http://ontologist.com1 the art of building useful ontologies barry smith

http://ontologist.com 1

The Art of Building Useful Ontologies

Barry Smith


where in the body ? where in the cell ?



what kind of organism ?



what kind of organism ?

what kind of disease process ?


Unified Medical Language System, Semantic Web, ontowiki, ...

let a million flowers bloom,

and rely for integration on post hoc mappings

problem: what to do with weeds ?

problem: how support reasoning across the annotated data?

how create broad-coverage semantic annotation systems for biomedicine?


for science

based on prospective standardization designed to support annotation of data in ways which will be

able to support reasoning with this data

an alternative approach


a family of interoperable gold standard biomedical reference ontologies built around the Gene Ontology at its core

http://obofoundry.org

The OBO Foundry


A prospective standard

designed to guarantee interoperability of ontologies from the very start (and to keep out weeds)

initial set of 10 criteria tested in the annotation of

scientific literature model organism databases life science experimental results

http://ontologist.com 11Karen Eilbecksong.sf.netproperties and features of

nucleic sequencesSequence Ontology

(SO)

RNA Ontology Consortium(under development)three-dimensional RNA

structuresRNA Ontology

(RnaO)

Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)

Protein Ontology Consortium(under development)protein types and

modificationsProtein Ontology

(PrO)

Michael Ashburner, Suzanna Lewis, Georgios Gkoutos

obo.sourceforge.net/cgi-bin/ detail.cgi?

attribute_and_valuequalities of biomedical entities

Phenotypic Quality Ontology

(PaTO)

Gene Ontology Consortiumwww.geneontology.orgcellular components, molecular functions, biological processes

Gene Ontology (GO)

FuGO Working Groupfugo.sf.netdesign, protocol, data

instrumentation, and analysis

Functional Genomics Investigation Ontology

(FuGO)

JLV Mejino Jr.,Cornelius Rosse

fma.biostr.washington.edu

structure of the human bodyFoundational Model of

Anatomy (FMA)

Melissa Haendel, Terry Hayamizu, Cornelius Rosse,

David Sutherland, (under development)

anatomical structures in human and model organisms

Common Anatomy Refer-

ence Ontology (CARO)

Paula Dematos,Rafael Alcantara

ebi.ac.uk/chebimolecular entitiesChemical Entities of Bio-logical Interest (ChEBI)

Jonathan Bard, Michael Ashburner, Oliver Hofman

obo.sourceforge.net/cgi-bin/detail.cgi?cell

cell types from prokaryotes to mammals

Cell Ontology (CL)

CustodiansURLScopeOntology


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 Componen

t(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule

(ChEBI, SO,RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)

Building out from the original GO


Ontologies being built to satisfy Foundry principles ab initio

Clinical Trial Ontology (CTO)Common Anatomy Reference Ontology (CARO, DB1

& DB2)Mosquito Anatomy Ontology (MAO)Ontology for Biomedical Investigations (OBI)Phenotypic Quality Ontology (PATO, DB1 & DB2)Protein Ontology (PRO)Relation Ontology (RO)RNA Ontology (RnaO)


Foundry Ontologies in planning phase

Biobank/Biorepository Ontology (BrO, part of OBI)

Environment Ontology (EnvO)

Fish Multi-Species Anatomy Ontology (funding received; no acronym yet)

Infectious Disease Ontology (IDO)

Mouse Adult Neurogenesis Ontology (MANGO)

Xenopus Anatomy Ontology (XAO)


CRITERIA

OPENNESS: The ontology is open and available to be used by all.

FORMAL LANGUAGE: The ontology is in, or can be instantiated in, a common formal language.

ORTHOGONALITY: The developers of the ontology agree in advance to collaborate with developers of other OBO Foundry ontology where domains overlap.

CONVERGENCE: The developers agree to work torwards a single ontology for each domain.

CRITERIA

http://obofoundry.org/http://obofoundry.org/


CRITERIA

UPDATE: The developers of each ontology commit to its maintenance in light of scientific advance, and to soliciting community feedback for its improvement.

