|
|
| (21 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| | == BFO OWL 2.0 == |
| | For BFO 2020 (= ISO standard) see [http://ncorwiki.buffalo.edu/index.php/BFO_2020 here] |
| | |
| | Release information on [https://github.com/bfo-ontology/BFO/wiki BFO github site] |
| | |
| | == VIDEO INTRODUCTION TO BFO 2.0 (2015) == |
| | |
| | [https://www.youtube.com/watch?v=iTNQYyh88-Y Part One] |
| | |
| | [https://www.youtube.com/watch?v=IMCBON2me3Y Part Two] |
| | |
| ==BACKGROUND INFORMATION== | | ==BACKGROUND INFORMATION== |
|
| |
|
| Line 9: |
Line 20: |
| 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. | | 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.
| | 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. |
|
| |
|
| 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. | | 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]. | | 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]. |
|
| |
|
| For further information please write to [mailto:phismith@buffalo.edu Barry Smith] or see [http://www.ifomis.uni-saarland.de/bfo/ here]. | | For further information please write to [mailto:phismith@buffalo.edu Barry Smith] or see [http://www.ifomis.uni-saarland.de/bfo/ here]. |
| | |
| '''FACULTY''': Alan Ruttenberg and Barry Smith (University at Buffalo)
| |
|
| |
|
| == DESCRIPTION == | | == DESCRIPTION == |
|
| |
|
| 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 draft version 2.0. | | 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 [http://purl.obolibrary.org/obo/bfo/Reference here]. | | The current version of the draft Specification and User Guide for BFO 2.0 is available [http://purl.obolibrary.org/obo/bfo/Reference here]. |
| Line 27: |
Line 36: |
| 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 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] |
|
| |
|
| These links, and also further information concerning the draft BFO 2.0 release can be found at the BFO page here: http://code.google.com/p/bfo/ | | 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 |
| | |
| == SCHEDULE ==
| |
| | |
| *[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Smith slides]
| |
| | |
| *[http://bfo.googlecode.com/svn/trunk/docs/BFO2-Tutorial-Implementation-Buffalo-2012-08-18-Ruttenberg.pdf Ruttenberg slides]
| |
| | |
| '''Saturday, August 18, 2012'''
| |
| | |
| [http://mediastream.buffalo.edu/Content/research/phismith/BFO-8-2012/Day1.wmv Streaming video]
| |
| | |
| *9:00 '''The main principles underlying Basic Formal Ontology'''
| |
| ::What BFO is used for
| |
| :::BFO is an upper-level ontology
| |
| :::Ontological realism: an evidence-based strategy for ontology development
| |
| :::Starting point for downward population
| |
| :::Annotation of scientific and administrative data
| |
| :::Part storehouse of lessons learned, part QWERTY keyboard
| |
| :::Basis for common training
| |
| :::Works best under the hood
| |
| ::Brief history of BFO
| |
| :::Pre-History
| |
| ::::Aristotle's Ontological Square
| |
| :::Edmund Husserl
| |
| :::Truthmakers
| |
| :::The Naive Physics Manifesto
| |
| :::Mereotopology
| |
| :::The Gene Ontology and the Foundational Model of Anatomy
| |
| | |
| ::BFO's competitors
| |
| :::DOLCE
| |
| :::SUMO
| |
| :::CYC
| |
| :::What BFO, DOLCE, SUMO, CYC have in common
| |
| :::Arguments in favor of using BFO
| |
| ::Important users of BFO
| |
| :::OBO Foundry
| |
| :::NIF Standard
| |
| :::OBI
| |
| :::IDO Consortium
| |
| :::Plant Ontology
| |
| :::Universal Core Semantic Layer
| |
| ::How BFO is constructed and maintained
| |
| :::Conservative evolution
| |
| :::Simplicity (two levels; no qualities of qualities)
| |
| :::Strict formality (no overlap with domain ontologies)
| |
| :::Asserted monohierarchy and inferred polyhierarchy
| |
| :::Truthmaker
| |
| :::Non-multiplicative (the statue is the portion of clay during the time when the latter has a certain role)
| |
| :::Perspectivalism
| |
| :::No reductionism, no phenomenalism
| |
| :::No 'context'
| |
| :::No meanings, fictions, non-existents
| |
| ::::The Semiotic Triangle
| |
| :::No 'possible worlds'
| |
| :::No abstracta
| |
| :::How to deal with thoughts, beliefs, information artifacts
| |
| | |
| *10:30 Break
| |
| | |
| *11:00 '''Overview of BFO 1.0'''
| |
| :::Instances and universals
| |
| :::Continuants and occurrents
| |
| :::Dependent entities and independent entities
| |
| ::::PATO qualities
| |
| :::Different kinds of relations
| |
| ::::Symmetry, asymmetry and inverses
| |
| ::::The all-some rule
| |
| ::::What to do with probabilistic and other some-some relations?
