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

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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.

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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.

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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)

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

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)

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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

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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