IDENTIFIERS: The ontology possesses a unique identifier space within OBO.

VERSIONING: The ontology provider has procedures for identifying distinct successive versions.

DEFINITIONS: The ontology includes textual definitions for all terms.

CRITERIA



CLEARLY BOUNDED: The ontology has a clearly specified and clearly delineated content.

DOCUMENTATION: The ontology is well-documented.

USERS: The ontology has a plurality of independent users.

COMMON ARCHITECTURE: The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.

CRITERIA



ORTHOGONALITY

annotations can be additive

ontologies do not need to create tiny theories of anatomy or chemistry within themselves

modularity ensures division of labor amongst domain experts


compare: legends for mapscompare: legends for maps


ontologies are legends for data


natural language labels organized in a graph-theoretic structure, designed to

make the data

• cognitively accessible to human beings• algorithmically accessible to machines• linked up to other data resources because the

same labels have been used


The OBO Foundry Idea

MouseEcotope GlyProt

DiabetInGene

GluChem

sphingolipid transporter

activity




DiabetInGene

GluChem

Holliday junction helicase complex


Five bangs for your GO buck

science base

cross-species database integration (human, mouse, fly ...)

cross-granularity database integration

through links to the entities in biological reality

semantic searchability links people to software


Applications for which GO has already been used:

• integrating genomic and proteomic information from different organisms

• finding functional similarities in genes that are overexpressed or underexpressed in diseases and as we age

• predicting the likelihood that a particular gene is involved in diseases that haven't yet been mapped to specific genes

• verifying models of genetic, metabolic and gene product interaction networks


Google: April 23, 2007

ontology 14.80 Mill.

“Gene Ontology” 0.96 Mill.

“Dublin Core” Ontology 0.65 Mill.

SUMO Ontology 0.30 Mill.




DiabetInGene

GluChem

sphingolipid transporter

activity


Reasons why GO has been successfulIt is a system for prospective standardization built

from the ground-up on the basis of what works and of real needs by domain specialists

It is built on the basis of community consensus but with considerable central leadership in imposition of best practice – authority is the only way to yield a coordinated system of interoperable ontologies

Subject to continuous update of content, documentation and formal architecture – updates every night

In such a way as to ensure backwards compatibility with prior annotations

Initially low-tech to encourage users, with movement to more powerful formal approaches (including OWL-DL – though GO community still recommending caution)


GO has learned the lessons of successful cooperation

Clear documentation

The ontology terms chosen are already familiar

Fully open source (no secrets, thorough testing in manifold combinations with other ontologies)

Subjected to considerable third-party critique

Embraces simple rules and simple technology wherever possible, but in such a way as to create an evolutionary path to logical reasoning and integration


Prospective standardization is a good thing

Prospective standardization is the only thing which will work in mission critical domains

Prospective standardization means that certain limits to tolerance must be imposed, authorities must be recognized


Prospective standardization is a good thing


But not every prospective standardization is a good thing

ISO 15926-2

http://ontology.buffalo.edu/bfo/west.pdfProceedings of FOIS 2006

http://ontology.buffalo.edu/bfo/west.pdf


How Not to Build Useful Ontologies

ISO/FDIS 15926-2

Lifecycle integration of process plant data including oil and gas production facilities


Heh ! Let’s reinvent the wheel


What ISO 15926 Part 2 says

What it is ...• rigorous 4D ontology• a full ISO standard (2003)• 201 entities in upper ontology • some 50,000 entities in all• limited axiomatisation• significant industrial support

from Oil and Process industries

... good for:– integrating diverse

information systems– engineering applications– applications involving time

and space– managing change– integrating/analyzing mid-

level ontologies


2006 NIST Upper Ontology Summit

March 14-15, 2006,Gaithersburg, MD

ISO 15926 proposed for general use as an upper level ontology – for ‘integrating diverse information systems’ and ‘integrating [and] analyzing mid-level ontologies’ without restriction.

