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[[Ontology Modules]]
The modules below are designed for use in teaching ontology to multidisciplinary audiences in domains such as government and administration, military and biomedical informatics. The content derives initially from the course "[http://ncorwiki.buffalo.edu/index.php/Problems_in_Ontology PHI:531 Problems in Ontology"] taught in the University at Buffalo in the fall of 2012. However, it will be continually expanded and up-dated where necessary.


[http://myub.buffalo.edu/course/public/scripts/crs_sched.cgi?switch=showclass&semester=fall&division=GRAD&dept=PHI&regnum=23893 PHI 531] Graduate Seminar: '''Problems in Ontology'''
----
Link to: [http://ncorwiki.buffalo.edu/index.php/Streaming_Video_Ontology_Training_Courses Streaming Video Ontology Training Courses]


Crosslisted with [http://myub.buffalo.edu/course/public/scripts/crs_sched.cgi?switch=showclass&semester=fall&division=UGRD&dept=PHI&regnum=23892 PHI 358] '''Problems in Ontology'''


Up to 4 Credit Hours


Principal faculty: [http://ontology.buffalo.edu/smith Barry Smith]
== General Ontology ==


'''Mondays, 4-6pm, Fall 2012, Jacobs 106, UB North Campus'''
'''Barry Smith: Introduction to Ontology (2012)''' [http://org.buffalo.edu/Ontology_in_Buffalo_Aug_27_2012.ppt Slides]
*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/1-Introduction-to-ontology.wmv Video]
:Provides a basic introduction to ontology by addressing questions such as: What is an ontology? What are the differences and interrelations between ontology (philosophy), ontology (science), and ontology (engineering)? How are ontologies used? We will also provide an introduction to Basic Formal Ontology (BFO), focusing on a discussion of the question: What is a musical score?


All sessions will be accessible both for face-to-face participants and on-line via webex.  
'''Werner Ceusters (Bioinformatics/Psychiatry): Particulars in Focus''' [http://www.referent-tracking.com/RTU/sendfile/?file=20120910-OntologyClassOnReferentTracking.ppt Slides]
*[https://buffalo.box.com/v/REFERENT-TRACKING Video]
:Referent Tracking (RT) is a methodology to create digital copies of the parts of the world we are interested in. It is based on Basic Formal Ontology, but focuses on particulars rather than universals. The goal is to create information systems in such a way that (1) the information they contain mimics the structure of the corresponding portions of reality and (2) they can make optimal use of ontologies and terminologies.  


----
'''Basic Formal Ontology'''


== Content ==
*[http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0 Teaching material on Basic Formal Ontology].


This class will consist of a mixture of:
*[http://ontology.buffalo.edu/smith/articles/ontologies.htm Introductory readings on General Ontology].


*presentations by ontologists from UB and elsewhere;
*[http://ontology.buffalo.edu/ Buffalo Ontology Site].
*ontology development and planning sessions;
*teaching on specific ontology topics (for examples see [http://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_2.0#DRAFT_SCHEDULE here]);
*video presentations (for example from [http://militaryontology.com/military-ontology-videos.html here]).  


We will cover a variety of topics in theoretical and applied ontology, paying special attention to applications in the areas of biology and medicine on the one hand, and defense and security on the other.
*[[2013 BFO Meeting]]


----
----


== Outcomes ==
== Ontology of Mind ==


By the end of the class students will be able to:
'''Mental Functioning Ontology'''


*understand the nature, utility and scope of contemporary applied ontology
:*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/3-Mental-functioning.wmv Video]
*understand methods and rules for ontology development, evaluation, planning and organization
*contribute to ontological development initiatives
*engage in discussion of major issues in theoretical and applied ontology


----
'''[http://www.affective-sciences.org/user/346 Janna Hastings] (Swiss Center for Affective Sciences and European Bioinformatics Institute): Representing Mental Functioning''' [http://ontology.buffalo.edu/12/MFO-hastings.pptx Hastings Slides]


