br />
** CBio_News|NCBO News<br />
** CBio_FAQ|NCBO FAQ<br />
** Public RQs|Public_Requirements<br />
** Shared_Materials|Shared Materials<br />
** Dissemination_Wiki|Dissemination Wiki<br />
** Education|Education/NCBO Lab<br />
** Outreach_and_Dev|Outreach and Sci Dev<br />
** Meetings_and_Events|Meetings and Events<br />
** recentchanges-url|recentchanges<br />
** helppage|help</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=4975Dissemination Wiki2007-02-02T17:57:22Z<p>Rubin: </p>
<hr />
<div>==NCBO Dissemination Core==<br />
<br />
What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to events relevant to the NCBO's mission.<br />
<br />
==Workshops==<br />
<br />
'''Feb 28-March 1, 2006'''<br />
<br />
[http://www.bioontology.org/wiki/index.php/BIRN_Ontology_workshop BIRN Ontology Workshop], Stanford University<br />
<br />
'''March 24-25, 2006'''<br />
<br />
[[Workshop on Ontology of Images]], Stanford University<br />
<br />
'''May 21-24, 2006'''<br />
<br />
[http://ontology.buffalo.edu/06/os2/index.html Training Course in Biomedical Ontology], Schloss Dagstuhl, Germany<br />
<br />
'''September 8-9, 2006'''<br />
<br />
[[Anatomy Ontology Workshop]], Seattle<br />
<br />
'''November 6-7, 2006'''<br />
<br />
[[Workshop on Ontology of Diseases]], Baltimore<br />
<br />
'''November 30-December 2, 2006'''<br />
<br />
[[PATO Meeting]] Stanford University Clark Center <br />
<br />
'''May 16-17, 2007'''<br />
<br />
[[Workshop on Clinical Trial Ontology]], venue tbd<br />
<br />
'''June 20-23, 2007'''<br />
<br />
[http://www.ifomis.uni-saarland.de/Events/OntospringIII.html Training Course on Logical and Computational Tools for Biomedical Ontology Development, Schloss Dagstuhl, Germany.]<br />
<br />
'''July 21, 2007'''<br />
<br />
[[Ontologies for Biomedicine – How to make and use them]], Tutorial by Barry Smith and Nigam Shah at ISMB 2007<br />
<br />
== Related Events ==<br />
<br />
'''July 19, 2006'''<br />
<br />
[http://www.bisti.nih.gov/ahm2006/ncbo_dissemination.htm Ontology: A Vision for the Future and Its Realization], National Institutes of Health NCBC All-Hands Meeting, Bethesda MD.<br />
*[[Media:Musen AHM Dissemination Event.pdf|Musen Slides]]<br />
<br />
*[http://obofoundry.org/Smith_OBOFoundry_071906.ppt Smith Slides]<br />
<br />
'''August 6, 2006'''<br />
<br />
[http://ismb2006.cbi.cnptia.embrapa.br/ Keynote Address by Suzanna Lewis], ISMB 2006.<br />
*[[Media:Lewis ISMB 2006 Keynote CSB.pdf|Lewis Slides]]<br />
<br />
'''August 15, 2006'''<br />
<br />
[http://www.lifesciencessociety.org/CSB2006/Abstracts/musenAbstract.pdf Keynote Address by Mark Musen], CSB 2006, Stanford 1:30-2:30pm.<br />
*[[Media:Musen Keynote CSB.pdf|Musen Slides]]<br />
<br />
'''August 27, 2006'''<br />
<br />
[http://ontology.buffalo.edu/06/MIE_Tutorial.htm Tutorial on Standards and Ontologies], Medical Informatics Europe, Maastricht, Netherlands.<br />
<br />
'''October 14-15, 2006'''<br />
<br />
[http://ontology.buffalo.edu/06/pob Workshop on Philosophy of Biology], Buffalo.<br />
<br />
'''October 25, 2006'''<br />
<br />
How to Build an Ontology. Tutorial by Barry Smith at NCBO project meeting<br />
*[[Media:BarrySmithTutorialNCBO.ppt | Smith Slides]] <br />
<br />
*Windows Media Player: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV<br />
<br />
*RealOne Player Streaming Video: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm<br />
<br />
'''November 8, 2006'''<br />
<br />
[http://www.imbi.uni-freiburg.de/medinf/kr-med-2006/index.html Biomedical Ontology in Action], KR-MED 2006, Baltimore.<br />
<br />
'''November 11, 2006'''<br />
<br />
[http://ontology.buffalo.edu/06/Biomedical_Imaging_Ontologies.pdf Biomedical Imaging Ontologies], AMIA, Washington DC<br />
<br />
'''November 12, 2006'''<br />
<br />
[http://ontology.buffalo.edu/06/AMIAWorkshop.htm Genomics Knowledge Representation for Clinical Trials], AMIA, Washington DC<br />
<br />
ISWC Workshop, Pathway Knowledge Base, Presentation by Nigam Shah<br />
*[[Media:Nigam-PKB.ppt|Shah Slides]]<br />
<br />
'''November 14, 2006'''<br />
<br />
[http://ontology.buffalo.edu/HL7/panel.htm Panel on the Future of HL7], AMIA, Washington, 3.30-5.00pm. <br />
*[http://www.org.buffalo.edu/RTU/papers/HL7-AMIA2006.ppt Ceusters Slides]<br />
*[http://ontology.buffalo.edu/HL7/AMIA_06_Audio/Ceusters.WMA Ceusters Audio]<br />
*[http://ontology.buffalo.edu/hl7/AMIA_06.ppt Smith Slides]<br />
