BFO-ECCB: Difference between revisions

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m (Created page with '== 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-Rut...')
 
 
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== SCHEDULE ==
*9:00 '''Introduction and Principles'''
 
::Why Large-Scale Data-Driven Science Needs Ontologies
*[http://ncor.buffalo.edu/2012/BFO_Tutorial_2012.pptx Smith slides]
::The need for a coordination strategy 1. Upper Level Coordination
*[http://bfo.googlecode.com/svn/trunk/docs/BFO2-Tutorial-Implementation-Buffalo-2012-08-18-Ruttenberg.pdf Ruttenberg slides]
:::BFO as domain-neutral upper-level ontology  
 
:::BFO as starting point for downward populationDomain-specific ontologies
'''Saturday, August 18'''
:::A common set of relations
 
:::Annotation of scientific data
[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21314907&rKey=e35d4e26d0ca7af3 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
:::Part storehouse of lessons learned, part QWERTY keyboard
:::Basis for common training
:::Basis for common training
:::Works best under the hood
:::Works best under the hood
::Brief history of BFO
::The need for a coordination strategy 2. Convergence on domain reference ontologies
:::Pre-History
:::OBO (Open Biomedical Ontologies) Foundry
::::Aristotle's Ontological Square
:::IDO Infectious Disease Ontology Consortium
:::Edmund Husserl
:::CROP Common Reference Ontologies for Plants
:::Truthmakers
:::The Naive Physics Manifesto
:::Mereotopology
:::The Gene Ontology and the Foundational Model of Anatomy


::BFO's competitors
'''Overview of BFO'''
:::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
:::Instances and universals
:::Continuants and occurrents
:::Continuants and occurrents
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::::Symmetry, asymmetry and inverses
::::Symmetry, asymmetry and inverses
::::The all-some rule
::::The all-some rule
::::What to do with probabilistic and other some-some relations?
::::What to do with probabilistic statements?
:::Realizables
:::Realizables
::::Roles
::::Roles
::::Dispositions and the treatment of modality
::::Dispositions and the treatment of modality
::::Functions
::::Functions
::Added in BFO 1.1
:::Generically and specifically dependent continuants, concretizations, and relations of dependence
:::Generically and specifically dependent continuants, concretizations, and relations of dependence
:::Information entities
:::Information entities
 
::Current state of BFO  
*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
:::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'''
'''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
:::Material and immaterial entities
:::Three subtypes of material entity: objects, object aggregates, and fiat object parts
:::Three subtypes of material entity: objects, object aggregates, and fiat object parts
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::::Cognitive selection in the realm of continuants
::::Cognitive selection in the realm of continuants
:::Granularity on the side 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)
*17:00 Close of Day 1
'''Sunday, August 19'''
[https://ub.webex.com/ub/lsr.php?AT=pb&SP=MC&rID=21315352&rKey=27ba15b47f3454cc Video]


*9:00 '''Process Profiles, Rates, and Process Measurement Data'''
'''Process Profiles, Rates, and Process Measurement Data'''
:::Mutual dependence of qualities: The case of color
::Full and partial processses
:::How quality instances change over time
:::Rigid and non-rigid universals
:::Universals and continuous change
::Complete and partial processses
:::Lives and other histories
:::Lives and other histories
:::A top is spinning and simultaneously warming up  
:::A top is spinning and simultaneously warming up  
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::::Cognitive selection
::::Cognitive selection
:::Quality process profiles
:::Quality process profiles
::::What did your temperature do since last night?
::::What did your temperature do since last night, Jim?
:::Rate process profiles
::::Relation to object aggregates
::::Relation to object aggregates
:::Other quantitative process profiles
:::Other quantitative process profiles
:::Process profiles and time-series graphs
:::Process profiles and time-series graphs
 
:::Process profiles and pathway diagrams
*10:30 Break
:::Process profiles and environmental niches
 
*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

Latest revision as of 15:17, 28 August 2012

  • 9:00 Introduction and Principles
Why Large-Scale Data-Driven Science Needs Ontologies
The need for a coordination strategy 1. Upper Level Coordination
BFO as domain-neutral upper-level ontology
BFO as starting point for downward populationDomain-specific ontologies
A common set of relations
Annotation of scientific data
Part storehouse of lessons learned, part QWERTY keyboard
Basis for common training
Works best under the hood
The need for a coordination strategy 2. Convergence on domain reference ontologies
OBO (Open Biomedical Ontologies) Foundry
IDO Infectious Disease Ontology Consortium
CROP Common Reference Ontologies for Plants

Overview of BFO

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 statements?
Realizables
Roles
Dispositions and the treatment of modality
Functions
Generically and specifically dependent continuants, concretizations, and relations of dependence
Information entities
Current state of BFO
How to migrate from BFO 1.0 to BFO 2.0

New Features of BFO 2.0

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

Process Profiles, Rates, and Process Measurement Data

Full 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, Jim?
Relation to object aggregates
Other quantitative process profiles
Process profiles and time-series graphs
Process profiles and pathway diagrams
Process profiles and environmental niches
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