Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO)

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Underlying Ontologies for Biomedical work - The
Relation Ontology (RO) and Basic Formal Ontology
(BFO)

• Thomas Bittner
• SUNY Buffalo
• bittner3_at_buffalo.edu

Disclaimer I recycle many slides originally made
by Barry Smith
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Overview

• Motivation
• BFO and RO
• Top-level categories and relations of BFO/RO
• Conclusions

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Why do we need a top-level ontology such as Basic
Formal Ontology (BFO) ?
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Jonathan Bard, Michael Ashburner, Oliver Hofman
cell types from prokaryotes to mammals
obo.sourceforge.net/cgi- bin/detail.cgi?cell
Paula Dematos, Rafael Alcantara
ebi.ac.uk/chebi
molecular entities
Melissa Haendel, Terry Hayamizu, Cornelius
Rosse, David Sutherland,
anatomical structures in human and model
organisms
(under development)
JLV Mejino Jr., Cornelius Rosse
fma.biostr.washington. edu
structure of the human body
design, protocol, data instrumentation, and
analysis
FuGO Working Group
fugo.sf.net
cellular components, molecular functions,
biological processes
Gene Ontology Consortium
www.geneontology.org
obo.sourceforge.net/cgi -bin/ detail.cgi? attribut
e_and_value
Michael Ashburner, Suzanna Lewis, Georgios
Gkoutos
qualities of biomedical entities
protein types and modifications
Protein Ontology Consortium
(under development)
Barry Smith, Chris Mungall
obo.sf.net/relationship
relations
three-dimensional RNA structures
RNA Ontology Consortium
(under development)
properties and features of nucleic sequences
Karen Eilbeck
song.sf.net
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Many partly independent efforts
Jonathan Bard, Michael Ashburner, Oliver Hofman
cell types from prokaryotes to mammals
obo.sourceforge.net/cgi- bin/detail.cgi?cell
Paula Dematos, Rafael Alcantara
ebi.ac.uk/chebi
molecular entities
Melissa Haendel, Terry Hayamizu, Cornelius
Rosse, David Sutherland,
anatomical structures in human and model
organisms
(under development)
JLV Mejino Jr., Cornelius Rosse
fma.biostr.washington. edu
structure of the human body
design, protocol, data instrumentation, and
analysis
FuGO Working Group
fugo.sf.net
cellular components, molecular functions,
biological processes
Gene Ontology Consortium
www.geneontology.org
obo.sourceforge.net/cgi -bin/ detail.cgi? attribut
e_and_value
Michael Ashburner, Suzanna Lewis, Georgios
Gkoutos
qualities of biomedical entities
protein types and modifications
Protein Ontology Consortium
(under development)
Barry Smith, Chris Mungall
obo.sf.net/relationship
relations
RNA Ontology Consortium
(under development)
three-dimensional RNA structures
properties and features of nucleic sequences
Karen Eilbeck
song.sf.net
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Domain ontologies specify the semantics of the
vocabulary of a particular domain

PaTO
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All domain ontologies use the same top level
notions

PaTO
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All domain ontologies use the same top level
notions

PaTO
Ontological principles
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All domain ontologies use the same top level
notions

PaTO
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All domain ontologies use the same top level
notions

PaTO
Facilitates interoperatibility
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All domain ontologies use the same top level
notions

PaTO
Facilitates interoperatibility
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All domain ontologies use the same top level
notions

PaTO
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More acronyms BFO vs. BFO-FOL vs. BFO-DL vs.
RO
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Kinds of Ontologies
ad hoc Hierarchies (Yahoo!)
Description Logics (DAMLOIL)
XML Schema
structured Glossaries
formal Taxonomies
XML DTDs
Terms
Thesauri
Data Models (UML, STEP)
Principled, informal hierarchies
ordinary Glossaries
Data Dictionaries (EDI)
General Logic
Frames (OKBC)
DB Schema
Glossaries Data Dictionaries
MetaData, XML Schemas, Data Models
Formal Ontologies Inference
Thesauri, Taxonomies
Michael Gruninger, gruning_at_nist.gov
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Kinds of Ontologies
ad hoc Hierarchies (Yahoo!)
Description Logics (DAMLOIL)
XML Schema
structured Glossaries
formal Taxonomies
XML DTDs
Terms
Thesauri
Data Models (UML, STEP)
Principled, informal hierarchies
ordinary Glossaries
Data Dictionaries (EDI)
General Logic
Frames (OKBC)
DB Schema
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Kinds of Ontology Languages
Description Logics (DAMLOIL)
General Logic
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Kinds of Ontology Languages
Description Logics (DAMLOIL)
General Logic
How well can we specify intended meaning of terms
What can we compute automatically
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Kinds of Ontology Languages
Description Logics (DAMLOIL)
General Logic
How well can we specify intended meaning of terms
What can we compute automatically
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We need BOTH kinds of languages
Description Logics (DAMLOIL)
Tradeoff between expressive power and
computability
General Logic
How well can we specify intended meaning
What can we compute automatically
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Computational representations of BFO
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Computational representations of BFO

