Difference between revisions of "BFO 2011"

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== Basic Formal Ontology Editorial Meeting ==
 
== Basic Formal Ontology Editorial Meeting ==
  
−
'''Venue:''' Room B1-360, Ground Floor, [http://www.bioinformatics.buffalo.edu/about_directions.php Center of Excellence in Bioinformatics and Life Sciences]
+
 
 +
'''Venue:''' Room B1-306, Ground Floor, [http://www.bioinformatics.buffalo.edu/about_directions.php 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 [http://www.bioinformatics.buffalo.edu/about_directions.php CeO]. The entrance is on Elicott Street between Goodell and Virginia.
 +
 
  
 
'''Date:''' November 10-11, 2011
 
'''Date:''' November 10-11, 2011
 +
 +
 +
'''[http://maps.google.com/maps?hl=en&rlz=1C1CHKZ_enUS440US440&nord=1&q=doubletree+hotel+buffalo+ny&gs_sm=&gs_upl=&bav=on.2,or.r_gc.r_pw.r_cp.,cf.osb&biw=623&bih=458&ion=1&um=1&ie=UTF-8&sa=N&tab=wl Walking directions from Doubletree Hotel]
  
 
----
 
----
−
'''Goal of This Meeting'''
+
 
 +
== '''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.
 
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.
  
 
----
 
----
−
'''Tentative Agenda'''
+
== '''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
 
Thursday November 10
  
−
'''9:00am Strategy for Future Development of BFO (Moderator: WC)'''
+
'''9:00am Strategy for Future Development of BFO (Moderator: Werner Ceusters)'''
  
 
:The BFO Reference   
 
:The BFO Reference   
  
 
:Universals and particulars
 
:Universals and particulars
−
:[http://ontology.buffalo.edu/smith/articles/vagueness.pdf Granularity and vagueness]
+
::::[http://ontology.buffalo.edu/smith/articles/vagueness.pdf Granularity and vagueness]
−
:Reductionism and perspectivalism
+
::::Reductionism and perspectivalism
 +
::::Predications in the category of substance vs. predications in other categories (how BFO differs from standard view of 'predicate' logic)
 +
::::[http://iospress.metapress.com/content/1551884412214u67/fulltext.pdf 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 [http://www.biomedcentral.com/1471-2105/11/441 TaillessMouse subClassOf: (not has-part some Tail)]
  
−
:BFO-conformant extensions
+
:BFO-conformant extensions  
−
::Governance process
+
::Certain categories that used to have closure axioms no longer do because we recognize that there may be other subtypes
−
:Rules for defined classes and abbreviations
+
:::Examples:
 +
:::Object, Fiat Object Part, Object Aggregate
 +
::::Governance process for this
 
:Relations
 
:Relations
−
::inside BFO
+
:Inside BFO
−
::outside BFO
+
:Outside BFO
 +
:::Governance process for this
 
:Formalization
 
:Formalization
 
::OWL, OBO, FOL
 
::OWL, OBO, FOL
−
::Definitions
+
::Treatment of definitions
 
::[http://userpages.umbc.edu/~fneuhaus/subquauni.pdf Axioms]
 
::[http://userpages.umbc.edu/~fneuhaus/subquauni.pdf Axioms]
 +
::Treatment of axioms
  
 
'''10:00am Coffee'''
 
'''10:00am Coffee'''
  
−
'''10:15am Material entity (Moderator: BS)'''
+
'''10:15am Treatment of Relations (Moderator: Alan Ruttenberg)
  
 +
:Presentation by Chris Mungall: "[http://ontology.buffalo.edu/BFO/Reference/Mungall_RO_2012.pptx 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
 
:Object; fiat object part; object aggregate
−
::Conjoined twins
+
::[http://www.ifomis.org/Downloads/Reports/IR-0303_Donnelly.pdf The relation of connection]
 
::Atoms, molecules
 
::Atoms, molecules
−
::Bodies of energy; fields; portions of matter
+
::Cells, organs, organisms (objects connected by surrounding membranes)
 +
:::Conjoined twins
 +
::Portions of matter
 +
::Planets
 +
:::Bodies of energy; fields; portions of matter
 
:Sites
 
:Sites
−
::The Environment Ontology
+
:::::The Environment Ontology
 
::Geographical entities
 
::Geographical entities
 
:Object boundaries
 
:Object boundaries
Line 51: Line 86:
 
'''12:00pm Lunch'''
 
'''12:00pm Lunch'''
  
−
'''1pm BFO Dependent Continuant (Moderator: BS)'''
+
'''1pm BFO Dependent Continuant (Moderator: Werner Ceusters)'''
  
