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

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


1
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Disclaimer I recycle many slides originally made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
2
Overview
  • Motivation
  • BFO and RO
  • Top-level categories and relations of BFO/RO
  • Conclusions

3
Why do we need a top-level ontology such as Basic
Formal Ontology (BFO) ?
4
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
5
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
6
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8
Domain ontologies specify the semantics of the
vocabulary of a particular domain

PaTO
9
All domain ontologies use the same top level
notions

PaTO
10
All domain ontologies use the same top level
notions

PaTO
Ontological principles
11
All domain ontologies use the same top level
notions

PaTO
12
All domain ontologies use the same top level
notions

PaTO
Facilitates interoperatibility
13
All domain ontologies use the same top level
notions

PaTO
Facilitates interoperatibility
14
All domain ontologies use the same top level
notions

PaTO
15
More acronyms BFO vs. BFO-FOL vs. BFO-DL vs.
RO
16
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
17
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
18
Kinds of Ontology Languages
Description Logics (DAMLOIL)
General Logic
19
Kinds of Ontology Languages
Description Logics (DAMLOIL)
General Logic
How well can we specify intended meaning of terms
What can we compute automatically
20
Kinds of Ontology Languages
Description Logics (DAMLOIL)
General Logic
How well can we specify intended meaning of terms
What can we compute automatically
21
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
22
Computational representations of BFO
23
Computational representations of BFO
  • BFO-FOL
  • implementation of BFO in first order logic

24
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

25
Computational representations of BFO
  • BFO-DL
  • implementation of BFO in OWL
  • BFO-FOL
  • implementation of BFO in first order logic

26
BFO vs. RO
  • RO Relation ontology
  • RO is a sub-set of BFO-DL that has been included
    in the OBO framework of ontologies

27
What is in the Relation Ontology (RO) ???
28
Two distinct kinds of entities
universals particulars
types tokens
classes instances

29
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30
ParticularsContinuants vs. occurrents
31
Persistent entities
32
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

33
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

34
Continuants have spatial parts
35
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36
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

37
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38
Kinds of continuants
39
Kinds of continuants
Independent continuants (substances)
Dependent continuants
40
Kinds of continuants
Independent continuants (substances)
Dependent continuants
41
Kinds of continuants
Independent continuants (substances)
Dependent continuants
  • the yellow color of this car
  • the maximal speed of this car

42
Kinds of continuants
Independent continuants (substances)
Dependent continuants
  • the mass of this planet
  • its disposition to sustain life

43
Kinds of continuants
Independent continuants (substances)
Dependent continuants
  • the mass of this molecule
  • its disposition to engage in chemical reactions

44
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46
Universals and particulars(cont.)
47
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48
Accidents Species and instances
Universals among dependent continuants
Barry Smith
49
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50
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51
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52
What is in the Relation Ontology (RO) ???
53
What is in the Relation Ontology (RO) ???
54
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61
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
62
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)

63
Important Individual-level relations
64
Individual-level relations
You, me, This molecule, My cat Misha
65
Individual-level relations
My temperature (now) My height My role as a
presenter
66
Individual-level relations
Processes My life, My presenting this talk
67
Individual-level relations
Occurrent
  • My heart part-of my body
  • Montana part-of United States

Dependent Continuant
Independent Continuant
68
Individual-level relations
Occurrent
  • the runner participates in the racing process
  • the molecule participates in the diffusion
    process

Dependent Continuant
Independent Continuant
69
Individual-level relations
Occurrent
  • the racing involves racers
  • the diffusion process involves molecules

Dependent Continuant
Independent Continuant
70
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
71
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
72
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

73
Individual-level relations
Occurrent
Dependent Continuant
Independent Continuant
  • Your height inheres in you
  • The role the antibiotics inheres in the
    antibiotics

74
Individual-level relations
Occurrent
Dependent Continuant
Independent Continuant
InheresIn
75
Relations among independent persistent entities
76
Conclusions
77
All domain ontologies use the same top level
notions

PaTO
78
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