== Schedule ==
Alternative streaming videos for all sessions are available [http://prmmcontent.acsu.buffalo.edu/silverlight_web/courses/fall2012/phi531/ here]
August 27: '''Introduction to Ontology'''
*[http://org.buffalo.edu/Ontology_in_Buffalo_Aug_27_2012.ppt Slides] | [https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21372047&rKey=551eac7161785dde Raw Webex Video] | [http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/1-Introduction-to-ontology.wmv Streaming Video]
:We will begin with a basic introduction to ontology by addressing questions such as: What is an ontology? What are the differences and interrelations between ontology (philosophy), ontology (science), and ontology (engineering)? How are ontologies used? We will also provide an introduction to Basic Formal Ontology (BFO), focusing on a discussion of the question: What is a musical score?
*Background  video: [http://southeastgenetics.org/presentation.php/20/How_to_Build_Useful_Ontologies_for_Clinical_and_Translational_Research Introduction to Biomedical Ontology].
September 10: '''Referent Tracking'''
*Presentation by Werner Ceusters (Bioinformatics/Psychiatry): Particulars in Focus
*[http://www.referent-tracking.com/RTU/sendfile/?file=20120910-OntologyClassOnReferentTracking.ppt Slides] |  [https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21463072&rKey=a30727e0f870a6e6 Raw Webex Video] |  [http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/2-Referent-Tracking.wmv Streaming Video]
:Referent Tracking (RT) is a methodology to create digital copies of the parts of the world we are interested in. It is based on Basic Formal Ontology, but focuses on particulars rather than universals. The goal is to create information systems in such a way that (1) the information they contain mimics the structure of the corresponding portions of reality and (2) they can make optimal use of ontologies and terminologies.
September 24: '''Mental Functioning Ontology'''
:[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/3-Mental-functioning.wmv Streaming Video]
:[http://www.affective-sciences.org/user/346 Janna Hastings] (Swiss Center for Affective Sciences and European Bioinformatics Institute): '''Representing Mental Functioning''' [http://ontology.buffalo.edu/12/MFO-Hastings.pptx Slides]
:Mental functioning includes all the faculties of the mind, e.g., perception, planning, language, memory, emotion, and self-representation. The study of these processes cuts across disciplines such as psychology, psychiatry, neuroscience, and biomedicine. The Mental Functioning Ontology (MFO) is designed to provide a means for the common description of data in all of these disciplines, in order to support data aggregation and comparison. For background material see [http://kr-med.org/icbofois2012/mfo/ here] (slides) and [http://kr-med.org/icbofois2012/proceedings/ICBOFOIS2012Workshops/ICBO2012MFO/ICBO-2012-MFO-WS.pdf here] (papers).
:Mental functioning includes all the faculties of the mind, e.g., perception, planning, language, memory, emotion, and self-representation. The study of these processes cuts across disciplines such as psychology, psychiatry, neuroscience, and biomedicine. The Mental Functioning Ontology (MFO) is designed to provide a means for the common description of data in all of these disciplines, in order to support data aggregation and comparison. For background material see [http://kr-med.org/icbofois2012/mfo/ here] (slides) and [http://kr-med.org/icbofois2012/proceedings/ICBOFOIS2012Workshops/ICBO2012MFO/ICBO-2012-MFO-WS.pdf here] (papers).
:Barry Smith: '''Mental Functioning and the Ontology of Language''' [http://ontology.buffalo.edu/12/Mind&LanguageSep24_2012.pptx Slides]
:In this section we will address those kinds of mental functioning which involve overt or covert use of language. We will focus especially on the issue of the directedness of thought and language to extra-mental objects.


September 27: '''How To Do Things With Diagrams'''
'''Barry Smith: Mental Functioning and the Ontology of Language''' [http://ontology.buffalo.edu/12/Mind&LanguageSep24_2012.pptx Slides]
*[http://ontology.buffalo.edu/12/How-to-do-things-with-diagrams-Sep25-2012.pptx Slides] | [https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21597707&rKey=45e4072f030cf44d Raw Webex Video] |  [http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/4-Diagrams.wmv Streaming Video] | [http://youtu.be/AaFnMesr6uQ Short Youtube Video]
:Addresses those kinds of mental functioning which involve overt or covert use of language focusing especially on the issue of the directedness of thought and language to extra-mental objects.
:The talk will explore some of the ways in which the theory of speech acts can throw light on the role of diagrams and of diagrammatic symbologies in areas such as chess, music, chemistry and military planning. The ontology of processes and process representations will play a central role.


October 1: '''Mental Functioning and the Ontology of Language'''
'''Barry Smith: How To Do Things With Diagrams''' [http://ontology.buffalo.edu/12/How-to-do-things-with-diagrams-Sep25-2012.pptx Slides]
*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/4-Diagrams.wmv Video]
*[http://www.youtube.com/watch?v=AaFnMesr6uQ Shorter Youtube Video]
:Explores some of the ways in which the theory of speech acts can throw light on the role of diagrams and of diagrammatic symbologies in areas such as chess, music, chemistry and military planning. The ontology of processes and process representations plays a central role.


*1. Ontology and the Austrian Tradition: A discussion of the theory of intentionality (or the directedness of mental processes), and of the roots of this theory in the philosophy of the Brentano school in Austria. Continues the discussions initiated on September 24 of how mental processes are interrelated in different ways with linguistic processes (for example of speaking, reading, and silent siloloquy).  
'''Barry Smith: Ontology and the Austrian Tradition''' [http://ontology.buffalo.edu/12/Mind&Language-1-Austria.pptx Slides]
:[http://ontology.buffalo.edu/12/Mind&Language-1-Austria.pptx Slides] | [http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/5-MindandLanguage-1-Austria.wmv Streaming Video]
*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/5-MindandLanguage-1-Austria.wmv Video]
:A discussion of the theory of intentionality (or the directedness of mental processes), and of the roots of this theory in the philosophy of the Brentano school in Austria. Continues the discussions initiated on September 24 of how mental processes are interrelated in different ways with linguistic processes (for example of speaking, reading, and silent siloloquy).  