*[http://ontology.buffalo.edu/HL7/AMIA_06_Audio/Smith.WMA Smith Audio]<br />
<br />
AMIA Workshop, Formal Structuring of Genomics Knowledge, Presentations by Nigam Shah and Barry Smith<br />
*[[Media:Nigam1.ppt|Shah Slides]]<br />
*[http://ontology.buffalo.edu/ontology/medo/ClinicalTrialOntology/AMIA_Genome_Nov06.ppt Smith Slides]<br />
<br />
Ontology-Driven Annotation of TMA Data, AMIA Presentation by Nigam Shah<br />
*[[Media:Nigam2.ppt|Shah Slides]]<br />
<br />
AMIA Tutorial on Ontologies by Mark Musen<br />
*[[Media:Musen-AMIA2006.ppt|Musen Slides]]<br />
<br />
'''November 20-21, 2006'''<br />
<br />
BioPAX Tutorial. [http://biopaxwiki.org/cgi-bin/moin.cgi/SmithWorkshopInformation exploratory workshop and tutorial] on '''Connecting BioPAX to Other Biomedical Ontologies''' at MIT.<br />
<br />
'''December 21, 2006'''<br />
<br />
Ontolog Forum Talk by Barry Smith on [http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2006_12_21#nidRW3 Ontology Evaluation in Biomedicine]: The OBO Foundry -- A Gold Standard Approach to Ontology Evaluation. <br />
*[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2006_12_21#nidRWB Smith Slides] <br />
*[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2006_12_21#nidRWQ Smith Audio]<br />
<br />
'''January 29, 2007'''<br />
<br />
Overview presentation of GO, NCBO, Phenotypes, and OBO Foundry by Suzi Lewis at the Ontologies for Biomedical Investigation Workshop, San Diego, CA<br />
*[[Media:OverviewJan07LaJollaCJM.ppt|Slide Presentation]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=4973Dissemination Wiki2007-01-30T18:33:59Z<p>Rubin: /* Related Events */</p>
<hr />
<div>==NCBO Dissemination Core==<br />
<br />
What follows is a list of events organized under the auspices of the NCBO's Dissemination Core (PI: [http://ontology.buffalo.edu/smith Barry Smith]), together with information pertaining to events relevant to the NCBO's mission.<br />
<br />
==Workshops==<br />
<br />
'''Feb 28-March 1, 2006'''<br />
<br />
[http://www.bioontology.org/wiki/index.php/BIRN_Ontology_workshop BIRN Ontology Workshop], Stanford University<br />
<br />
'''March 24-25, 2006'''<br />
<br />
[[Workshop on Ontology of Images]], Stanford University<br />
<br />
'''May 21-24, 2006'''<br />
<br />
[http://ontology.buffalo.edu/06/os2/index.html Training Course in Biomedical Ontology], Schloss Dagstuhl, Germany<br />
<br />
'''September 8-9, 2006'''<br />
<br />
[[Anatomy Ontology Workshop]], Seattle<br />
<br />
'''November 6-7, 2006'''<br />
<br />
[[Workshop on Ontology of Diseases]], Baltimore<br />
<br />
'''November 30-December 2, 2006'''<br />
<br />
[[PATO Meeting]] Stanford University Clark Center <br />
<br />
'''May 16-17, 2007'''<br />
<br />
[[Workshop on Clinical Trial Ontology]], venue tbd<br />
<br />
'''June 20-23, 2007'''<br />
<br />
[http://www.ifomis.uni-saarland.de/Events/OntospringIII.html Training Course on Logical and Computational Tools for Biomedical Ontology Development, Schloss Dagstuhl, Germany.]<br />
<br />
'''July 21, 2007'''<br />
<br />
[[Ontologies for Biomedicine – How to make and use them]], Tutorial by Barry Smith and Nigam Shah at ISMB 2007<br />
<br />
== Related Events ==<br />
<br />
'''July 19, 2006'''<br />
<br />
[http://www.bisti.nih.gov/ahm2006/ncbo_dissemination.htm Ontology: A Vision for the Future and Its Realization], National Institutes of Health NCBC All-Hands Meeting, Bethesda MD.<br />
*[[Media:Musen AHM Dissemination Event.pdf|Musen Slides]]<br />
<br />
*[http://obofoundry.org/Smith_OBOFoundry_071906.ppt Smith Slides]<br />
<br />
'''August 6, 2006'''<br />
<br />
[http://ismb2006.cbi.cnptia.embrapa.br/ Keynote Address by Suzanna Lewis], ISMB 2006.<br />
*[[Media:Lewis ISMB 2006 Keynote CSB.pdf|Lewis Slides]]<br />
<br />
'''August 15, 2006'''<br />
<br />
[http://www.lifesciencessociety.org/CSB2006/Abstracts/musenAbstract.pdf Keynote Address by Mark Musen], CSB 2006, Stanford 1:30-2:30pm.<br />
*[[Media:Musen Keynote CSB.pdf|Musen Slides]]<br />
<br />
'''August 27, 2006'''<br />
<br />
[http://ontology.buffalo.edu/06/MIE_Tutorial.htm Tutorial on Standards and Ontologies], Medical Informatics Europe, Maastricht, Netherlands.<br />
<br />
'''October 14-15, 2006'''<br />
<br />
[http://ontology.buffalo.edu/06/pob Workshop on Philosophy of Biology], Buffalo.<br />
<br />
'''October 25, 2006'''<br />
<br />
How to Build an Ontology. Tutorial by Barry Smith at NCBO project meeting<br />