Matthew West, “ISO 15926 – Integration of Lifecycle Data” http://ontolog.cim3.net /file/work/UpperOntologySummit/UO-Summit-Meeting_20050315/UOS--west_ 20060315.ppt


ISO 15926

Common Objects

TimeProperties

Products and Materials

Organizations

Locations

Agreements

Intentional Thing

Buy/Sell

Manufacture

Subjec

t Areas

ISO

Process

Areas

Commo

n Interes

t

ISO 15926 as foundation

Entity Types can be referenced in one subject area from another

Accounts General Management

CarrierCRM Demand

Movement

Project/Activity

Transport Constraint

Total of 1546 entity types so far.


“The purpose of ISO 15926 is to provide a Lingua Franca for computer systems, thereby integrating the information produced by them.”


The importance of consensus-based uptake

An ontology is like a telephone network: it is designed to support exchange of information.

Its value depends on the number of users who agree to adopt and to help maintain this common network

Thus it depends also on the existence of a straightforward learning path for new users, and of clear and easily accessible documentation.


The importance of consensus-based uptake

is even greater in the case of an upper level ontology

which is designed to support exchange of information about all subjects


This is not a problem of money

Robust ontologies need to be thoroughly tested by being critically examined and pulled apart, and above all by being combined dynamically with other artifacts in real use cases à la GO

An upper ontology should not be proprietary


Confusion of Data Models and Ontologies

Data Model

mass of plunger: an integer

location of plunger: a string

Ontology

mass of plunger: a quality (which can be measured)

location of plunger: a place (which can have a name)


Is ISO 15926 an ontology or a data model?

I do not know


Principle of intelligibility

an ontology that is advocated for general use should be understandable to its intended users. Its features should be explained in clear, simple English, extended where necessary with technical terms.


First Great Mystery

Of the 201 terms included in the ISO 15926 upper-level ontology, 88 are of the form ‘class of X’, for example:

class_of_composite_materialclass_of_compoundclass_of_dimension_for_shape class_of_featureclass_of_feature_whole_partclass_of_functional_objectclass_of_inanimate_physical_objectclass_of_indirect_connection


Definition of ‘class’

A <class> is a <thing> that is an understanding of the nature of things and that divides things into those which are members of the class and those which are not according to one or more criteria.

Example: ‘Centrifugal pump is a <class>’.


What logic governs classes in ISO 15926?

Not, say, ZF set theory

but the theory of ‘non-well-founded sets’ devised for the special purposes of logical modeling of certain non-terminating computational processes;

allows sets to contain themselves, thereby generating infinitely descending chains of the form:

… A A A A A A A A A A


The principle of simple tools

An ontology is an artifact created to support exchange of information; it is not the place to try out the latest new bits of mathematics you learned about last week


But worse

ISO 15926 complicates its theory of classes by allowing classes with both actual and possible members:

‘Although there is only one <class> that has no members, there can be a <class> that has no members in the actual world, but which does have members in other possible worlds.’

No standard theory of modal logic is addressed by ISO 15926


The principle of re-using available resources

if an ontology deals with what is dealt with perfectly well already in some recognized resource, then it should utilize this recognized resource.


Example

There is a perfectly good theory of relations, ranges, domains, ordered pairs, and of the transitivity, symmetry, etc. of such relations, which is part of standard set theory.

What does ISO 15926-2 do here?


‘class_of_ relationship_with_related_end_1’

DEFINITION: a <class_of_ relationship> where a particular <thing> is related in the <class_of_relationship>, rather than the members of a <class>. The related <thing> plays the <role_ and_domain> indicated by the class_of_end_1 attribute.


The principle of terminological moderation

Stay as close as possible to the terms already used by your intended audience and to their already established meanings. Use only terms for which either (1) there is a reasonable expectation that intended users of the ontology will have a need for them, or (2) such terms are required to fill gaps in the ontology in order to create a complete hierarchy.


The principle of intelligible definitions

Use definitions which are both (1) humanly intelligible (to avoid error in human use and maintenance) and (2) formally specifiable (as far as possible in such a way as to support one or other standard type of software e.g. for error-checking of the ontology).