*2. Mental Functioning Ontology and the ICF: A survey of the WHO's Internal Classification of Functioning
'''Barry Smith: Mental Functioning Ontology and the ICF: A survey of the WHO's Internal Classification of Functioning''' [http://ontology.buffalo.edu/12/Mind&Language-2-ICF.pptx Slides]  
:[http://ontology.buffalo.edu/12/Mind&Language-2-ICF.pptx Slides] | [http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/5-MindandLanguage-2-ICF.wmv Streaming Audio] - to be used together with slides [http://ontology.buffalo.edu/12/Mind&Language-2-ICF.pptx here]


*3. Neuroscience and the Ontology of Mind: A discussion of the mainstream neuroscience approach to mental directedness.
*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/5-MindandLanguage-2-ICF.wmv Audio] - to be used together with slides [http://ontology.buffalo.edu/12/Mind&Language-2-ICF.pptx here]
:[http://ontology.buffalo.edu/12/Mind&Language-3-Neuroscience.pptx Slides]| [http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/5-MindandLanguage-3-Neuroscience.wmv Streaming Video] (for first five minutes see slides [http://ontology.buffalo.edu/12/Mind&Language-3-Neuroscience.pptx here])


<!--  [https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21622297&rKey=8a7500e254868745 Raw Webex Video1] | [https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21622307&rKey=5e0d03fe51b6d300 Raw Webex Video2] | [http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/5-MindandLanguage-1-Austria.wmv Streaming Video]
'''Barry Smith: Neuroscience and the Ontology of Mind: A discussion of the mainstream neuroscience approach to mental directedness''' [http://ontology.buffalo.edu/12/Mind&Language-3-Neuroscience.pptx Slides]
-->
October 8: '''Special session on research collaborations in military, healthcare and other fields of information-driven science'''
:Further details are available [[Information Infrastructure Collaboration Meeting | here]].
October 15: '''Social Ontology'''
:[https://ub.webex.com/ub/ldr.php?AT=pb&SP=MC&rID=21719072&rKey=3f2807ad74940c57 Raw Webex Video] | [http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/6-Social-ontology.wmv Streaming Video]
:We will address the foundations of social ontology, considering topics such as the nature of obligations, credentials, authority, and the role of documents in the construction of social reality.
*'''The Ontology of Social Reality''': Barry Smith
:focusing on debts, obligations, prices, the Dow Jones Industrial Average, and the views of John Searle [http://ontology.buffalo.edu/12/SocialOntology-Oct2012.pptx Slides]
:[http://ontology.buffalo.edu/document_ontology/ Background reading]
*'''Social Ontology and the Biomedical Domain''': Mathias Brochhausen and William Hogan (University of Arkansas for Medical Sciences) [http://ontology.buffalo.edu/12/Brochhausen.pptx Slides]
:includes treatment of the Ontology of Medically Related Social Entities ([http://ceur-ws.org/Vol-833/paper20.pdf OMRSE]) and related work on demographics, including [http://hl7-watch.blogspot.com/2010/12/demographics-hl7-vs-reality-part-2.html gender] and [http://hl7-watch.blogspot.com/2010/11/demographics-hl7-vs-reality-part-1.html marital status], organizations, [http://ontology.buffalo.edu/document_ontology/Almeida_Rome_2012.pdf document acts], and guidelines


October 22: Information on this session provided only to students registered for credit
*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/5-MindandLanguage-3-Neuroscience.wmv Video] (for first five minutes see slides [http://ontology.buffalo.edu/12/Mind&Language-3-Neuroscience.pptx here])


October 29: '''From the Gene Ontology to the Neurological Disease Ontology''' with Alexander Diehl (Neurology)
----
:[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21818962&rKey=f84d9eda6e5c3d31 Raw Webex Video] | [http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/7-GO.wmv Streaming Video]
:The first part of the talk will cover the Gene  (GO) and Cell Ontologies (CL), covering issues of ontology structure, development, use in annotation, and exploitation for biological research. The second part will cover the Neurological Disease (ND) and  Neuropsychological Testing Ontologies (NPT).
:'''Introduction to bio-ontology for absolute beginners''' [http://southeastgenetics.org/presentation.php/20/How_to_Build_Useful_Ontologies_for_Clinical_and_Translational_Research Click on: Video/Audio Stream]
'''Background Reading'''
:The Gene Ontology Consortium, "[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037419/ Gene Ontology: tool for the unification of biology]", Nat Genet. 2000 May; 25(1): 25–29.
:Mungall CJ, el al., "[http://www.sciencedirect.com/science/article/pii/S1532046410000171 Cross-product extensions of the Gene Ontology]", J Biomed Inform. 2011 Feb;44(1):80-6. 
:Hill DP, et al., "[http://www.biomedcentral.com/1471-2105/9/S5/S2 Gene Ontology annotations: what they mean and where they come from]", BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S2. 
:Meehan TF, et al., "[http://www.biomedcentral.com/1471-2105/12/6 Logical development of the cell ontology]", BMC Bioinformatics. 2011 Jan 5;12:6.
:Cox AP, et al., "[http://bit.ly/T6TkZB Ontologies for the study of neurological disease]", ICBO 2012.
:[http://www.everythingbio.com/glos/ Glossary of biological terms]