*[[Media:BarrySmithTutorialNCBO.ppt | Smith Slides]] <br />
<br />
*Windows Media Player: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.WMV<br />
<br />
*RealOne Player Streaming Video: rtsp://stream.buffalo.edu/shared/research/phismith/Stanford10-25-06/Tutorial.rm<br />
<br />
'''November 8, 2006'''<br />
<br />
[http://www.imbi.uni-freiburg.de/medinf/kr-med-2006/index.html Biomedical Ontology in Action], KR-MED 2006, Baltimore.<br />
<br />
'''November 11, 2006'''<br />
<br />
[http://ontology.buffalo.edu/06/Biomedical_Imaging_Ontologies.pdf Biomedical Imaging Ontologies], AMIA, Washington DC<br />
<br />
'''November 12, 2006'''<br />
<br />
[http://ontology.buffalo.edu/06/AMIAWorkshop.htm Genomics Knowledge Representation for Clinical Trials], AMIA, Washington DC<br />
<br />
ISWC Workshop, Pathway Knowledge Base, Presentation by Nigam Shah<br />
*[[Media:Nigam-PKB.ppt|Shah Slides]]<br />
<br />
'''November 14, 2006'''<br />
<br />
[http://ontology.buffalo.edu/HL7/panel.htm Panel on the Future of HL7], AMIA, Washington, 3.30-5.00pm. <br />
*[http://www.org.buffalo.edu/RTU/papers/HL7-AMIA2006.ppt Ceusters Slides]<br />
*[http://ontology.buffalo.edu/HL7/AMIA_06_Audio/Ceusters.WMA Ceusters Audio]<br />
*[http://ontology.buffalo.edu/hl7/AMIA_06.ppt Smith Slides]<br />
*[http://ontology.buffalo.edu/HL7/AMIA_06_Audio/Smith.WMA Smith Audio]<br />
<br />
AMIA Workshop, Formal Structuring of Genomics Knowledge, Presentations by Nigam Shah and Barry Smith<br />
*[[Media:Nigam1.ppt|Shah Slides]]<br />
*[http://ontology.buffalo.edu/ontology/medo/ClinicalTrialOntology/AMIA_Genome_Nov06.ppt Smith Slides]<br />
<br />
Ontology-Driven Annotation of TMA Data, AMIA Presentation by Nigam Shah<br />
*[[Media:Nigam2.ppt|Shah Slides]]<br />
<br />
AMIA Tutorial on Ontologies by Mark Musen<br />
*[[Media:Musen-AMIA2006.ppt|Musen Slides]]<br />
<br />
'''November 20-21, 2006'''<br />
<br />
BioPAX Tutorial. [http://biopaxwiki.org/cgi-bin/moin.cgi/SmithWorkshopInformation exploratory workshop and tutorial] on '''Connecting BioPAX to Other Biomedical Ontologies''' at MIT.<br />
<br />
'''December 21, 2006'''<br />
<br />
Ontolog Forum Talk by Barry Smith on [http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2006_12_21#nidRW3 Ontology Evaluation in Biomedicine]: The OBO Foundry -- A Gold Standard Approach to Ontology Evaluation. <br />
*[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2006_12_21#nidRWB Smith Slides] <br />
*[http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2006_12_21#nidRWQ Smith Audio]<br />
<br />
'''January 29, 2007'''<br />
<br />
Overview presentation of GO, NCBO, Phenotypes, and OBO Foundry by Suzi Lewis at the Ontologies for Biomedical Investigation Workshop, San Diego, CA<br />
*[[Media:Suzi_OBI_2007.ppt|Slide Presentation]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Outreach_and_Dev&diff=4931Outreach and Dev2007-01-24T05:40:53Z<p>Rubin: </p>
<hr />
<div>==Communities for NCBO Outreach==<br />
*OBO<br />
*NCI<br />
*W3C Health Care Life Sci SIG<br />
*BIRN<br />
*(Suzi DAC? community)<br />
*CTSA informatics community</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=4930MediaWiki:Sidebar2007-01-24T05:39:20Z<p>Rubin: </p>
<hr />
<div>* navigation<br />
** mainpage|mainpage<br />
** CBio_News|NCBO News<br />
** CBio_FAQ|NCBO FAQ<br />
** Shared_Materials|Shared Materials<br />
** Dissemination_Wiki|Dissemination Wiki<br />
** Education|Education/NCBO Lab<br />
** Outreach_and_Dev|Outreach and Sci Dev<br />
** Meetings_and_Events|Meetings and Events<br />
** recentchanges-url|recentchanges<br />
** helppage|help</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=4929MediaWiki:Sidebar2007-01-24T05:38:49Z<p>Rubin: </p>
<hr />
<div>* navigation<br />
** mainpage|mainpage<br />
** CBio_News|NCBO News<br />
** CBio_FAQ|NCBO FAQ<br />
** Shared_Materials|Shared Materials<br />
** Dissemination_Wiki|Dissemination Wiki<br />
** Education|Education/NCBO Lab<br />
** Outreach_and_Dev|Outreach &amp; Scientific Dev<br />
** Meetings_and_Events|Meetings and Events<br />
** recentchanges-url|recentchanges<br />
** helppage|help</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=MediaWiki:Sidebar&diff=4928MediaWiki:Sidebar2007-01-24T05:38:26Z<p>Rubin: </p>
<hr />
<div>* navigation<br />
