BFO 2011
Basic Formal Ontology Editorial Meeting
Venue: Room B1-306, Ground Floor, Center of Excellence (CoE) in Bioinformatics and Life Sciences
Parking: Parking is available for $5 per day in the large lot immediately in front of the CeO. The entrance is on Elicott Street between Goodell and Virginia.
Date: November 10-11, 2011
Walking directions from Doubletree Hotel
Goal of This Meeting
To define a strategy for the future maintenance of Basic Formal Ontology. To create a BFO Reference, designed as an authoritative documentation of the BFO ontology, including an updated version of the BFO 1.0 taxonomy together with the top level relations of the Relation Ontology. To define a strategy to create BFO OWL, including a treatment of temporal relations, based on BFO Reference.
Agenda
(This agenda is designed to provide a list of topics which need to be addressed in due course; the agenda for the meeting itself will be a selection herefrom; indented items marked &&& will be dealt with at most in cursory fashion)
On both days the café adjacent to the meeting room is open from 8am to 10:30am and from 11am to 3pm.
Thursday November 10
9:00am Strategy for Future Development of BFO (Moderator: Werner Ceusters)
- The BFO Reference
- Universals and particulars
- &&&Granularity and vagueness
- &&&Reductionism and perspectivalism
- &&&Predications in the category of substance vs. predications in other categories (how BFO differs from standard view of 'predicate' logic)
- &&&Classes, universals, extensions, laws of nature
- Attributive classes, abbreviations, disjunctions of convenience
- Inferred classes
- Nomenclature for membership in attributive and inferred classes
- Relation between Is_a and OWL:SubClassOf
- &&&That 'Is_a' in BFO Reference (and in GO, and many other ontologies) does not mean the same as SubClassOf in OWL because the latter allows statements such as TaillessMouse subClassOf: (not has-part some Tail)
- Relation between Is_a and OWL:SubClassOf
- BFO-conformant extensions
- Certain categories that used to have closure axioms no longer do because we recognize that there may be other subtypes
- Examples:
- Object, Fiat Object Part, Object Aggregate
- Governance process for this
- Certain categories that used to have closure axioms no longer do because we recognize that there may be other subtypes
- Relations
- Inside BFO
- Outside BFO
- Governance process for this
- Formalization
- OWL, OBO, FOL
- Treatment of definitions
- Axioms
- Treatment of axioms
10:00am Coffee
10:15am Treatment of Relations (Moderator: Alan Ruttenberg)
- Presentation by Chris Mungall: "RO.owl and Shortcut Relations"
10:45 Material entity (Moderator: Werner Ceusters)
- Material entity
- Can contain parts which are not material entities (e.g. FMA: lumen of gut part_of gut)
- Object; fiat object part; object aggregate
- The relation of connection
- Atoms, molecules
- Cells, organs, organisms (objects connected by surrounding membranes)
- Conjoined twins
- Portions of matter
- Planets
- Bodies of energy; fields; portions of matter
- Sites
- &&&The Environment Ontology
- Geographical entities
- Object boundaries
- Spatial region boundaries
- Granularity
12:00pm Lunch
1pm BFO Dependent Continuant (Moderator: Werner Ceusters)
- Dependence, inherence
- Qualities
- Quality
- Reciprocal quality pair
- Relational quality
- Comparison of qualities
- Realizable dependent continuant
- Disposition and its subcategories
- Reciprocal disposition pair
- Relational disposition
- Physical basis (cf. OGMS:Disorder)
- Generically dependent continuant (GDC)
- GDC as bearer of quality?
2.30pm Break
2.45pm BFO Occurrent (Moderator: Fabian Neuhaus)
- Predicates applied to processes
- The general strategy: processes have profiles as parts (e.g. beat profile, sound profile, ...) and when we predicate e.g. '60 bpm' of a heart beating process p, then we are asserting that p has a beat profile which instantiates the universal: 60bpm process.
- Rates Paper by BS
- Synchronous, asynchronous
- Blood pressure
- Relation to DOLCE theory of quality spaces
- Wavelength, frequency
- Process profile universals and information artifacts
- State (State of rest as limit case of motion process) (vs. State as continuant)
- Treatment of information artifacts such as peak current, peak voltage, etc.
- Course / life / history / projection
4:00-6:00pm Special session on Mental and Neurological Ontologies (Moderator: Alex Diehl)
- Janna Hastings: From brain science to mind science with the Mental Functioning Ontology (MFO)
- Werner Ceusters: The Mental Disease Ontology (MDO)
- Alex Diehl: The Neurological Disease Ontology (NDO)
Friday November 11
9:00am: Continued discussion of object aggregates and process profiles (Moderator: Janna Hastings)
10:00am Coffee
10:15 Regions (Moderator: Fabian Neuhaus)
- Region and frame of reference
- BFO-Reference
- Versioning
- Spatial region
- Spatio-temporal and temporal region
- Location and containment
- Incorporation of RCC8 and Allen Calculus?
12:00pm Lunch
1:00pm: BFO OWL (Moderator: Alan Ruttenberg)
- Relations, including short-cut relations
- Axioms relating to relations
2:00pm Break
2:30pm: Development and governance strategy (Moderator: Barry Smith)
- Modules and working groups
- Spatial, temporal and spatiotemporal regions
- Process profiles, PATO and units of measure
- Terminology for referring to release versions of BFO Reference, of BFO OWL, and eventually of other variants.
- Working groups for documentation and formalization
- of BFO Reference
- of BFO FOL
- of BFO OWL
- Infrastructure
- BFO and OBO Foundry
Participants
- Thomas Bittner
- Mathias Brochhausen
- Carmelo Gaudioso
- Werner Ceusters
- Alexander Cox
- Randall Dipert
- Alexander Diehl
- Albert Goldfain
- Janna Hastings
- Amanda Hicks
- Leonard Jacuzzo
- Mark Jensen
- David Molik
- Darren Natale
- Fabian Neuhaus
- Mark Ressler
- Ron Rudnicki
- Alan Ruttenberg
- Stefan Schulz
- Barry Smith
- Neil Williams