Ontological Engineering

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Ontological Engineering

• Barry Smith
• http//ontology.buffalo.edu
• Computers and Information in Engineering
  Conference, Buffalo
• August 19, 2014

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GO is amazingly successful in overcoming problems
of balkanization, especially for retrieval of data

• but it covers only generic biological entities of
  three sorts
• cellular components
• molecular functions
• biological processes
• and it does not provide representations of
  diseases, symptoms, anatomy, pathways,

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RELATION TO TIME GRANULARITY CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT
RELATION TO TIME GRANULARITY INDEPENDENT INDEPENDENT DEPENDENT DEPENDENT
ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality(PaTO) Biological Process (GO)
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Phenotypic Quality(PaTO) Biological Process (GO)
MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO)
Original OBO Foundry ontologies (Gene Ontology
in yellow)
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RELATION TO TIME GRANULARITY CONTINUANT CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT
RELATION TO TIME GRANULARITY INDEPENDENT INDEPENDENT INDEPENDENT DEPENDENT DEPENDENT
ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality(PaTO) Biological Process (GO)
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Phenotypic Quality(PaTO) Biological Process (GO)
MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO)
Environments
Environment Ontology (EnvO)
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domain ontologies created by specialization from
BFO
Basic Formal Ontology (BFO)
top level mid-level domain level
Information Artifact Ontology (IAO) Ontology for Biomedical Investigations (OBI) Spatial Ontology (BSPO)
Anatomy Ontology (FMA, CARO) Anatomy Ontology (FMA, CARO) Environment Ontology (ENVO) Infectious Disease Ontology (IDO) Biological Process Ontology (GO)
Cell Ontology (CL) Cellular Component Ontology (FMA, GO) Environment Ontology (ENVO) Infectious Disease Ontology (IDO) Biological Process Ontology (GO)
Cell Ontology (CL) Cellular Component Ontology (FMA, GO) Environment Ontology (ENVO) Phenotypic Quality Ontology(PATO) Biological Process Ontology (GO)
Subcellular Anatomy Ontology (SAO) Subcellular Anatomy Ontology (SAO) Subcellular Anatomy Ontology (SAO) Phenotypic Quality Ontology(PATO) Biological Process Ontology (GO)
Sequence Ontology (SO) Sequence Ontology (SO) Sequence Ontology (SO) Molecular Function (GO) Biological Process Ontology (GO)
Protein Ontology (PRO) Protein Ontology (PRO) Protein Ontology (PRO) Molecular Function (GO) Biological Process Ontology (GO)
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domain ontologies created by specialization from
BFO
Basic Formal Ontology (BFO) core nodes
Independent continuants Dependent continuants Occurrents
Classes Object types Attribute types Process types
Particulars Individual objects Individual attributes Individual processes
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• BFO 2.0

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http//obofoundry.org

• CHEBI Chemical Entities of Biological Interest
• GO Gene Ontology
• OBI Ontology for Biomedical Investigations
• PATO Phenotypic Quality Ontology
• PO Plant Ontology
• PATO Phenotypic Quality Ontology
• PRO Protein Ontology
• XAO Xenopus Anatomy Ontology
• ZFA Zebrafish Anatomy Ontology

http//www.ifomis.org/bfo/
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OBO Foundry approach extended into other domains
NIF Standard Neuroscience Information Framework
IDO Consortium Infectious Disease Ontology
cROP Common Reference Ontologies for Plants
MilPortal.org Military Ontology
AIRS Ontology Suite Actionable Intelligence Retrieval System
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• MilPortal
• http//milportal.ncor.buffalo.edu/ontologies

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How classify this?
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or this?
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The Emotion Ontology
http//bioportal.bioontology.org/ontologies/49078
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physiological response to emotion

• need link to a physiology ontology

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emotion process
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BFO als standard upper-level Ontologie