** mainpage|mainpage<br />
** CBio_News|NCBO News<br />
** CBio_FAQ|NCBO FAQ<br />
** Shared_Materials|Shared Materials<br />
** Dissemination_Wiki|Dissemination Wiki<br />
** Education|Education/NCBO Lab<br />
** Outreach_and_Dev|Outreach & Scientific Dev<br />
** Meetings_and_Events|Meetings and Events<br />
** recentchanges-url|recentchanges<br />
** helppage|help</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=File:FmaToOwl.zip&diff=4924File:FmaToOwl.zip2007-01-23T16:48:26Z<p>Rubin: </p>
<hr />
<div></div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=FMAInOwl&diff=4922FMAInOwl2007-01-23T04:13:19Z<p>Rubin: </p>
<hr />
<div>We have created a transformation for the FMA into OWL that pursues the following two goals:<br />
<br />
1. representing only the information that is explicitly present in the frames representation of the FMA or that can be directly inferred from the semantics of Protege frames; <br />
<br />
2. representing al l the information that is present in the frames representation of the FMA, thus producing an OWL representation for the complete FMA.<br />
<br />
The '''description''' of the transformation is available as an SMI Technical report [http://smi.stanford.edu/smi-web/research/details.jsp?PubId=1234 SMI-2007-1234]<br />
<br />
The '''OWL representation''' of the FMA is available at [http://www.bioontology.org/projects/ontologies/fma http://www.bioontology.org/projects/ontologies/fma]<br />
<br />
If you want to access the OWL file directly, point your OWL tool (e.g. the Protege OWL ontology editor) to<br />
<br />
[http://www.bioontology.org/projects/ontologies/fma/fmaOwlFullCopmonent_1_4_0.owl http://www.bioontology.org/projects/ontologies/fma/fmaOwlFullCopmonent_1_4_0.owl]<br />
<br />
Note that it will use owl:imports to import another OWL ontology in the same directory ([http://www.bioontology.org/projects/ontologies/fma/fmaOwlDlCopmonent_1_4_0.owl http://www.bioontology.org/projects/ontologies/fma/fmaOwlDlCopmonent_1_4_0.owl]).<br />
<br />
The '''conversion script''' is also available: download the [[Media:fmaToOwl.zip|FMA-TO-OWL Converter]]<br />
<br />
The conversion script takes the following arguments:<br />
<br />
- the path to the Protege project with the frames version of the FMA<br />
<br />
- the namespace to use for the OWL DL component<br />
<br />
- the namespace to use for the OWL Full component<br />
<br />
Note: the following files (available in the Protege installation directory must also be on the classpath): icu4j_3_4.jar:iri.jar:xercesImpl.jar:protege.jar:commons-logging.jar:jena.jar:driver.jar:protege-owl.jar</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=FMAInOwl&diff=4921FMAInOwl2007-01-23T04:12:16Z<p>Rubin: </p>
<hr />
<div>We have created a transformation for the FMA into OWL that pursues the following two goals:<br />
<br />
1. representing only the information that is explicitly present in the frames representation of the FMA or that can be directly inferred from the semantics of Protege frames; <br />
<br />
2. representing al l the information that is present in the frames representation of the FMA, thus producing an OWL representation for the complete FMA.<br />
<br />
The '''description''' of the transformation is available as an SMI Technical report [http://smi.stanford.edu/smi-web/research/details.jsp?PubId=1234 SMI-2007-1234]<br />
<br />
The '''OWL representation''' of the FMA is available at [http://www.bioontology.org/projects/ontologies/fma http://www.bioontology.org/projects/ontologies/fma]<br />
<br />
If you want to access the OWL file directly, point your OWL tool (e.g. the Protege OWL ontology editor) to<br />
<br />
[http://www.bioontology.org/projects/ontologies/fma/fmaOwlFullCopmonent_1_4_0.owl http://www.bioontology.org/projects/ontologies/fma/fmaOwlFullCopmonent_1_4_0.owl]<br />
<br />
Note that it will use owl:imports to import another OWL ontology in the same directory ([http://www.bioontology.org/projects/ontologies/fma/fmaOwlDlCopmonent_1_4_0.owl http://www.bioontology.org/projects/ontologies/fma/fmaOwlDlCopmonent_1_4_0.owl]).<br />
<br />
The '''conversion script''' is also available: download the [[Media:fmaToOwl.jar|FMA-TO-OWL Converter]]<br />
<br />
The conversion script takes the following arguments:<br />
<br />
- the path to the Protege project with the frames version of the FMA<br />
<br />
- the namespace to use for the OWL DL component<br />
<br />
- the namespace to use for the OWL Full component<br />
<br />
