View source for Problems in Ontology

[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'''

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]	

'''Mondays, 4-6pm, Fall 2012, Jacobs 106, UB North Campus'''

All sessions will be accessible both for face-to-face participants and on-line via webex. 

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== Content ==

This class will consist of a mixture of:

*presentations by ontologists from UB and elsewhere; 
*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. 

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== Outcomes ==

By the end of the class students will be able to:

*understand the nature, utility and scope of contemporary applied ontology
*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

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== Schedule ==

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?

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'''
*See link to Video/audio stream [http://southeastgenetics.org/presentation.php/20/How_to_Build_Useful_Ontologies_for_Clinical_and_Translational_Research here].
:4:00pm [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).
:4:45pm 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'''
*[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]
: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''' 
*[http://ontology.buffalo.edu/12/Mind&LanguageOct1_2012.pptx Slides] | [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-Mind-and-Language.wmv Streaming Video]
:We will continue 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) and linguistic artifacts (for example scientific and literary texts, instruction manuals, contracts). This session will include a survey of the WHO's Internal Classification of Functioning. 
*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.
*4:00-5:00pm '''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]
*5:00-6:00pm '''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
*October 29: Alexander Diehl (Neurology): From the Gene Ontology to the Neurological Disease Ontology
:[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21818962&rKey=f84d9eda6e5c3d31 Raw Webex 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'''
::1) 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. 
::2) 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.  
::3) 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.  
::4) 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. 
::5) 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>
*November 5: The Infectious Disease Ontology (IDO)

[https://ub.webex.com/ub/j.php?ED=143342182&UID=491437657&PW=NNTRiNjY4ZjY3&RT=MiMxMQ%3D%3D Webex]

:1. Background in the [http://code.google.com/p/ogms/ Ontology for General Medical Science] (Barry Smith)
:2. The IDO Core and Its Extensions - Coordination and Interoperability (Lindsay Cowell)
::IDO as an extension of the OGMS Framework (Lindsay Cowell)
:::(infectious) disease
:::(infectious) disorder
:::(infectious) disease course 
::Granularity Issues in IDO  (Barry Smith / Lindsay Cowell)
:::Defining 'Infection' (a) as an aggregate/collective and (b) as a unified object

:3. The IDO-Staph Extension (Albert Goldfain)
::''Staph aureus'' diseases and their differentiation 
::Antibiotic Resistance (Blocking, Complemenatary and Reciprocal Dispositions) (Albert Goldfain)(
::A Lattice of Staph aureus Infectious Diseases 

:4. Interesting Types of Entities Required by IDO (open discussion with Barry Smith, Lindsay Cowell and Albert Goldfain)
::'herd immunity', 
::'long term non-progressor'
::'obligate symbiont'

*'''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.

<div id="IAO"></div>
*November 12: Symposium on the Information Artifact Ontology with Alan Ruttenberg (UB)
:[https://ub.webex.com/ub/j.php?ED=143583622&UID=491437657&PW=NZmMzZDZkNmRl&RT=MiMxMQ%3D%3D Webex]

*November 19: Symposium on the Information Artifact Ontology with Ron Rudnicki (CUBRC) and Werner Ceusters (UB)
[https://ub.webex.com/ub/j.php?ED=143583822&UID=491437657&PW=NNWM2NWNmYjli&RT=MiMxMQ%3D%3D Webex]

<div id="SO"></div>
*November 26: Social Ontology
:[https://ub.webex.com/ub/j.php?ED=143583827&UID=491437657&PW=NZDEzNGE5MzM3&RT=MiMxMQ%3D%3D Webex]

:Barry Smith: Introduction

:Ramona Walls: The Population and Community Ontology (PCO) 

::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 community health care, plant pathology, behavioral studies, sociology, and ecology.

:Shahim Essaid (Oregon Health and Sciences University): TBD

*December 3: TBD
:[https://ub.webex.com/ub/j.php?ED=143583837&UID=491437657&PW=NZTIzZTcxMWY4&RT=MiMxMQ%3D%3D Webex]
 
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'''Grading'''
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. 

'''All students taking the class for credit should make an appointment with Dr Smith to discuss further details.
'''

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'''Literature'''

Introductory readings are provided [http://ontology.buffalo.edu/smith/articles/ontologies.htm here].

See also the [http://ontology.buffalo.edu/ Buffalo Ontology Site].