• Wie Ontologien die wissenschaftliche Forschung
  unterstützen
• Warum wissenschaftliche Ontologien
  zusammenarbeiten müssen
• Basic Formal Ontology (BFO) die Vorteil der
  Koordination
• Benützer von BFO
• Kontinuanten, Okkurrenten, RealisierungenArten
  der Abhängigkeit

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The idea of ontological realism

• Before we build a data model we need to look at
  the reality we are trying to represent ( lets
  look at the best scientific theory we have of
  this reality)
• Lets constrain our data models so that our
  databases are veridical representations of the
  world outside

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Scientific ontologies have special features

• Every term in a scientific ontology must be such
  that the developers of the ontology believe it to
  refer to some entity in reality on the basis of
  the best current evidence
• in first approximation instances of a type

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Universals and Instances (from Bill Mandrick)
Geographic Coordinates Set
designates
Geopolitical Entity
Spatial Region
instance_of
has location
is_a
Village Name
has location
Distance Measurement Result
designates
Village
Well
Latrine
instance_of
instance_of
instance_of
instance_of
instance_of
16 meters
VT 334 569
Khanabad Village
measurement_of
located in
located near
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For science, and thus for scientific ontologies,

• it is generalizations that are of prime important
  universals, types, kinds, species

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For scientific ontologies

• reusability, openness is crucial
• intelligibility to humans is crucial
• revisability is crucial
• there is always an open world assumption
• testability is crucial
• compatibility with neighboring scientific
  ontologies is crucial ? it should not be too easy
  to add new terms to an ontology

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For scientific ontologies

• the issue of how the ontology will be used is
  not a factor relevant for determining how
  entities are treated by the ontology
• If this decision is made to reflect specific,
  local practical needs, this will thwart
  reusability of the data the ontology is used to
  annotate

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BFO

• A simple top-level ontology to support
  information integration in scientific research
• Defining a framework that will help to ensure
  consistency and non-redundancy of the ontologies
  created in its terms

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Three Fundamental Dichotomies

• Continuant vs. occurrent
• Dependent vs. independent
• Type vs. instance
• http//ontology.buffalo.edu/bfo/

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Continuant thing, quality
Occurrent process, event
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depends_on
Continuant
Occurrent process, event
Independent Continuant thing
Dependent Continuant quality
quality depends on bearer

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depends_on
Continuant
Occurrent process, event
Independent Continuant thing
Dependent Continuant quality,
event depends on participant
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instance_of
types
Continuant
Occurrent process, event
Independent Continuant thing
Dependent Continuant quality
.... ..... .......
instances
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depends_on
Continuant
Occurrent process
Independent Continuant thing
Dependent Continuant quality
temperature depends on bearer
.... ..... .......
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3 kinds of (binary) relations

• Between types
• human is_a mammal
• human heart part_of human
• Between an instance and a type
• this human instance_of the type human
• this human allergic_to the type tamiflu
• Between instances
• Marys heart part_of Mary
• Marys aorta connected_to Marys heart

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Definitions of relations
Clark et al., 2005
is_a
part_of
Barry Smith, et al., Relations in Biomedical
Ontologies, Genome Biology 2005, 6 (5), R46.
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Type-level relations presuppose the underlying
instance-level relations

• A part_of B def. All instances of A are
  instance-level-parts-of some instance of B
• e.g. human heart part_of human
• A has_participant B def. All instances of A
  have an instance of B as instance-level
  participant
• e.g. cell binding has_participant cell

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Blinding Flash of the Obvious
Continuant
Occurrent (Process, Event)
Independent Continuant
Dependent Continuant
How to create an ontology from the top down
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Example The Cell Ontology
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Benefits of coordination

• No need to reinvent the wheel
• Can profit from lessons learned through mistakes
  made by others
• Can more easily reuse what is made by others
• Can more easily inspect and criticize results of
  others work (PATO)
• Leads to innovations (e.g. Mireot) in strategies
  for combining ontologies

