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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] |
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| | Release information on [https://github.com/bfo-ontology/BFO/wiki BFO github site] |
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| ----
| | == VIDEO INTRODUCTION TO BFO 2.0 (2015) == |
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| == IMPORTANT NOTE FOR INTENDING PARTICIPANTS == | | [https://www.youtube.com/watch?v=iTNQYyh88-Y Part One] |
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| '''If you intend to participate in this tutorial and have not received an email with instructions please write to phismith@buffalo.edu immediately'''
| | [https://www.youtube.com/watch?v=IMCBON2me3Y Part Two] |
| ----
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| | ==BACKGROUND INFORMATION== |
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| | '''[http://www.ifomis.uni-saarland.de/bfo/ BFO Website]''' |
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| '''VENUE for FACE-TO-FACE PARTICIPATION''': 141 [http://www.buffalo.edu/buildings/building?id=PARK Park Hall], University at Buffalo [http://www.buffalo.edu/home/visiting-ub/north-campus-directions.html North Campus], Amherst, NY.
| | 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. |
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| Suggested hotels: [http://www.expedia.ca/Amherst-Buffalo-Hotels.0-n6056530-0.Travel-Guide-Filter-Hotels]
| | 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. |
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| '''ONLINE PARTICIPATION''': Instructions will for Webex participation will be sent by e-mail. The Webex sessions will be recorded and the recordings will be linked from this page. | | 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. |
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| '''FACULTY''': Alan Ruttenberg and Barry Smith (University at Buffalo) | | 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. |
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| == DESCRIPTION ==
| | 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. |
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| 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.
| | 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]. |
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| The current version of the draft Specification and User Guide for BFO 2.0 is available [http://purl.obolibrary.org/obo/bfo/Reference here].
| | For further information please write to [mailto:phismith@buffalo.edu Barry Smith] or see [http://www.ifomis.uni-saarland.de/bfo/ here]. |
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| The current version of the BFO 2.0 OWL file is available [http://purl.obolibrary.org/obo/bfo.owl here].
| | == DESCRIPTION == |
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| 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/
| | 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. |
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| == DRAFT SCHEDULE ==
| | The current version of the draft Specification and User Guide for BFO 2.0 is available [http://purl.obolibrary.org/obo/bfo/Reference here]. |
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| *[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Smith slides]
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| *[http://bfo.googlecode.com/svn/trunk/docs/BFO2-Tutorial-Implementation-Buffalo-2012-08-18-Ruttenberg.pdf Ruttenberg slides]
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| '''Saturday, August 18'''
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| *9:00 '''The main principles underlying Basic Formal Ontology'''
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| ::What BFO is used for
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| :::BFO is an upper-level ontology
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| :::Ontological realism: an evidence-based strategy for ontology development
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| :::Starting point for downward population
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| :::Annotation of scientific and administrative data
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| :::Part storehouse of lessons learned, part QWERTY keyboard
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| :::Basis for common training
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| :::Works best under the hood
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| ::Brief history of BFO
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| :::Pre-History
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| ::::Aristotle's Ontological Square
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| :::Edmund Husserl
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| :::Truthmakers
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| :::The Naive Physics Manifesto
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| :::Mereotopology
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| :::The Gene Ontology and the Foundational Model of Anatomy
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| ::BFO's competitors
| | 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] |
| :::DOLCE
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| :::SUMO
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| :::CYC
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| :::What BFO, DOLCE, SUMO, CYC have in common
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| :::Arguments in favor of using BFO
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| ::Important users of BFO
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| :::OBO Foundry
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| :::NIF Standard
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| :::OBI
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| :::IDO Consortium
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| :::Plant Ontology
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| :::Universal Core Semantic Layer
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| ::How BFO is constructed and maintained
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| :::Conservative evolution
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| :::Simplicity (two levels; no qualities of qualities)
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| :::Strict formality (no overlap with domain ontologies)
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| :::Asserted monohierarchy and inferred polyhierarchy
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| :::Truthmaker
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| :::Non-multiplicative (the statue is the portion of clay during the time when the latter has a certain role)
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| :::Perspectivalism
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| :::No reductionism, no phenomenalism
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| :::No 'context'
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| :::No meanings, fictions, non-existents
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| ::::The Semiotic Triangle
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| :::No 'possible worlds'
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| :::No abstracta
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| :::How to deal with thoughts, beliefs, information artifacts
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| *10:30 Break
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| *11:00 '''Overview of BFO 1.0'''
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| :::Instances and universals
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| :::Continuants and occurrents
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| :::Dependent entities and independent entities
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| ::::PATO qualities
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| :::Different kinds of relations
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| ::::Symmetry, asymmetry and inverses
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| ::::The all-some rule
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| ::::What to do with probabilistic and other some-some relations?
