Basic Formal Ontology 2.0: Difference between revisions

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'''DATE''': Saturday and Sunday, August 18-19, 2012.
== BFO OWL 2.0 ==
For BFO 2020 (= ISO standard) see [http://ncorwiki.buffalo.edu/index.php/BFO_2020 here]


'''VENUE for FACE-TO-FACE PARTICIPATION''': Room14A, Basement, [http://www.buffalo.edu/buildings/building?id=BALDY Baldy Hall], University at Buffalo [http://www.buffalo.edu/home/visiting-ub/north-campus-directions.html North Campus], Amherst, NY.
Release information on [https://github.com/bfo-ontology/BFO/wiki BFO github site]


Suggested hotels: [http://www.expedia.ca/Amherst-Buffalo-Hotels.0-n6056530-0.Travel-Guide-Filter-Hotels]
== VIDEO INTRODUCTION TO BFO 2.0 (2015) ==


'''FACULTY''': Alan Ruttenberg and Barry Smith (University at Buffalo)
[https://www.youtube.com/watch?v=iTNQYyh88-Y Part One]


== DESCRIPTION ==
[https://www.youtube.com/watch?v=IMCBON2me3Y Part Two]


Basic Formal Ontology is currently being used by over 100 ontology-based research projects in biomedical informatics and increasingly in other fields. The course will provide an introduction to the content and use of BFO in ontology development. Attendees will acquire knowledge of the ontology and of its use as top-level ontology in multiple ontology development projects in a variety of fields. They will learn about the most recent developments in the ontology and acquire basic knowledge of the new formalizations of BFO in first-order logic (FOL) and in OWL.
==BACKGROUND INFORMATION==


The current version of the draft Specification and User Guide for BFO 2.0 is available [http://purl.obolibrary.org/obo/bfo.owl here].
'''[http://www.ifomis.uni-saarland.de/bfo/ BFO Website]'''
The current version of the BFO 2.0 OWL file is available [http://purl.obolibrary.org/obo/bfo.owl here].


These links, and also further information concerning the BFO 2.0 release can be found at the BFO page here: http://code.google.com/p/bfo/
For introductory reading see: Pierre Grenon and Barry Smith: "[http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf SNAP and SPAN: Towards Dynamic Spatial Ontology]", ''Spatial Cognition and Computation'', 4 (2004), 69-103.


== DRAFT SCHEDULE ==
For introductory reading on relations see: Barry Smith, Werner Ceusters, et al., “[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]”, ''Genome Biology'' (2005), 6 (5), R46.


Saturday, August 18: 9am-5pm
For (optional) philosophical discussion of core BFO issues see: Barry Smith and Werner Ceusters, “[http://iospress.metapress.com/content/1551884412214u67/fulltext.pdf Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies]”, ''Applied Ontology'', 5 (2010), 139–188.
:*The main idea of BFO
:*Existing domain ontologies extending BFO
:*The development of BFO 2.0
:*Overview of BFO 2.0 architecture
::::Instances and universals
::::Continuants and occurrents
::::Dependence and independence
::::Generic dependence and information entities
::::Processes and process profiles


Sunday, August 19: 9am-5pm
This paper contains some material pertaining to process profiles: “[https://philpapers.org/rec/SMICPA-5 Classifying Processes: An Essay in Applied Ontology]”, ''Ratio'', 25:4 (2012), 463-488.
:*Examples of uses of BFO
:*Creating a domain ontology by extending BFO
:*BFO in First Order Logic
:*BFO in OWL (Alan Ruttenberg)
:*Applications of BFO in OWL (Alan Ruttenberg)
:*Concluding discussion (Alan Ruttenberg and Barry Smith)


== PARTICIPATION ==
And the paper [http://ontology.buffalo.edu/smith/articles/Material_Entities.pdf here] contains material on the proposed BFO 2.0 classification of objects: “On Classifying Material Entities in Basic Formal Ontology”, in Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting, Tokyo: Keio University Press, 2012, 1-13.


Participants should have some background in ontology (including either philosophical or applied ontology). No specific knowledge of BFO is presupposed. This tutorial allows both face-to-face and on-line participation. Participation may be for credit (with an official university transcript), or the tutorial may be audited (with a certificate of completion if needed). The course will take place on the weekend of August 18-19, 2012, with follow-up meetings as necessary for those taking the course for credit.  
The current draft version of the BFO 2.0 Specification is available [https://github.com/BFO-ontology/BFO/raw/master/docs/bfo2-reference/BFO2-Reference.pdf here].  
Log-on/dial-in instructions for on-line participation will be provided by email to registered participants prior to the meeting.


'''FOR CREDIT'''
For further information please write to [mailto:phismith@buffalo.edu Barry Smith] or see [http://www.ifomis.uni-saarland.de/bfo/ here].


Participation in this tutorial will yield 1 credit hour; up to 3 further credit hours can be received through completion of a project under the guidance of an assigned faculty member. Projects must be completed before November 30, 2012. 
== DESCRIPTION ==
 
::Registration details for students taking this course for credit are available:
:::[http://myub.buffalo.edu/course/public/scripts/crs_sched.cgi?switch=showclass&semester=summer&division=NON&dept=PHI&regnum=12518 here], for face-to-face participation;
:::[http://myub.buffalo.edu/course/public/scripts/crs_sched.cgi?switch=showclass&semester=summer&division=NON&dept=PHI&regnum=12708 here], for on-line participation.
 