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Users of BFO

• PharmaOntology (W3C HCLS SIG)
• MediCognos / Microsoft Healthvault
• Cleveland Clinic Semantic Database in
  Cardiothoracic Surgery
• Major Histocompatibility Complex (MHC) Ontology
  (NIAID)
• Neuroscience Information Framework Standard
  (NIFSTD) and Constituent Ontologies

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Users of BFO

• Interdisciplinary Prostate Ontology (IPO)
• Nanoparticle Ontology (NPO) Ontology for Cancer
  Nanotechnology Research
• Neural Electromagnetic Ontologies (NEMO)
• ChemAxiom Ontology for Chemistry
• Ontology for Risks Against Patient Safety
  (RAPS/REMINE) (EU FP7)
• IDO Infectious Disease Ontology (NIAID)

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Users of BFO

• National Cancer Institute Biomedical Grid
  Terminology (BiomedGT)
• US Army Universal Core Semantic Layer (UCore SL)
• US Army Biometrics Ontology
• US Army Command and Control Ontology
• Ontology for General Medical Science (OGMS)

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Infectious Disease Ontology Consortium

• MITRE, Mount Sinai, UTSouthwestern Influenza
• IMBB/VectorBase Vector borne diseases (A.
  gambiae, A. aegypti, I. scapularis, C. pipiens,
  P. humanus)
• Colorado State University Dengue Fever
• Duke University Tuberculosis, Staph. aureus,
  HIV
• Case Western Reserve Infective Endocarditis
• University of Michigan Brucilosis

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OBO Open Biomedical Ontologies

• GO Gene Ontology
• CL Cell Ontology
• SO Sequence Ontology
• ChEBI Chemical Ontology
• PATO Phenotype (Quality) Ontology
• FMA Foundational Model of Anatomy
• ChEBI Chemical Entities of Biological Interest
• PRO Protein Ontology
• Plant Ontology
• Environment Ontology
• Ontology for Biomedical Investigations
• RNA Ontology

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RELATION TO TIME GRANULARITY CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT
RELATION TO TIME GRANULARITY INDEPENDENT INDEPENDENT DEPENDENT DEPENDENT
ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality(PaTO) Biological Process (GO)
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Phenotypic Quality(PaTO) Biological Process (GO)
MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO)
The Open Biomedical Ontologies (OBO) Foundry
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maintained by

• Werner Ceusters, Buffalo
• Pierre Grenon, Open University
• Chris Mungall, Berkeley
• Fabian Neuhaus, NIST
• Holger Stenzhorn, IFOMIS, Saarland University
• Alan Ruttenberg, Science Commons
• plus 103 other members of BFO Discussion Group
• http//groups.google.com/group/bfo-discuss?

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inspired by

• Aristotle
• Husserl
• Roman Ingarden
• Ingvar Johansson
• Kevin Mulligan, University of Geneva
• Cornelius Rosse
• Peter Simons, Trinity College, Dublin
• Wittgensteins Tractatus (picture theory of
  language)
• Wolfgang Degen, Nicola Guarino, Patrick Hayes

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Blinding Flash of the Obvious
Continuant
Occurrent (Process, Event)
Independent Continuant
Dependent Continuant
How to create an ontology from the top down
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Specifically Dependent Continuant
Red color of my skin
Red color of your skin
Accidens non migrat de subjecto in
subjectum. Accidents do not migrate from one
substance to another
depends_on
depends_on
You
Me
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Continuant
Independent Continuant
Dependent Continuant
Non-realizable Dependent Continuant (quality)
Realizable Dependent Continuant (function, role,
disposition)
..... .....
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Realizable dependent continuants

• plan
• function
• role
• disposition
• capability
• tendency

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Their realizations

• execution
• expression
• exercise
• realization
• application
• course

occurrents
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Continuant
Independent Continuant
Dependent Continuant
Non-realizable Dependent Continuant (quality)
Realizable Dependent Continuant (function, role,
disposition)
..... .....
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realization depends_on realizable
Continuant
Occurrent
Independent Continuant bearer
Dependent Continuant disposition
Process of realization
.... ..... .......
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Specific Dependence

• on the instance level
• a depends_on b def. a is necessarily such that
  if b ceases to exist than a ceases to exist
• on the type level
• A specifically_depends_on B def. for every
  instance a of A, there is some instance b of B
  such that a depends_on b.