<div id="IDO"></div>
== Information Ontology ==
November 5: '''The Infectious Disease Ontology (IDO)'''
*1.[http://code.google.com/p/ogms/ OGMS]: The Ontology for General Medical Science (Barry Smith) [http://ontology.buffalo.edu/12/OGMS-Nov2012.pptx Slides]
'''Alan Ruttenberg: The Basics of the Information Artifact Ontology'''  
:[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/8-OGMS-Nov2012.wmv Streaming Video]
*2. The IDO Core and Its Extensions - Coordination and Interoperability (Lindsay Cowell) [http://ontology.buffalo.edu/12/IDO_Nov-5.pdf Slides]
:[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/8-IDO-Nov2012.wmv Streaming Video]
*3. The IDO-Staph Extension (Albert Goldfain) [http://ontology.buffalo.edu/12/IDO-Staph.pptx Slides]
:[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/8-IDO-Staph-Nov2012.wmv Streaming Video] (for initial 10 minutes use slides from [http://ontology.buffalo.edu/12/IDO-Staph*.pptx here])
::''Staph aureus'' diseases and their differentiation
::Antibiotic Resistance (Blocking, Complemenatary and Reciprocal Dispositions) (Albert Goldfain)
::A Lattice of Staph aureus Infectious Diseases
*Background Reading
:[http://infectiousdiseaseontology.org/ IDO website]
:LG Cowell, B Smith, "[http://www.springerlink.com/content/n2l5141m4306n8l0/fulltext.pdf Infectious Disease Ontology]", Chapter 19 in ''Infectious Disease Informatics'', V Sintchenko (ed.), 2010, 373-395.
:A Goldfain, B Smith and LG Cowell, “[http://ontology.buffalo.edu/ido/Dispositions_and_IDO.pdf Dispositions and the Infectious Disease Ontology]”, in Antony Galton and Riichiro Mizoguchi (eds.), ''Formal Ontology in Information Systems. Proceedings of the Sixth International Conference'' (FOIS 2010), Amsterdam: IOS Press, 2010, 400-413.
 
November 12: '''Symposium on the Information Artifact Ontology: Part 1''' with Alan Ruttenberg (UB)
[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21913277&rKey=08e83d74bdf8a315 Raw Webex Video]
 
The Information Artifact Ontology (IAO) is an ontology of information entities, originally inspired by needs of the Ontology for Biomedical Investigations ([http://obi-ontology.org/page/Main_Page OBI]) to represent measurement data and other information entities associated with investigations such as reports and protocols. A number of issues that have emerged and we are developing a second version to address these issues.
 
'''Basic ideas'''
:1. information artifacts are about, or are intended to be about, some entity
:2. genes are not information artifacts; gene sequences as recorded in computers are information artifacts
:3. information artifacts are copyable
:4. information artifacts are generically dependent continuants which have concretizations, for example in specifically dependent patterns of ink on a piece of paper or of magnetization on a hard drive
 
*'''Schedule'''
The session is in two parts. First, an introduction by Alan Ruttenberg; second, a series of 15-second chess discussions of major issues, moderated by Barry Smith, as follows:
 
*4:00pm '''Introduction''' outlining the basics of IAO, focusing on cases where it works well, such as measurement data.
 
*4:30pm Discussion: How can we define the 'is about' relation, which forms the core of IAO? What is the current strategy, and what breaks? What can information artifacts be about? Non-problematic is the case of particulars. Can information artifacts be about types and if so, what does that mean?
 
*4:45pm What is a copying process - the process that results in a new concretization of an information content entity (ICE)? How is copying defined? Is there a constraint on how complicated the copying process can be it can be considered not as copying but as new creation? What happens when the copying is partial?


*5:00pm How should IAO deal with information artifacts for which the putative ''topic'' does not, or might not, exist? Examples are (written) hypotheses, fiction, diagrams of chemical compounds that can't be synthesized, terms such as 'ether' or 'phlogiston' from the history of science, terms such as 'the soup I plan to have for dinner' used in planning. 
*[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21913277&rKey=08e83d74bdf8a315 Raw Webex Video]


*5:15pm How can we define information artifacts in order to circumscribe the scope of IAO? What primitives do we need to rely on?Candidates include: intention, communication, (cognitive) mental function, output (of realization of cognitive mental function).
:The Information Artifact Ontology (IAO) is an ontology of information entities, originally inspired by needs of the Ontology for Biomedical Investigations ([http://obi-ontology.org/page/Main_Page OBI]) to represent measurement data and other information entities associated with investigations such as reports and protocols. A number of issues that have emerged and we are developing a second version to address these issues.  


*5:30 How do we deal with ''[http://en.wikipedia.org/wiki/Syncategorematic_term syncategorematica]'' (for example the 'the' and the 'not' in 'the table not beside my bed')?
:Basic ideas:
::1. information artifacts are about, or are intended to be about, some entity
::2. genes are not information artifacts; gene sequences as recorded in computers are information artifacts
::3. information artifacts are copyable
::4. information artifacts are generically dependent continuants which have concretizations, for example in specifically dependent patterns of ink on a piece of paper or of magnetization on a hard drive.


*5:45 How do we deal with different encodings of what is putatively the same information artifact, for example resulting from use of different character sets such as ASCII or Unicode?  
:Discussion:
::How can we define the 'is about' relation, which forms the core of IAO? What is the current strategy, and what breaks? What can information artifacts be about? Non-problematic is the case of particulars. Can information artifacts be about types and if so, what does that mean?
::What is a copying process - the process that results in a new concretization of an information content entity (ICE)? How is copying defined? Is there a constraint on how complicated the copying process can be it can be considered not as copying but as new creation? What happens when the copying is partial?
::How should IAO deal with information artifacts for which the putative ''topic'' does not, or might not, exist? Examples are (written) hypotheses, fiction, diagrams of chemical compounds that can't be synthesized, terms such as 'ether' or 'phlogiston' from the history of science, terms such as 'the soup I plan to have for dinner' used in planning. 
::How can we define information artifacts in order to circumscribe the scope of IAO? What primitives do we need to rely on?Candidates include: intention, communication, (cognitive) mental function, output (of realization of cognitive mental function).
::How do we deal with ''[http://en.wikipedia.org/wiki/Syncategorematic_term syncategorematica]'' (for example the 'the' and the 'not' in 'the table not beside my bed')?
::How do we deal with different encodings of what is putatively the same information artifact, for example resulting from use of different character sets such as ASCII or Unicode?  