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| :::Realizables
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| ::::Roles
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| ::::Dispositions and the treatment of modality
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| ::::Functions
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| ::Added in BFO 1.1
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| :::Generically and specifically dependent continuants, concretizations, and relations of dependence
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| :::Information entities
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| *12:30 Lunch
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| *13:30 '''Introduction to OWL and to the Semantic Web''' (Alan Ruttenberg)
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| *15:00 Break
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| *15:30 '''Formalization of Basic Formal Ontology''' (Alan Ruttenberg)
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| :::Relations between the BFO Specification and BFO FOL, BFO CLIF, BFO OWL
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| :::BFO in First Order Logic
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| :::BFO in OWL
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| :::Applications of BFO in OWL
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| :::How to migrate from BFO 1.0 to BFO 2.0
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| :::The BFO 2.0 OWL temporalization strategy
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| *16:00 '''New Features of BFO 2.0'''
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| ::The BFO 2.0 Specification and Its Status
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| :::Relation to FOL and OWL realizations
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| :::Definitions and elucidations
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| :::New treatment of Relations
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| ::::Incorporation of top-level relations into BFO 2.0
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| ::::Focus primarily on instance-instance relations
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| ::::Added relation of concretization
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| :::::::A musical work and its performance
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| :::Sites and regions
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| :::Representation of boundaries
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| ::::Frames of reference; space, time and spacetime
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| :::SpaceR, TimeR and Spacetime
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| :::Material and immaterial entities
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| :::Three subtypes of material entity: objects, object aggregates, and fiat object parts
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| :::Continuant fiat boundaries
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| ::::Coordinate systems and frames of reference
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| :::Object aggregates and the member_of relation, with an application to groups and organizations
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| ::::Cognitive selection in the realm of continuants
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| :::Granularity on the side of continuants
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| ::::Modeling and simulation
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| :::Map-based partitions of reality and the fiat entities they create
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| ::::Map layers
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| ::::Cadaster
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| ::::Environments and ecology
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| ::::Habitats, niches
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| *17:00 Close of Day 1
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| '''Sunday, August 19'''
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| *9:00 '''Process Profiles, Rates, and Process Measurement Data'''
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| :::Mutual dependence of qualities: The case of color
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| :::How quality instances change over time
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| :::Rigid and non-rigid universals
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| :::Universals and continuous change
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| ::Complete and partial processses
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| :::Lives and other histories
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| :::A top is spinning and simultaneously warming up
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| ::Process profiles as targets of process measurements
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| :::The Wiggers diagram
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| ::::Cognitive selection
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| :::Quality process profiles
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| ::::What did your temperature do since last night?
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| :::Rate process profiles
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| ::::Relation to object aggregates
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| :::Other quantitative process profiles
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| :::Process profiles and time-series graphs
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| *10:30 Break
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| *11:00 '''Qualitative process profiles, granularity and the partitioning of reality'''
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| :::Map-based partitions of occurrent reality and the fiat entities they create
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| ::::Weather
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| :::Granularity on the side of occurrents
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| ::::Journalism, history
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| ::::Napoleon's March to Moscow
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| :::Many map-based fiat entities existed trillions of years before the technology of maps
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| :::Music
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| ::::Focusing on the cello part when you listen to a string quartet
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| :::Dance
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| :::Planning
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| :::Chess
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| :::Football
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| :::Experiments and experimental protocols
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| :::Language
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| ::::Speech acts
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| :::Zeno Vendler
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| ::::Accomplishments: processes which have an endpoint and are incremental or gradual (paint a picture, build a house)
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| ::::Achievements: occur instantaneously (recognize, notice)
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| ::::Basic Actions
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| :*12:00 Lunch
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| :*13:00 '''BFO Applied to Disease'''
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| :::Creating a domain ontology by extending BFO
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| :::An overview of the Ontology for General Medical Science
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| :::Disease courses are process profiles
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| :::Occurrent symptoms are process profiles
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| :*14:30 Break
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| :*15:00 '''Concluding Discussion'''
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| :*17:00 Close
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| == PARTICIPATION ==
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| 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.
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| Log-on/dial-in instructions for on-line participation will be provided by email to registered participants prior to the meeting.
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| '''FOR CREDIT'''
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| 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.
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| ::Registration details for students taking this course for credit are available:
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| :::[http://myub.buffalo.edu/course/public/scripts/crs_sched.cgi?switch=showclass&semester=summer&division=NON&dept=PHI®num=12518 here], for face-to-face participation;
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| :::[http://myub.buffalo.edu/course/public/scripts/crs_sched.cgi?switch=showclass&semester=summer&division=NON&dept=PHI®num=12708 here], for on-line participation.
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| ::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].
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| '''AUDITING'''
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| 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.
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| ==FACULTY==
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| '''[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.
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| '''[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.
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| ==FURTHER INFORMATION==
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| 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.
| |
| | |
| 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.
| |
| | |
| 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 paper [http://ontology.buffalo.edu/smith/articles/Classifying_Processes.pdf here] contains some material pertaining to process profiles: “Classifying Processes: An Essay in Applied Ontology”, ''Ratio'', in press.
| |
| | |
| 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.
| |
|
| |
|
| 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] |
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