::External (non-UB) participants who wish to take this course for credit, either on-line or through face-to-face participation, should use the links above and follow the procedures outlined [http://registrar.buffalo.edu/registration/procedures/index.php here] under 'Non-matriculated student'. External students will be able to apply credits from participation in this tutorial to the UB [http://philosophy.buffalo.edu/graduate/areas_of_study/ma_ontology/ Masters] and [http://philosophy.buffalo.edu/graduate/areas_of_study/phd_ontology/ PhD] Programs in Ontology, and also to the planned on-line UB Advanced Graduate Certificate Program in Ontology which is currently being established. Further details can be obtained from [mailto:phismith@buffalo.edu Barry Smith].
 
'''AUDITING'''
 
Auditing, both on-line and face-to-face, is free to registered participants.  All those wishing to audit this tutorial should fill in the registration form provided [http://ncor.buffalo.edu/Tutorial_Registation_Form.pdf here] as soon as possible. A certificate of participation will be supplied on request, but auditing the course does not count for credit.
 
==FACULTY==
 
'''[http://ontology.buffalo.edu/smith Barry Smith]''' is a prominent contributor to both theoretical and applied research in ontology. He is the author of some 500 publications, and his research has been funded by the National Institutes of Health, the US, Swiss and Austrian National Science Foundations, the US Department of Defense, the Volkswagen Foundation, and the European Union. In 2010 he was awarded the first Paolo Bozzi Prize in Ontology by the University of Turin. Smith is one of the principal scientists of the NIH National Center for Biomedical Ontology, a Scientific Advisor to the Gene Ontology Consortium, and a PI on the Protein Ontology and Infectious Disease Ontology projects. He has organized over 100 ontology conferences, workshops and tutorials.


'''[http://sciencecommons.org/about/whoweare/ruttenberg/ Alan Ruttenberg]''' is a Principal Scientist at Science Commons and the Director of the University at Buffalo Clinical and Translational Data Exchange. His project, the Neurocommons, prototypes the use of Semantic Web technology for integrating and querying biomedical knowledge, working on structuring and using biological and clinical knowledge to answer questions and computationally interpret experimental data. He is a Coordinating Editor of the OBO Foundry and a former chair of the OWL Working Group.
Basic Formal Ontology is currently being used by over 450 ontology-based research projects in biomedical informatics and increasingly in other fields. The course will provide an introduction to the content and use of BFO in ontology development. Attendees will acquire knowledge of the ontology and of its use as top-level ontology in multiple ontology development projects in a variety of fields. They will learn about the most recent developments in the ontology and acquire basic knowledge of the draft version 2.0.


==FURTHER INFORMATION==
The current version of the draft Specification and User Guide for BFO 2.0 is available [http://purl.obolibrary.org/obo/bfo/Reference here].
Background information concerning BFO is available [http://www.ifomis.uni-saarland.de/bfo/ here].  


For introductory reading see: Pierre Grenon and Barry Smith: "[http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf SNAP and SPAN: Towards Dynamic Spatial Ontology]", Spatial Cognition and Computation, 4 (2004), 69-103.
The current version of the draft BFO 2.0 OWL file is available [http://purl.obolibrary.org/obo/bfo.owl here]. Please read the [http://purl.obolibrary.org/obo/bfo/2012-07-20/ReleaseNotes release notes]


The current draft version of the BFO 2.0 Specification is available [http://bfo.googlecode.com/svn/trunk/docs/bfo2-reference/BFO2-Reference.docx here].
These links, and also further information concerning the draft BFO 2.0 release can be found at the BFO page here: https://github.com/BFO-ontology/BFO


For further information please write to [mailto:phismith@buffalo.edu Barry Smith].
[http://ncorwiki.buffalo.edu/index.php/WORKSHOP,_Buffalo,_August_18-19,_2012#WORKSHOP.2C_Buffalo.2C_August_18-19.2C_2012 BFO Workshop 2012]

Latest revision as of 12:19, 16 November 2023

BFO OWL 2.0

For BFO 2020 (= ISO standard) see here

Release information on BFO github site

VIDEO INTRODUCTION TO BFO 2.0 (2015)

Part One

Part Two

BACKGROUND INFORMATION

BFO Website

For introductory reading see: Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Dynamic Spatial Ontology", Spatial Cognition and Computation, 4 (2004), 69-103.

For introductory reading on relations see: Barry Smith, Werner Ceusters, et al., “Relations in Biomedical Ontologies”, Genome Biology (2005), 6 (5), R46.

For (optional) philosophical discussion of core BFO issues see: Barry Smith and Werner Ceusters, “Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies”, Applied Ontology, 5 (2010), 139–188.

This paper contains some material pertaining to process profiles: “Classifying Processes: An Essay in Applied Ontology”, Ratio, 25:4 (2012), 463-488.

And the paper here contains material on the proposed BFO 2.0 classification of objects: “On Classifying Material Entities in Basic Formal Ontology”, in Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting, Tokyo: Keio University Press, 2012, 1-13.

The current draft version of the BFO 2.0 Specification is available here.

For further information please write to Barry Smith or see here.

DESCRIPTION

Basic Formal Ontology is currently being used by over 450 ontology-based research projects in biomedical informatics and increasingly in other fields. The course will provide an introduction to the content and use of BFO in ontology development. Attendees will acquire knowledge of the ontology and of its use as top-level ontology in multiple ontology development projects in a variety of fields. They will learn about the most recent developments in the ontology and acquire basic knowledge of the draft version 2.0.

The current version of the draft Specification and User Guide for BFO 2.0 is available here.

The current version of the draft BFO 2.0 OWL file is available here. Please read the release notes

These links, and also further information concerning the draft BFO 2.0 release can be found at the BFO page here: https://github.com/BFO-ontology/BFO

BFO Workshop 2012

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