:'''Background materials'''
:'''Background materials'''
Line 150: Line 86:
*http://www.bioontology.org/wiki/index.php/From_BFO_to_IAO
*http://www.bioontology.org/wiki/index.php/From_BFO_to_IAO


'''[http://www.referent-tracking.com/RTU/?page=ceusters_vita Werner Ceusters]: [http://www.referent-tracking.com/RTU/sendfile/?file=or_submission_125_2.pdf Proposed Definitions of IAO Terms]'''


'''[http://www.linkedin.com/pub/ron-rudnicki/4/b00/957 Ron Rudnicki] (CUBRC): [http://ontology.buffalo.edu/12/information-ontologies.pptx A Discussion of Two Information Ontologies]'''


<div id="IAO"></div>
[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21963527&rKey=aa1c762058fff21e Raw Webex Video]
November 19: '''Symposium on the Information Artifact Ontology: Part 2''' with [http://www.referent-tracking.com/RTU/?page=ceusters_vita] Werner Ceusters (UB) and [http://www.linkedin.com/pub/ron-rudnicki/4/b00/957 Ron Rudnicki] (CUBRC)


[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21963527&rKey=aa1c762058fff21e Raw Webex Video]
----
 
== Ontology Evaluation ==


Werner Ceusters will lead a discussion of the proposed definitions of IAO terms set forth [http://www.referent-tracking.com/RTU/sendfile/?file=or_submission_125_2.pdf here]
'''Fabian Neuhaus''' (National Institute of Standards and Technologies): Introduction to Ontology Evaluation [http://ontology.buffalo.edu/12/Neuhaus-Evalution2012.pdf Slides]
*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/Evaluation/Neuhaus.wmv Video]


Ron Rudnicki will lead a discussion of the two information ontologies represented [http://ontology.buffalo.edu/12/information-ontologies.pptx here], with a view to formulating a plan for the merger of these ontologies within an improved IAO framework. [http://ontology.buffalo.edu/12/Rudnicki-Information-Ontologies.pptx Slides]
'''Barry Smith''': Basic Formal Ontology as a Tool for the Evaluation of Ontologies [http://ontology.buffalo.edu/12/HL7-and-BFO.pdf Paper] [http://ontology.buffalo.edu/12/HL7-BFO.ppt Slides]
*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/Evaluation/Smith-HL7.wmv Video]
:A Practical Example: Evaluation of the [http://bioportal.bioontology.org/ontologies/47171?p=terms HL7 RIM Ontology]
:Relation to OntoClean
:Alternatives to BFO
:[http://ontology.buffalo.edu/medo/biodynamic.pdf Introduction to BFO]


'''Werner Ceusters: A Realism-Based Approach to the Evaluation of Ontologies''' [http://www.referent-tracking.com/RTU/sendfile/?file=2012RBOntoEval.pptx Slides]
*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/Evaluation/Ceusters.wmv Video]


<div id="SO"></div>
:We present a novel methodology for calculating the improvements obtained in successive versions of ontologies, using examples from biomedicine. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records.


November 26: '''Social Ontology'''
*[http://ontology.buffalo.edu/bfo/Versioning.pdf Paper]
:[http://prmmcontent.acsu.buffalo.edu/silverlight_web/courses/fall2012/phi531/ Video]


This session continues the discussion of social ontology initiated on October 15, with a view to coordination and integration of social ontologies being developed by different groups, especially in the biological and medical domains.
*[http://ontology.buffalo.edu/evaluation.html Background Readings on Ontology Evaluation]


*Barry Smith: Introduction
----


*Ramona Walls: The Population and Community Ontology (PCO) [http://ontology.buffalo.edu/12/PCO_Nov2012.pptx Slides]
==Social Ontology ==
:The Population and Community Ontology ([http://code.google.com/p/popcomm-ontology/ PCO]) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include ecology, community health care, epidemiology, plant pathology, behavioral studies, and sociology. This presentation will describe the domain of the PCO and how the PCO relates to other OBO Foundry Library ontologies such as PATO, GO, and EnvO. It will conclude with a brief discussion of the utility of the PCO.