Note: the following files (available in the Protege installation directory must also be on the classpath): icu4j_3_4.jar:iri.jar:xercesImpl.jar:protege.jar:commons-logging.jar:jena.jar:driver.jar:protege-owl.jar</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4912Education2007-01-22T01:45:05Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum Myhre-S, Additional gene ontology structure for improved biological reasoning]<br />
*Jan 26 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16554186&query_hl=3&itool=pubmed_docsum Melton-GB et al, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*Feb 12, 2007: [http://www.biomedcentral.com/1471-2105/8/17 Publishing perishing? Towards tomorrow's information architecture]<br />
*Feb 19, 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15892875&query_hl=4&itool=pubmed_docsum Goldberg-AG, The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging]<br/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12677061&query_hl=4&itool=pubmed_docsum Swedlow-JR Informatics and quantitative analysis in biological imaging]<br />
*Feb 26, 2007:<br />
*Mar 5, 2007:<br />
*Mar 12, 2007<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4911Education2007-01-22T01:44:51Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum Myhre-S, Additional gene ontology structure for improved biological reasoning]<br />
*Jan 26 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16554186&query_hl=3&itool=pubmed_docsum Melton-GB et al, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*Feb 12, 2007: [http://www.biomedcentral.com/1471-2105/8/17 Publishing perishing? Towards tomorrow's information architecture]<br />
*Feb 19, 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15892875&query_hl=4&itool=pubmed_docsum Goldberg-AG, The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging]<br/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12677061&query_hl=4&itool=pubmed_docsum Swedlow-JR Informatics and quantitative analysis in biological imaging]<br />
*Feb 26, 2007:<br />
*Mar 5, 2007:<br />
*Mar 12, 2007<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4910Education2007-01-22T01:44:36Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum Myhre-S, Additional gene ontology structure for improved biological reasoning]<br />
*Jan 26 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16554186&query_hl=3&itool=pubmed_docsum Melton-GB et al, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*Feb 12, 2007: [http://www.biomedcentral.com/1471-2105/8/17 Publishing perishing? Towards tomorrow's information architecture]<br />
*Feb 19, 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15892875&query_hl=4&itool=pubmed_docsum Goldberg-AG, The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging]<br/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12677061&query_hl=4&itool=pubmed_docsum Swedlow-JR Informatics and quantitative analysis in biological imaging]<br />
*Feb 26, 2007:<br />
*Mar 5, 2007:<br />
*Mar 12, 2007<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4909Education2007-01-22T01:44:10Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum Myhre-S, Additional gene ontology structure for improved biological reasoning]<br />
*Jan 26 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16554186&query_hl=3&itool=pubmed_docsum Melton-GB et al, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*Feb 12, 2007: [http://www.biomedcentral.com/1471-2105/8/17 Publishing perishing? Towards tomorrow's information architecture]<br />
*Feb 19, 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15892875&query_hl=4&itool=pubmed_docsum Goldberg-AG, The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging]<br/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12677061&query_hl=4&itool=pubmed_docsum Swedlow-JR Informatics and quantitative analysis in biological imaging]<br />
*Feb 26, 2007:<br />
*Mar 5, 2007:<br />
*Mar 12, 2007<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4908Education2007-01-22T01:43:57Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum Myhre-S, Additional gene ontology structure for improved biological reasoning]<br />
*Jan 26 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16554186&query_hl=3&itool=pubmed_docsum Melton-GB et al, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*Feb 12, 2007: [http://www.biomedcentral.com/1471-2105/8/17 Publishing perishing? Towards tomorrow's information architecture]<br />
