An Introduction to Ontology as a Strategy for Data Integration

Barry Smith

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The problem

• legacy idiosyncracies in handling data

complicated progressively by• changes in available hardware and software• turnover of personnel and of collaborations• explosion of data• need to get funding (inhibits reuse)

2

The result: balkanization

• systems are poorly integrated• deliver redundant capabilities• foster error and waste• prevent comparison and aggregation• prevent secondary use of data• lowers ROI on software

3

The proposed solution• vocabulary and meanings change more

slowly than hardware and software (and scientific theory*)

• semantic interoperability has high initial cost (governance, commitment) but considerable long-term value

*atom, electron, cell, bacteria, organism …

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How to do it right?

• how create an incremental, evolutionary process, where what is good survives, and what is bad fails

• create a scenario in which people will find it profitable to reuse ontologies, terminologies and coding systems which have been tried and tested

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Uses of ‘ontology’ in PubMed abstracts

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By far the most successful: GO (Gene Ontology)

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GO provides a controlled vocabulary of terms for use in annotating (describing, tagging) data

• multi-species, multi-disciplinary, open source

• contributing to the cumulativity of scientific results obtained by distinct research communities

• compare use of kilograms, meters, seconds in formulating experimental results

• natural language and logical definitions for all terms to support consistent human application and computational exploitation

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What is the key to GO’s success?• multi-species, multi-disciplinary, open source

• clear rules for ontology development and maintenance

• over 11 million annotations relating gene products described in the UniProt, Ensembl and other databases to terms in the GO

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Extending GO’s success to other fields

Open Biological and Biomedical Ontologies (OBO) Foundry

• Best practice principles• Governance• Review process• Two-tier membership

http://obofoundry.org11

http://ontology.buffalo.edu/smith

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RELATION TO TIME

GRANULARITY

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO)

OrganFunction

(FMP, CPRO) Phenotypic

Quality(PaTO)

Biological Process

(GO)CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Compone

nt(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule

(ChEBI, SO,RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)

OBO (Open Biomedical Ontology) Foundry proposal(Gene Ontology in yellow) 13

RELATION TO TIME

GRANULARITY

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

COMPLEX OFORGANISMS

Family, Community, Deme, Population

OrganFunction

(FMP, CPRO)

Population Phenotype

PopulationProcess

ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO) Phenotypic

Quality(PaTO)

Biological Process

(GO)CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Componen

t(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule

(ChEBI, SO,RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)

Population-level ontologies 14

RELATION TO TIME

GRANULARITY

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO)

OrganFunction

(FMP, CPRO) Phenotypic

Quality(PaTO)

Biological Process

(GO)CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Compone

nt(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule

(ChEBI, SO,RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)

Environment Ontology

envi

ron

men

ts

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The Environment OntologyThe Environment Ontology

Barry Smithhttp://ontology.buffalo.edu/smith

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The Spatial-Structural NicheA Hole Story

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Places are holes

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DIGESTIVE SYSTEM

the interior of your gut: an environment for more than1013 microorganisms

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Positive and negative parts

positivepart

negativepart

or hole

(made of matter)

(not made of matter)

A site

intuitively: a spatial entity that can contain a material entity

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A spatial environment

is a site that

1. contains a medium (air, water)

2. can contain an organism or a population of organisms

Some sites are supported and demarcated by some solid object

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Stationary Sites

1: your office when the door is closed; a closed mouth

2: a rabbit hole; an open mouth

3: the surface of a leaf

4: the Klingon Empire

1 2 3 4

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Mobile Sites

1 2 3 4

1: a womb; a spaceship2: a snail’s shell; a 3: the home range of a migrating herd of buffalo; 4: the niche around a flying buzzard

At any given instant

a site is coincident with some spatial region

But because there are mobile sites

not: site spatial region

For stationary sites we can associate latitute/longitude specifications

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Double hole structure of a Spatial Environment

Medium (filling the environing hole)

Tenant (occupying the central hole)

Retainer (a boundary of some surrounding structure)

……… (soil, cheese …)

Anatomy Ontology(FMA*, CARO)

Environment

Ontology(EnvO)

Infectious Disease

Ontology(IDO*)

Biological Process

Ontology (GO*)

Cell Ontology

(CL)

CellularComponentOntology

(FMA*, GO*) Phenotypic Quality

Ontology(PaTO)

Subcellular Anatomy Ontology (SAO)Sequence Ontology

(SO*) Molecular Function

(GO*)Protein Ontology(PRO*) Extension Strategy + Modular Organization 40

top level

mid-level

domain level

Information Artifact Ontology

(IAO)

Ontology for Biomedical

Investigations(OBI)

Spatial Ontology

(BSPO)

Basic Formal Ontology (BFO)

How to fit EnvO under BFO

• http://www.ifomis.org/bfo/

Populating downwards from BFO

Continuant Occurrent(Process, Event)

IndependentContinuant

DependentContinuant

Basic Formal Ontology

Continuant Occurrent(Process, Event)

IndependentContinuant

DependentContinuant

organism

CONTINUANT OCCURRENT

INDEPENDENT DEPENDENT

ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity

(FMA, CARO)

OrganFunction

(FMP, CPRO) Phenotypic

Quality(PaTO)

Organism-Level Process

(GO)

CELL AND CELLULAR

COMPONENT

Cell(CL)

Cellular Compone

nt(FMA, GO)

Cellular Function

(GO)

Cellular Process

(GO)

MOLECULEMolecule

(ChEBI, SO,RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)

obofoundry.org

GRANULARITY

RELATION TO TIME

Hydraulic System

CIRCULATORY SYSTEM (Principal Organs)

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Genus-species definitions

System =def. an independent continuant which is composed of interacting material entities forming an integrated whole

Ecosystem =def. a system which includes organisms and the site in which they live as components

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Biome =def. An ecosystem which contains populations adapted to the environmental conditions conserved over its spatial extent.

Microbiome =def. A biome which contains the totality of microscopic organisms, their genetic elements, and interactions in a given environment.

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Aligning EnvO to the Basic Formal Ontology

habitat

Habitat =def. An ecosystem which can support the life of a given organism, population, or community

Realized niche =def. An ecosystem which is that part of a habitat which supports the life of a given organism, population or community

Aligning EnvO to the Basic Formal Ontology

Hutchinsonion niche(niche as volume in a functionally defined hyperspace)

=def. an n-dimensional hyper-volume whose dimensions correspond to resource gradients over which species are distributed– degree of slope, exposure to sunlight,

soil fertility, foliage density, salinity...

G.E. Hutchinson (1957, 1965)

Aligning EnvO to the Basic Formal Ontology

part_of

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GAZ. An open source gazetteer based on ontological principles

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http://gensc.org/gc_wiki/index.php/GAZ_Project

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Applications of EnvO in biology