*Shahim Essaid (Oregon Health and Sciences University): [http://ontology.buffalo.edu/12/ctsa-social.pptx Slides]
See [[Social Ontology 2012 | here]]
:[https://www.eagle-i.net/ eagle-i] and [http://vivoweb.org/ VIVO] are two initiatives whose goal is to help scientists and others discover information, especially information on the web. Each uses ontologies to help achieve this goal:
:*the eagle-i ontology is focused on representing research-related resources such as biological specimens, human studies, equipment and software;
:*the VIVO ontology is focused on researchers themselves, for example their activities, expertise, and publications. 
:The [http://ctsaconnect.org/ CTSAconnect] project is developing an integrated framework that merges the eagle-i and VIVO ontologies into a single integrated ontology to support the work of clinical and translational scientists. Suppose, for example, that you are a scientist in city X working on a certain disease, and you notice that some of your patients show a particular reaction to a certain drug. How would you identify other researchers living in or near X who have studied responses to this specific drug? CTSAconnect is developing a module to represent the expertise of clinicians inferred from data generated during clinical encounters. This presentation will be a brief overview of the project with a focus on discussing some of the social entities that need to be represented within the ontology framework. Examples include:
:*agreement
:*credential
:*authorship
:*position


<div id="EVAL"></div>
----


== Biomedical Ontology ==


December 3: '''Symposium on Ontology Evaluation''' with Barry Smith, Werner Ceusters, Alan Ruttenberg (UB) and Fabian Neuhaus (National Institute of Standards and Technology)
:[https://ub.webex.com/ub/j.php?ED=143583837&UID=491437657&PW=NZTIzZTcxMWY4&RT=MiMxMQ%3D%3D Webex]
:[http://ontology.buffalo.edu/evaluation.html Background readings]


Presentations will include:
'''Alexander Diehl (Department of Neurology, University at Buffalo): From the Gene Ontology to the Neurological Disease Ontology''' [http://ontology.buffalo.edu/12/Diehl-GO-CL-ND.pptx Slides]
*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/7-GO.wmv Video]
:The first part of the talk covers the Gene (GO) and Cell Ontologies (CL), covering issues of ontology structure, development, use in annotation, and exploitation for biological research. The second part will cover the Neurological Disease (ND) and  Neuropsychological Testing Ontologies (NPT).


*'''Fabian Neuhaus''' (National Institute of Standards and Technologies): Introduction to Ontology Evaluation [http://ontology.buffalo.edu/12/Neuhaus-Evalution2012.pdf Slides]
*Background videos:  


*'''Barry Smith''': Basic Formal Ontology as a Tool for the Evaluation of Ontologies [http://ontology.buffalo.edu/12/HL7-and-BFO.doc Paper] [http://ontology.buffalo.edu/12/HL7-BFO.ppt Slides]
*[http://southeastgenetics.org/presentation.php/20/How_to_Build_Useful_Ontologies_for_Clinical_and_Translational_Research Introduction to Biomedical Ontology].
:A Practical Example: Evaluation of the [http://bioportal.bioontology.org/ontologies/47171?p=terms HL7 RIM Ontology]
:Relation to OntoClean
:Alternatives to BFO
:[http://ontology.buffalo.edu/medo/biodynamic.pdf Introduction to BFO]


*'''Werner Ceusters''': A Realism-Based Approach to the Evaluation of Ontologies”,  
*Background Reading'''
:We present a novel methodology for calculating the improvements obtained in successive versions of ontologies, using examples from biomedicine. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records.
:The Gene Ontology Consortium, "[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037419/ Gene Ontology: tool for the unification of biology]", Nat Genet. 2000 May; 25(1): 25–29.
:[http://www.referent-tracking.com/RTU/sendfile/?file=2012RBOntoEval.pptx Slides]  
:Mungall CJ, el al., "[http://www.sciencedirect.com/science/article/pii/S1532046410000171 Cross-product extensions of the Gene Ontology]", J Biomed Inform. 2011 Feb;44(1):80-6.
:[http://ontology.buffalo.edu/bfo/Versioning.pdf Paper]
:Hill DP, et al., "[http://www.biomedcentral.com/1471-2105/9/S5/S2 Gene Ontology annotations: what they mean and where they come from]", BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S2.
:Meehan TF, et al., "[http://www.biomedcentral.com/1471-2105/12/6 Logical development of the cell ontology]", BMC Bioinformatics. 2011 Jan 5;12:6.
:Cox AP, et al., "[http://bit.ly/T6TkZB Ontologies for the study of neurological disease]", ICBO 2012.
:[http://www.everythingbio.com/glos/ Glossary of biological terms]


: '''The Infectious Disease Ontology (IDO)'''
*1.[http://code.google.com/p/ogms/ OGMS]: The Ontology for General Medical Science (Barry Smith) [http://ontology.buffalo.edu/12/OGMS-Nov2012.pptx Slides]
:[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/8-OGMS-Nov2012.wmv Video]


December 10: '''Social Ontology'''
'''Lindsay Cowell (University of Texas Southwestern Medical Center): The IDO Core and Its Extensions - Coordination and Interoperability''' [http://ontology.buffalo.edu/12/IDO_Nov-5.pdf Slides]
:'''NOTE CHANGE OF VENUE: THIS SESSION IS IN PARK 141 (UB NORTH CAMPUS)'''
*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/8-IDO-Nov2012.wmv Video]
:[https://ub.webex.com/ub/j.php?ED=144235497&UID=491437657&PW=NZGY3MmMyNzli&RT=MiMxMQ%3D%3D Webex]


We will continue the discussions of social ontology initiated on October 15 and November 26 (see videos and other background material above). Content will include:
'''Albert Goldfain: The IDO-Staph Extension [http://ontology.buffalo.edu/12/IDO-Staph.pptx Slides]