• BFO-FOL
• implementation of BFO in first order logic

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Computational representations of BFO

• BFO-DL
• implementation of BFO in the description logic
  OWL (Ontology WEB language)

• BFO-FOL
• implementation of BFO in first order logic

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Computational representations of BFO

• BFO-DL
• implementation of BFO in OWL

• BFO-FOL
• implementation of BFO in first order logic

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BFO vs. RO

• RO Relation ontology
• RO is a sub-set of BFO-DL that has been included
  in the OBO framework of ontologies

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What is in the Relation Ontology (RO) ???
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Two distinct kinds of entities
universals particulars
types tokens
classes instances

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ParticularsContinuants vs. occurrents
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Persistent entities
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Persistent entities

• Continuant
• Persists through time in virtue of being wholly
  present at every time at which it exists at all.
• I exist in full at this moment in time

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Persistent entities

• Continuant
• Persists through time in virtue of being wholly
  present at every time at which it exists at all.
• I exist in full at this moment in time

• Occurrent
• Evolve over time
• Do not exist in full at any given moment
• This presentation does not exist in full right now

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Continuants have spatial parts
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Continuants do NOT have spatio-temporal parts

• I am a continuant
• The first 5-minute phase of my existence is not a
  spatio-temporal part of me
• It is a spatio-temporal part of my life
• My life is a process

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Kinds of continuants
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Kinds of continuants
Independent continuants (substances)
Dependent continuants
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Kinds of continuants
Independent continuants (substances)
Dependent continuants
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Kinds of continuants
Independent continuants (substances)
Dependent continuants

• the yellow color of this car
• the maximal speed of this car

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Kinds of continuants
Independent continuants (substances)
Dependent continuants

• the mass of this planet
• its disposition to sustain life

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Kinds of continuants
Independent continuants (substances)
Dependent continuants

• the mass of this molecule
• its disposition to engage in chemical reactions

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Universals and particulars(cont.)
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Accidents Species and instances
Universals among dependent continuants
Barry Smith
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What is in the Relation Ontology (RO) ???
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What is in the Relation Ontology (RO) ???
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The semantics of universal parthood
X PART-OF Y iff For every instance x of X
there exists an instance y of Y such that x
part-of y AND For every instance y of Y there
exists an instance x of X such that x part-of y
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General framework for defining universal-level
relations in terms of relations between
individuals

• Rall-some(A, B)
• ?x (Inst(x, A) ? ?y( Inst(y, B) Rxy))
• For every instance x of A there is some instance
  y of B such that R(x,y) holds
• Rsome-all(A, B)
• ?y (Inst(y, B) ? ?x( Inst(x, A) Rxy))
• For every instance y of B there is some instance
  x of A such that R(x,y) holds
• Rall-all(A, B) Rall-some(A, B) Rsome-all(A,
  B)

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Important Individual-level relations
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Individual-level relations
You, me, This molecule, My cat Misha
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Individual-level relations
My temperature (now) My height My role as a
presenter
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Individual-level relations
Processes My life, My presenting this talk
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Individual-level relations
Occurrent

• My heart part-of my body
• Montana part-of United States

Dependent Continuant
Independent Continuant
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Individual-level relations
Occurrent

• the runner participates in the racing process
• the molecule participates in the diffusion
  process

Dependent Continuant
Independent Continuant
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Individual-level relations
Occurrent

• the racing involves racers
• the diffusion process involves molecules

Dependent Continuant
Independent Continuant
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Individual-level relations

• the first 10 minutes of the presentation are
  part of the presentation
• my childhood is part of
• my life

Occurrent
Dependent Continuant
Independent Continuant
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Individual-level relations
Occurrent

• The power of a catalytic RNA to catalyze a
  reaction is realized through a complex process of
  binding substrates in the correct orientation and
  stabilizing reaction intermediates
• The role of antibiotics in treating
  infections is realized via the killing of
  bacteria

Dependent Continuant
Independent Continuant
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Individual-level relations
Occurrent
Dependent Continuant
Independent Continuant

• A warming process yields a rise in
  temperature
• The tenure process yields a rise in Johns
  status

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Individual-level relations
Occurrent
Dependent Continuant
Independent Continuant

• Your height inheres in you
• The role the antibiotics inheres in the
  antibiotics

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Individual-level relations
Occurrent
Dependent Continuant
Independent Continuant
InheresIn
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Relations among independent persistent entities
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Conclusions
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All domain ontologies use the same top level
notions

PaTO
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