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depends_on
Continuant
Occurrent process, event
Independent Continuant thing
Dependent Continuant quality
temperature depends on bearer
.... ..... .......
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The (Aristotelian) Ontological Sextet
Substances Quality entities Processes
Universals Substance-universals Quality-universals Process-universals
Particulars Individual Substances Quality-instances (Tropes) Process-instances
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Specifically dependent continuants

• the quality of whiteness of this cheese
• your role as lecturer
• the disposition of this patient to experience
  diarrhea

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color
anatomical structure
is_a
is_a
red
eye
instantiates
instantiates
the particular case of redness (of a particular
fly eye)
an instance of an eye (in a particular fly)
depends on
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depends_on
Continuant
Occurrent process
Independent Continuant thing
Dependent Continuant quality
temperature depends on bearer
.... ..... .......
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Specifically Dependent Continuants
Specifically Dependent Continuant
if the bearer ceases to exist, then its quality,
function, role ceases to exist the color of my
skin the function of my heart to pump blood my
weight
Quality, Pattern
Realizable Dependent Continuant
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RELATION TO TIME GRANULARITY CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT
RELATION TO TIME GRANULARITY INDEPENDENT INDEPENDENT DEPENDENT DEPENDENT
ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality(PaTO) Biological Process (GO)
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Phenotypic Quality(PaTO) Biological Process (GO)
MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO)
The Open Biomedical Ontologies (OBO) Foundry
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CONTINUANT CONTINUANT CONTINUANT CONTINUANT OCCURRENT
INDEPENDENT INDEPENDENT DEPENDENT DEPENDENT
ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality(PaTO) Organism-Level Process (GO)
CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Phenotypic Quality(PaTO) Cellular Process (GO)
MOLECULE Molecule (ChEBI, SO, RNAO, PRO) Molecule (ChEBI, SO, RNAO, PRO) Molecular Function (GO) Molecular Function (GO) Molecular Process (GO)
rationale of OBO Foundry coverage
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Continuant
Independent Continuant
Specifically Dependent Continuant
Quality
Realizable Dependent Continuant (function, role,
disposition)
..... .....
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Specific Dependence

• on the instance level
• a depends_on b def. a is necessarily such that
  if b ceases to exist than a ceases to exist
• on the type level
• A specifically_depends_on B def. for every
  instance a of A, there is some instance b of B
  such that a depends_on b.

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Generically Dependent Continuants
if one bearer ceases to exist, then the entity
can survive, because there are other
bearers (copyability) the pdf file on my
laptop the DNA (sequence) in this chromosome
Generically Dependent Continuant
Information Object
Gene Sequence
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Continuant
Independent Continuant
Specifically Dependent Continuant
Quality
Realizable Dependent Continuant (function, role,
disposition)
..... .....
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Realizable dependent continuants

• plan
• function
• role
• disposition
• capability
• tendency

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Their realizations

• execution
• expression
• exercise
• realization
• application
• course

occurrents
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Generically Dependent Continuant
Realizable
Information Artifact
Sequence
Role
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IAO

• IAO The Information Artifact Ontology, developed
  by scientific researchers as a vehicle for
  annotating data about measurement results,
  publications, protocols, databases, consent
  forms, licenses
• in a way that will allow discovery, integration
  and analysis
• Two kinds of data about data
• 1. what are the data about ? Domain Ontologies
• 2. how the data are packaged (collected,
  presented, formatted, stored) ? IAO Ontologies