*Shahim Essaid (Oregon Health and Sciences University): Continuation from November 26 [http://ontology.buffalo.edu/12/ctsa-social.pptx Draft Slides]
*[http://mediastream.buffalo.edu/Content/research/phismith/Ontology2012/8-IDO-Staph-Nov2012.wmv Video] (for initial 10 minutes use slides from [http://ontology.buffalo.edu/12/IDO-Staph_.pptx here])
::''Staph aureus'' diseases and their differentiation
::Antibiotic Resistance (Blocking, Complemenatary and Reciprocal Dispositions) (Albert Goldfain)
::A Lattice of Staph aureus Infectious Diseases
*Background Reading
:[http://infectiousdiseaseontology.org/ IDO website]
:LG Cowell, B Smith, "[http://www.springerlink.com/content/n2l5141m4306n8l0/fulltext.pdf Infectious Disease Ontology]", Chapter 19 in ''Infectious Disease Informatics'', V Sintchenko (ed.), 2010, 373-395.
:A Goldfain, B Smith and LG Cowell, “[http://ontology.buffalo.edu/ido/Dispositions_and_IDO.pdf Dispositions and the Infectious Disease Ontology]”, in Antony Galton and Riichiro Mizoguchi (eds.), ''Formal Ontology in Information Systems. Proceedings of the Sixth International Conference'' (FOIS 2010), Amsterdam: IOS Press, 2010, 400-413.


*William Hogan and Mathias Brochhausen (University of Arkansas for Medical Sciences): "OMRSE: Current status and our strategy for future development" [http://ontology.buffalo.edu/12/HoganBrochhausen.pptx Slides]
----


:[http://code.google.com/p/omrse/ OMRSE]: The Ontology for Medically Related Social Entities
== Military Ontology ==


Video presentations on military ontology are provided [http://militaryontology.com/military-ontology-videos.html here].
----
----


'''Grading'''
== [[Ontological Engineering]] ==
Requirements for this class will depend on the selected number of credit hours, but will include active class participation and completion of some written work or ontology project.
 
Modules from Fall 2013 Graduate Seminar, Buffalo, NY
 
== Military Intelligence Ontology==


'''All students taking the class for credit should make an appointment with Dr Smith to discuss further details.
A tutorial on ontology for intelligence analysis is [http://ncorwiki.buffalo.edu/index.php/Ontology_for_Intelligence,_Defense_and_Security here]
'''


----
----


'''Literature'''
== Ontology Software ==
 
Introductory readings are provided [http://ontology.buffalo.edu/smith/articles/ontologies.htm here].


See also the [http://ontology.buffalo.edu/ Buffalo Ontology Site].
Teaching material on ontology software is provided [http://ncorwiki.buffalo.edu/index.php/Introduction_to_Prot%C3%A9g%C3%A9 here]

Latest revision as of 22:39, 30 October 2022

The modules below are designed for use in teaching ontology to multidisciplinary audiences in domains such as government and administration, military and biomedical informatics. The content derives initially from the course "PHI:531 Problems in Ontology" taught in the University at Buffalo in the fall of 2012. However, it will be continually expanded and up-dated where necessary.

Link to: Streaming Video Ontology Training Courses


General Ontology

Barry Smith: Introduction to Ontology (2012) Slides

Provides a basic introduction to ontology by addressing questions such as: What is an ontology? What are the differences and interrelations between ontology (philosophy), ontology (science), and ontology (engineering)? How are ontologies used? We will also provide an introduction to Basic Formal Ontology (BFO), focusing on a discussion of the question: What is a musical score?

Werner Ceusters (Bioinformatics/Psychiatry): Particulars in Focus Slides

Referent Tracking (RT) is a methodology to create digital copies of the parts of the world we are interested in. It is based on Basic Formal Ontology, but focuses on particulars rather than universals. The goal is to create information systems in such a way that (1) the information they contain mimics the structure of the corresponding portions of reality and (2) they can make optimal use of ontologies and terminologies.

Basic Formal Ontology

Ontology of Mind

Mental Functioning Ontology

Janna Hastings (Swiss Center for Affective Sciences and European Bioinformatics Institute): Representing Mental Functioning Hastings Slides

Mental functioning includes all the faculties of the mind, e.g., perception, planning, language, memory, emotion, and self-representation. The study of these processes cuts across disciplines such as psychology, psychiatry, neuroscience, and biomedicine. The Mental Functioning Ontology (MFO) is designed to provide a means for the common description of data in all of these disciplines, in order to support data aggregation and comparison. For background material see here (slides) and here (papers).

Barry Smith: Mental Functioning and the Ontology of Language Slides

Addresses those kinds of mental functioning which involve overt or covert use of language focusing especially on the issue of the directedness of thought and language to extra-mental objects.

Barry Smith: How To Do Things With Diagrams Slides

Explores some of the ways in which the theory of speech acts can throw light on the role of diagrams and of diagrammatic symbologies in areas such as chess, music, chemistry and military planning. The ontology of processes and process representations plays a central role.

Barry Smith: Ontology and the Austrian Tradition Slides

A discussion of the theory of intentionality (or the directedness of mental processes), and of the roots of this theory in the philosophy of the Brentano school in Austria. Continues the discussions initiated on September 24 of how mental processes are interrelated in different ways with linguistic processes (for example of speaking, reading, and silent siloloquy).