*Feb 19, 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15892875&query_hl=4&itool=pubmed_docsum Goldberg-AG, The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging]<br/><br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12677061&query_hl=4&itool=pubmed_docsum Swedlow-JR Informatics and quantitative analysis in biological imaging]<br />
*Feb 26, 2007:<br />
*Mar 5, 2007:<br />
*Mar 12, 2007<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4907Education2007-01-22T01:43:18Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum Myhre-S, Additional gene ontology structure for improved biological reasoning]<br />
*Jan 26 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16554186&query_hl=3&itool=pubmed_docsum Melton-GB et al, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*Feb 12, 2007: [http://www.biomedcentral.com/1471-2105/8/17 Publishing perishing? Towards tomorrow's information architecture]<br />
*Feb 19, 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15892875&query_hl=4&itool=pubmed_docsum Goldberg-AG, The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging]<br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12677061&query_hl=4&itool=pubmed_docsum Swedlow-JR Informatics and quantitative analysis in biological imaging]<br />
*Feb 26, 2007:<br />
*Mar 5, 2007:<br />
*Mar 12, 2007<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4906Education2007-01-22T01:42:48Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum Myhre-S, Additional gene ontology structure for improved biological reasoning]<br />
*Jan 26 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16554186&query_hl=3&itool=pubmed_docsum Melton-GB et al, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*Feb 12, 2007: [http://www.biomedcentral.com/1471-2105/8/17 Publishing perishing? Towards tomorrow's information architecture]<br />
*Feb 19, 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15892875&query_hl=4&itool=pubmed_docsum Goldberg-AG, The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging]<br />
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12677061&query_hl=4&itool=pubmed_docsum Swedlow-JR Informatics and quantitative analysis in biological imaging]<br />
*Feb 26, 2007:<br />
*Mar 5, 2007:<br />
*Mar 12, 2007<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4905Education2007-01-22T01:42:12Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum Myhre-S, Additional gene ontology structure for improved biological reasoning]<br />
*Jan 26 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16554186&query_hl=3&itool=pubmed_docsum Melton-GB et al, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*Feb 12, 2007: [http://www.biomedcentral.com/1471-2105/8/17 Publishing perishing? Towards tomorrow's information architecture]<br />
*Feb 19, 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15892875&query_hl=4&itool=pubmed_docsum &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Goldberg-AG, The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging]<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12677061&query_hl=4&itool=pubmed_docsum Swedlow-JR Informatics and quantitative analysis in biological imaging]<br />
*Feb 26, 2007:<br />
*Mar 5, 2007:<br />
*Mar 12, 2007<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4904Education2007-01-22T01:41:15Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum Myhre-S, Additional gene ontology structure for improved biological reasoning]<br />
*Jan 26 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16554186&query_hl=3&itool=pubmed_docsum Melton-GB et al, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*Feb 12, 2007: [http://www.biomedcentral.com/1471-2105/8/17 Publishing perishing? Towards tomorrow's information architecture]<br />
*Feb 19, 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=15892875&query_hl=4&itool=pubmed_docsum Goldberg-AG, The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging]<br />
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12677061&query_hl=4&itool=pubmed_docsum Swedlow-JR Informatics and quantitative analysis in biological imaging]<br />
*Feb 26, 2007:<br />
*Mar 5, 2007:<br />
*Mar 12, 2007<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4903Education2007-01-21T03:04:45Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum Myhre-S, Additional gene ontology structure for improved biological reasoning]<br />