| |
| :::Realizables
| |
| ::::Roles
| |
| ::::Dispositions and the treatment of modality
| |
| ::::Functions
| |
| ::Added in BFO 1.1
| |
| :::Generically and specifically dependent continuants, concretizations, and relations of dependence
| |
| :::Information entities
| |
| | |
| *12:30 Lunch
| |
| | |
| *13:30 '''Introduction to OWL and to the Semantic Web''' (Alan Ruttenberg)
| |
| | |
| *15:00 Break
| |
| | |
| *15:30 '''Formalization of Basic Formal Ontology''' (Alan Ruttenberg)
| |
| :::Relations between the BFO Specification and BFO FOL, BFO CLIF, BFO OWL
| |
| :::BFO in First Order Logic
| |
| :::BFO in OWL
| |
| :::Applications of BFO in OWL
| |
| :::How to migrate from BFO 1.0 to BFO 2.0
| |
| :::The BFO 2.0 OWL temporalization strategy
| |
| | |
| *16:00 '''New Features of BFO 2.0'''
| |
| ::The BFO 2.0 Specification and Its Status
| |
| :::Relation to FOL and OWL realizations
| |
| :::Definitions and elucidations
| |
| :::New treatment of Relations
| |
| ::::Incorporation of top-level relations into BFO 2.0
| |
| ::::Focus primarily on instance-instance relations
| |
| ::::Added relation of concretization
| |
| :::::::A musical work and its performance
| |
| :::Sites and regions
| |
| :::Representation of boundaries
| |
| ::::Frames of reference; space, time and spacetime
| |
| :::SpaceR, TimeR and Spacetime
| |
| :::Material and immaterial entities
| |
| :::Three subtypes of material entity: objects, object aggregates, and fiat object parts
| |
| :::Continuant fiat boundaries
| |
| ::::Coordinate systems and frames of reference
| |
| :::Object aggregates and the member_of relation, with an application to groups and organizations
| |
| ::::Cognitive selection in the realm of continuants
| |
| :::Granularity on the side of continuants
| |
| ::::Modeling and simulation
| |
| :::Map-based partitions of reality and the fiat entities they create
| |
| ::::Map layers
| |
| ::::Cadaster
| |
| ::::Environments and ecology
| |
| ::::Habitats, niches
| |
| :::Partitions of occurrent reality
| |
| ::::Partition sequences
| |
| ::::Partitions and plans (two sorts of direction of fit)
| |
| | |
| | |
| | |
| '''Sunday, August 19, 2012'''
| |
| | |
| [http://mediastream.buffalo.edu/Content/research/phismith/BFO-8-2012/Day2.wmv Streaming video]
| |
| | |
| *9:00 '''Process Profiles, Rates, and Process Measurement Data'''
| |
| :::Mutual dependence of qualities: The case of color
| |
| :::How quality instances change over time
| |
| :::Rigid and non-rigid universals
| |
| :::Universals and continuous change
| |
| ::Complete and partial processses
| |
| :::Lives and other histories
| |
| :::A top is spinning and simultaneously warming up
| |
| ::Process profiles as targets of process measurements
| |
| :::The Wiggers diagram
| |
| ::::Cognitive selection
| |
| :::Quality process profiles
| |
| ::::What did your temperature do since last night?
| |
| :::Rate process profiles
| |
| ::::Relation to object aggregates
| |
| :::Other quantitative process profiles
| |
| :::Process profiles and time-series graphs
| |
| | |
| *10:30 Break
| |
| | |
| *11:00 '''Qualitative process profiles, granularity and the partitioning of reality'''
| |
| :::Map-based partitions of occurrent reality and the fiat entities they create
| |
| ::::Weather
| |
| :::Granularity on the side of occurrents
| |
| ::::Journalism, history
| |
| ::::Napoleon's March to Moscow
| |
| :::Many map-based fiat entities existed trillions of years before the technology of maps
| |
| :::Music
| |
| ::::Focusing on the cello part when you listen to a string quartet
| |
| :::Dance
| |
| :::Planning
| |
| :::Chess
| |
| :::Football
| |
| :::Experiments and experimental protocols
| |
| :::Language
| |
| ::::Speech acts
| |
| :::Zeno Vendler
| |
| ::::Accomplishments: processes which have an endpoint and are incremental or gradual (paint a picture, build a house)
| |
| ::::Achievements: occur instantaneously (recognize, notice)
| |
| ::::Basic Actions
| |
| | |
| :*12:00 Lunch
| |
| | |
| :*13:00 '''BFO Applied to Disease''' [http://ncor.buffalo.edu/2012/BFO-Disease-Tutorial-August2012.pptx Slides]
| |
| :::Creating a domain ontology by extending BFO
| |
| :::An overview of the Ontology for General Medical Science
| |
| :::Disease courses are process profiles
| |
| :::Occurrent symptoms are process profiles
| |
| | |
| :*14:30 Break
| |
| | |
| :*15:00 '''Concluding Discussion'''
| |
| | |
| :*17:00 Close
| |
| | |
| Participation details: [[BFO 2.0 Meeting August 18-19, 2012]]
| |
| | |
| ==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://alan.ruttenbergs.com Alan Ruttenberg]''' was a Principal Scientist at Creative Commons for 5 years and is now 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.
| | [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