Barry Smith: Mental Functioning Ontology and the ICF: A survey of the WHO's Internal Classification of Functioning Slides

Barry Smith: Neuroscience and the Ontology of Mind: A discussion of the mainstream neuroscience approach to mental directedness Slides

  • Video (for first five minutes see slides here)

Information Ontology

Alan Ruttenberg: The Basics of the Information Artifact Ontology

The Information Artifact Ontology (IAO) is an ontology of information entities, originally inspired by needs of the Ontology for Biomedical Investigations (OBI) to represent measurement data and other information entities associated with investigations such as reports and protocols. A number of issues that have emerged and we are developing a second version to address these issues.
Basic ideas:
1. information artifacts are about, or are intended to be about, some entity
2. genes are not information artifacts; gene sequences as recorded in computers are information artifacts
3. information artifacts are copyable
4. information artifacts are generically dependent continuants which have concretizations, for example in specifically dependent patterns of ink on a piece of paper or of magnetization on a hard drive.
Discussion:
How can we define the 'is about' relation, which forms the core of IAO? What is the current strategy, and what breaks? What can information artifacts be about? Non-problematic is the case of particulars. Can information artifacts be about types and if so, what does that mean?
What is a copying process - the process that results in a new concretization of an information content entity (ICE)? How is copying defined? Is there a constraint on how complicated the copying process can be it can be considered not as copying but as new creation? What happens when the copying is partial?
How should IAO deal with information artifacts for which the putative topic does not, or might not, exist? Examples are (written) hypotheses, fiction, diagrams of chemical compounds that can't be synthesized, terms such as 'ether' or 'phlogiston' from the history of science, terms such as 'the soup I plan to have for dinner' used in planning.
How can we define information artifacts in order to circumscribe the scope of IAO? What primitives do we need to rely on?Candidates include: intention, communication, (cognitive) mental function, output (of realization of cognitive mental function).
How do we deal with syncategorematica (for example the 'the' and the 'not' in 'the table not beside my bed')?
How do we deal with different encodings of what is putatively the same information artifact, for example resulting from use of different character sets such as ASCII or Unicode?
Background materials

Werner Ceusters: Proposed Definitions of IAO Terms

Ron Rudnicki (CUBRC): A Discussion of Two Information Ontologies

Raw Webex Video

Ontology Evaluation

Fabian Neuhaus (National Institute of Standards and Technologies): Introduction to Ontology Evaluation Slides

Barry Smith: Basic Formal Ontology as a Tool for the Evaluation of Ontologies Paper Slides

A Practical Example: Evaluation of the HL7 RIM Ontology
Relation to OntoClean
Alternatives to BFO
Introduction to BFO

Werner Ceusters: A Realism-Based Approach to the Evaluation of Ontologies Slides

We present a novel methodology for calculating the improvements obtained in successive versions of ontologies, using examples from biomedicine. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records.

Social Ontology

See here

Biomedical Ontology

Alexander Diehl (Department of Neurology, University at Buffalo): From the Gene Ontology to the Neurological Disease Ontology Slides

The first part of the talk covers the Gene (GO) and Cell Ontologies (CL), covering issues of ontology structure, development, use in annotation, and exploitation for biological research. The second part will cover the Neurological Disease (ND) and Neuropsychological Testing Ontologies (NPT).
  • Background videos:
  • Background Reading
The Gene Ontology Consortium, "Gene Ontology: tool for the unification of biology", Nat Genet. 2000 May; 25(1): 25–29.
Mungall CJ, el al., "Cross-product extensions of the Gene Ontology", J Biomed Inform. 2011 Feb;44(1):80-6.
Hill DP, et al., "Gene Ontology annotations: what they mean and where they come from", BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S2.
Meehan TF, et al., "Logical development of the cell ontology", BMC Bioinformatics. 2011 Jan 5;12:6.
Cox AP, et al., "Ontologies for the study of neurological disease", ICBO 2012.
Glossary of biological terms
The Infectious Disease Ontology (IDO)
  • 1.OGMS: The Ontology for General Medical Science (Barry Smith) Slides
Video

Lindsay Cowell (University of Texas Southwestern Medical Center): The IDO Core and Its Extensions - Coordination and Interoperability Slides

Albert Goldfain: The IDO-Staph Extension Slides

  • Video (for initial 10 minutes use slides from here)
Staph aureus diseases and their differentiation
Antibiotic Resistance (Blocking, Complemenatary and Reciprocal Dispositions) (Albert Goldfain)
A Lattice of Staph aureus Infectious Diseases
  • Background Reading
IDO website
LG Cowell, B Smith, "Infectious Disease Ontology", Chapter 19 in Infectious Disease Informatics, V Sintchenko (ed.), 2010, 373-395.
A Goldfain, B Smith and LG Cowell, “Dispositions and the Infectious Disease Ontology”, in Antony Galton and Riichiro Mizoguchi (eds.), Formal Ontology in Information Systems. Proceedings of the Sixth International Conference (FOIS 2010), Amsterdam: IOS Press, 2010, 400-413.

Military Ontology

Video presentations on military ontology are provided here.

Ontological Engineering

Modules from Fall 2013 Graduate Seminar, Buffalo, NY

Military Intelligence Ontology

A tutorial on ontology for intelligence analysis is here

Ontology Software

Teaching material on ontology software is provided here

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