*Jan 26 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16554186&query_hl=3&itool=pubmed_docsum Melton-GB et al, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*Feb 5, 2007: [http://www.biomedcentral.com/1471-2105/8/17 Publishing perishing? Towards tomorrow's information architecture]<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4902Education2007-01-21T03:03:46Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum Myhre-S, Additional gene ontology structure for improved biological reasoning]<br />
*Jan 26 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16554186&query_hl=3&itool=pubmed_docsum Melton-GB et al, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*Feb 5, 2007: [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?tmpl=NoSidebarfile&db=PubMed&cmd=Retrieve&list_uids=16554186&dopt=Abstract Melton-GB, Inter-patient distance metrics using SNOMED CT defining relationships]<br />
*when?: [http://www.biomedcentral.com/1471-2105/8/17 Publishing perishing? Towards tomorrow's information architecture]<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed Location]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4888Education2007-01-19T19:22:56Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: Myhre-S, Additional gene ontology structure for improved biological reasoning, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum<br />
*Jan 26 2007: Oliver-DE, Representation of change in controlled medical terminologies, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed<br />
*Feb 5, 2007: Melton-GB, Inter-patient distance metrics using SNOMED CT defining relationships, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?tmpl=NoSidebarfile&db=PubMed&cmd=Retrieve&list_uids=16554186&dopt=Abstract<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=4884Education2007-01-18T03:27:30Z<p>Rubin: /* Articles of Interest for Journal Clubs */</p>
<hr />
<div>===Educational Events and Presentations===<br />
[[Media:CSB2006.pdf|Slides from tutorial on Bio-ontologies at CSB 2006]]<br />
<br />
===Articles of Interest for Journal Clubs===<br />
*Jan 8 2007: Myhre-S, Additional gene ontology structure for improved biological reasoning, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16787968&query_hl=4&itool=pubmed_docsum<br />
*Jan 22 2007: Oliver-DE, Representation of change in controlled medical terminologies, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pubmed<br />
*Feb 5, 2007: Melton-GB, Inter-patient distance metrics using SNOMED CT defining relationships, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?tmpl=NoSidebarfile&db=PubMed&cmd=Retrieve&list_uids=16554186&dopt=Abstract<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*Journal of American Medical Informatics Association<br />
*Journal of Biomedical Informatics<br />
*Bioinformatics<br />
*BMC Bioinformatics<br />
*Briefings in Bioinformatics<br />
*Journal of Bioinformatics and Computational Biology<br />
*International Journal of Medical Informatics<br />
<br />
====Ontologies====<br />
*Journal of Applied Ontology<br />
<br />
====Biomedical====<br />
*Genome Biology<br />
*Nature Biotechnology<br />
*Computers in Biology and Medicine<br />
*Omics: A journal of Integrative Biology<br />
*Applied Bioinformatics<br />
*Artificial Intelligence in Medicine<br />
<br />
===Symposia and Meetings===<br />
*ISWC<br />
*AMIA<br />
*ESWC<br />
*ISMB<br />
*PSB<br />
*WWW Conference<br />
*KCAP/EKAW<br />
*KR-MED<br />
*HCLSIG</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Shared_Materials&diff=4877Shared Materials2007-01-17T16:20:00Z<p>Rubin: </p>
<hr />
<div>This page lists materials shared among members of NCBO<br />
==NCBO Documents==<br />
[[Public Requirements]]<br />
<br />
[[Media:cbio-r01-plan.v11.doc|Collaboration Plan]]<br />
<br />
[[Media:cBiO-5-pg Center Overview.v3.doc|Center Overview 5-page document]]<br />
<br />
[[Media:cbio_flyer_v3.pdf|NCBO Brochure]]<br />
<br />
[[Media:OBO-Foundry.doc|OBO Foundry]]<br />
<br />
==NCBO Policies and Guidelines==<br />
[[Citing the Center]]<br />
<br />
[[Acknowledgements in NCBO Papers]]<br />
<br />
==PowerPoint Presentations==<br />
<br />
===Project meeting March 2006 Talks===<br />
<br />
*[[Media:OBO-Core-Criteria.ppt|OBO Core Criteria, Barry Smith slides]]<br />
*[[Media:AHM_Ashburner.ppt|Cambridge: Ashburner]]<br />
*[[Media:AHM_Barry.ppt|Buffalo: Smith]]<br />
*[[Media:AHM_Core1.ppt|Stanford: Murphy]]<br />