 
:Dependence, inherence
 
:Dependence, inherence
−
:Quality;
+
:Qualities
 +
:Quality  
 
::Reciprocal quality pair  
 
::Reciprocal quality pair  
 
::Relational quality
 
::Relational quality
−
::State
 
 
::Comparison of qualities
 
::Comparison of qualities
−
::Wavelength, frequency
 
 
:Realizable dependent continuant
 
:Realizable dependent continuant
 
::Disposition and its subcategories
 
::Disposition and its subcategories
 
::Reciprocal disposition pair
 
::Reciprocal disposition pair
 
::Relational disposition
 
::Relational disposition
−
::Physical basis
+
::Physical basis (cf. OGMS:Disorder)
 
:Generically dependent continuant (GDC)
 
:Generically dependent continuant (GDC)
−
::GDC as bearer of quality
+
::GDC as bearer of quality?
  
 
'''2.30pm Break'''
 
'''2.30pm Break'''
  
−
'''2.45pm BFO Occurrent (Moderator BS)'''
+
'''2.45pm BFO Occurrent (Moderator: Fabian Neuhaus)'''
  
 
:Predicates applied to processes
 
:Predicates applied to processes
−
::Rates
+
::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. 
−
::Flows
+
::Rates [http://ontology.buffalo.edu/BFO/Reference/rates.docx Paper by BS]
−
:Course / life / history / projection
+
::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 / [http://ontology.buffalo.edu/smith/articles/cornucopia.pdf projection]
  
 
'''4:00-6:00pm Special session on Mental and Neurological Ontologies (Moderator: Alex Diehl)'''
 
'''4:00-6:00pm Special session on Mental and Neurological Ontologies (Moderator: Alex Diehl)'''
Line 82: Line 123:
 
:Werner Ceusters: The Mental Disease Ontology (MDO)
 
:Werner Ceusters: The Mental Disease Ontology (MDO)
 
:Alex Diehl: The Neurological Disease Ontology (NDO)
 
:Alex Diehl: The Neurological Disease Ontology (NDO)
 +
 +
----
  
 
Friday November 11
 
Friday November 11
  
−
'''9am BFO OWL (Moderator AR)'''
+
'''9:00am: Continued discussion of object aggregates and process profiles (Moderator: Janna Hastings)'''
−
 
+
−
:Relations, including short-cut relations
 
−
:Axioms relating to relations
 
−
 
 
 
'''10:00am Coffee'''
 
'''10:00am Coffee'''
  
−
:Other aspects of BFO OWL
+
'''10:15 Regions (Moderator: Fabian Neuhaus)'''
 +
:Region and frame of reference
 +
:BFO-Reference
 +
:Versioning
 +
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1560437/ Spatial region]
 +
:Spatio-temporal and temporal region
 +
:Location and containment
 +
::Incorporation of RCC8 and Allen Calculus?
  
 
'''12:00pm Lunch'''
 
'''12:00pm Lunch'''
  
−
'''1:00pm Regions (Moderator WC)'''
+
'''1:00pm: BFO OWL (Moderator: Alan Ruttenberg)'''
−
:[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1560437/ Spatial region]
+
 
−
:Spatio-temporal and temporal region
+
:Relations, including short-cut relations
−
:Region and frame of reference
+
:Axioms relating to relations
−
::Incorporation of RCC8 and Allen Calculus?
 
  
−
'''3:00pm Final Session on Future Plans (Moderator BS)'''
+
'''2:00pm Break'''
−
:BFO-Reference
 
−
:Versioning
 
−
:Governance
 
  
 +
'''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'''
+
 
 +
== '''Participants''' ==
  
 
*Thomas Bittner
 
*Thomas Bittner
 
*Mathias Brochhausen
 
*Mathias Brochhausen
 +
*Carmelo Gaudioso
 
*Werner Ceusters
 
*Werner Ceusters
 
*Alexander Cox
 
*Alexander Cox
Line 119: Line 175:
 
*Albert Goldfain
 
*Albert Goldfain
 
*Janna Hastings
 
*Janna Hastings
 +
*Amanda Hicks
 +
*Leonard Jacuzzo
 
*Mark Jensen
 
*Mark Jensen
 +
*David Molik
 +
*Darren Natale
 
*Fabian Neuhaus
 
*Fabian Neuhaus
 
*Mark Ressler
 
*Mark Ressler
 +
*Ron Rudnicki
 
*Alan Ruttenberg
 
*Alan Ruttenberg
 
*Stefan Schulz
 
*Stefan Schulz
 
*Barry Smith
 
*Barry Smith
 
*Neil Williams
 
*Neil Williams
−
 
−
{{Hidden
 
−
 
−
'''Remotely:'''
 
−
 
−
*Larry Hunter
 
−
*Chris Mungall
 
−
}}
 

Latest revision as of 08:02, 22 January 2012

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)
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)

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
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