*[[Media:AHM_LexGrid.ppt|Mayo: Buntrock]]<br />
*[[Media:AHM_Monte.ppt|UOregon: Westerfield]]<br />
*[[Media:AHM_Sim.ppt|UCSF: Sim]]<br />
*[[Media:AHM_Peggy.ppt|UVic: Storey]]<br />
*[[Media:AHM_Suzi.ppt|Berkeley: Lewis]]<br />
*[[Media:AHM_OBD.ppt|Berkeley: Mungall]]<br />
<br />
===AMIA 2005 Talks===<br />
#[[Media:Musen AMIA Panel.ppt|Mark Musen slides]]<br />
#[[Media:AMIA_Bioontology_05.pdf|Chris Chute slides]]<br />
#[[Media:SmithpanelSemantics.ppt|Barry Smith slides]]<br />
#[[Media:AMIA_Oct2005_SLewis.ppt|Suzi Lewis slides]]<br />
<br />
===CSH Talks===<br />
#[[Media:CSHL_22Oct2005_SLewis.ppt|Suzi Lewis slides]]<br />
<br />
===NCOR Talks===<br />
#[[Media:cBio-NCOR_SLewis.ppt|Suzi Lewis slides]]<br />
<br />
===Phenotype November 2005 Talks===<br />
#[[Media:Westerfield_Pheno_CSH.ppt|Monte Westerfield slides]]<br />
#[[Media:Drysdale_Pheno_CSH.ppt|Rachel Drysdale slides]]<br />
#[[Media:Mungall_Pheno_CSH.ppt|Chris Mungall slides]]<br />
<br />
===Phenotype December 2005 Talks===<br />
* [[Media:cBioMockup_ZFIN0512.pdf|Erik Segerdell mockup]]<br />
* [[Media:cBioRequirements_ZFIN0512.doc|Melissa Haendel and Erik Segerdell requirements]]<br />
* [[Media:Uvic_viztools_Asimilar_Dec2005.ppt|Peggy Storey's (UVic) presentation on visualization]]<br />
<br />
===SMI Talk===<br />
* [[Media:OntologyJoy.ppt|Suzi SMI Talk]]<br />
<br />
===NIH Kickoff Meeting Talks Dec 2005===<br />
* [[Media:cBiO NCBC kickoff mtg.ppt|Kickoff Meeting Slides]]<br />
<br />
===HCLS===<br />
* [[Media:Musen W3C HCLS-converted.ppt|HCLS meeting]]<br />
<br />
===NIH Dissemination Event July 2006===<br />
*[http://www.bisti.nih.gov/ahm2006/Presentations/NCBO/Dissemination/Musen_AHM_Dissemination_Event.pdf Mark A. Musen: Ontology: A Vision for the Future and Its Realization]<br />
* [http://www.bisti.nih.gov/ahm2006/Presentations%5CNCBO%5CDissemination%5CSmith_OBOFoundry_071906.ppt Barry Smith: The OBO Foundry]<br />
<br />
===PATO meeting May 2006, Hinxton===<br />
*[[Media:Phenote-pato-hinxton-may-2006.ppt|Phenote slides, Mark Gibson]]<br />
<br />
===Berkeley-Stanford July 10 meeting===<br />
*[[Media:Phenote-stanford-july-2006.ppt|Phenote slides,Mark Gibson]]<br />
<br />
===ZFin early August 2006 meeting===<br />
*[[Media:Phenote-zfin-aug-1-2006.ppt|Phenote slides,Mark Gibson]]<br />
<br />
===CARO September 2006 meeting===<br />
[[Media:CARO_minutes.doc|MEETING MINUTES]]<br />
<br />
<br />
PRESENTATIONS:<br />
*[http://ontology.buffalo.edu/medo/CARO_Smith.ppt OBO Foundry Principles, Barry Smith]<br />
*[[Media:ncbo-anatomy-2006-intro-cjm.ppt|OBO Foundry principles in GO, Chris Mungall]]<br />
*[[Media:anatomy-and-stages.ppt|Stages,Chris Mungall]]<br />
*[[Media:MODs-anatomy-mah.ppt|MODs Anatomy,Melissa Haendel]]<br />
*[[Media:DOS_Seattle_SessionII.ppt|Part relationships during development, David Sutherland]]<br />
*[[Media:Homology-review.ppt|Homology Review, Melissa Haendel]]<br />
*[[Media:developing_structure_types.ppt|Classifying Developing Structures, David Sutherland]]</div>Rubinhttps://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=4876Main Page2007-01-17T16:19:15Z<p>Rubin: </p>
<hr />
<div>Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, <br><br />
dissemination events conducted by the NCBO and publically shared materials from the NCBO.<br />
<br />
<br />
=== NCBO Links ===<br />
*[http://www.bioontology.org/ NCBO Home page]<br />
*[http://www.bioontology.org/wiki/index.php/CBio_FAQ NCBO FAQ]<br />
*[[Meetings and Events]]<br />
<br />
=== Shared Materials===<br />
<br />
*[[Public Requirements]]<br />
<br />
*[[Shared Materials]]<br />
<br />
*[[Evaluation Activities]]<br />
<br />
=== Other NCBC Links ===<br />
<br />
*[http://www.bisti.nih.gov/ncbc/ NCBC Home page]<br />
<br />
*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]<br />
<br />
=== Ontology Development Area ===<br />
<br />
Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki<br />
<br />
*[[PATO:Main_Page]] - An ontology of phenotypic qualities<br />
<br />
*[[RO:Main_Page]] - OBO Relations ontology<br />
<br />
*[[CARO:Main_Page]] - Reference anatomical ontology<br />
<br />
*[[CL:Main_Page]] - OBO Cell ontology<br />
<br />
*[[SO:Main_Page]] - Sequence Ontology<br />
<br />
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders<br />
<br />
Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.<br />
<br />
*[[OboInOwl:Main_Page]] - Mapping between Obo and OWL</div>Rubin