The principle of terminological coherence

For any expression ‘E’ in an ontology, ‘E’ means E.

The principle of univocityEach expression in an ontology should have the same meaning on every occasion of use.


Hence:

an ontology should construct its complex terms in such a way that their constituent parts preserve their ordinary meanings. In the ISO 15926 documentation however the expression ‘individual’ is often used to mean, not: individual, but rather: possible individual. Thus:

‘class_of_individual’ = ‘a class whose members are instances of <possible_individual>’.

‘possible individual’ = ‘thing that exists in space and time’.


Follow rules for formulating definitions

If ‘A’ does not mean: A, but rather: possible A, then ‘possible A’ itself means something like: possible possible A, and so on, ad exasperandum.


‘Class_of_class_of_X’ terms

*class_of_class_of_compositionclass_of_class_of_definitionclass_of_class_of_descriptionclass_of_class_of_identificationclass_of_class_of_individualclass_of_class_of_information_ representationclass_of_class_of_relationshipclass_of_class_of_relationship_with_signature*,†class_of_class_of_representationclass_of_class_of_representation_translationclass_of_class_of_responsibility_for_ representationclass_of_class_of_usage_of_representation

*have no corresponding ‘class of’ term in the ontology, †contains a reference to such a term in its definition


‘Class_of_class_of_X’ terms in ISO 15926

if one needs to iterate the ‘class_of’ operator, then why not do this by means of some general facility, rather than by giving names in ad hoc fashion to just those ‘class of class of’ terms one thinks one needs?


<class_of_class_of_composition>

DEFINITION: a <class_of_class_of_ relationship> whose members are instances of <class_of_composition>. It indicates that a member of a member of the class_of_class_of_part is a part of a member of an instance of the class_of_class_of_whole,

EXAMPLE: Toxicity description is a class_of_class_of_part of a material data sheet, where the description “has carcinogenic components” is a class_of_part on the Mogas Material Safety Data Sheet, and copy #5 of the Mogas Material Safety Data Sheet has “has carcinogenic components” as a part.

From this we learn that: a description is a class ...


Believe me, this is not the best way to deal with part-whole relations in an

ontology


Pleural Cavity

Pleural Cavity

Interlobar recess

Interlobar recess

Mesothelium of Pleura

Mesothelium of Pleura

Pleura(Wall of Sac)

Pleura(Wall of Sac)

VisceralPleura

VisceralPleura

Pleural SacPleural Sac

Parietal Pleura

Parietal Pleura

Anatomical SpaceAnatomical Space

OrganCavityOrganCavity

Serous SacCavity

Serous SacCavity

AnatomicalStructure

AnatomicalStructure

OrganOrgan

Serous SacSerous Sac

MediastinalPleura

MediastinalPleura

TissueTissue

Organ PartOrgan Part

Organ Subdivision

Organ Subdivision

Organ Component

Organ Component

Organ CavitySubdivision

Organ CavitySubdivision

Serous SacCavity

Subdivision

Serous SacCavity

Subdivision

part

_of

is_a


The principle of non-circularity

avoid circular definitions; and, a fortiorissimo, avoid nonsense-definitions of the forms:

‘an a is the b of an a’

(A disease is the observation of a disease [HL7])

or:

‘an a is an a which is b’

(A person is a person with an identity document [HL7])


The ISO 15926 tiny theory of arithmetic

DEFINITION: A <class_of_number> is a <class_of_class> whose members are members of <arithmetic_number>

DEFINITION: An <integer_number> is an <arithmetic_number> that is an integer number.


The ISO 15926 tiny theory of geometry

DEFINITION: A <class_of_dimension_for_shape> is a <class_of_class_of_ relationship> that indicates that members of the class_of_shape have a dimension that is a member of the class_of_dimension.

ELUCIDATION Specifying that members of the “class of circle” have members of “class of diameter” is an instance of <class_of_dimension_for_shape>.’

DEFINITION: a <dimension_of_shape> is a <class_of_class_of_relationship> that indicates that members of the <shape_dimension> are dimensions of the <shape> members.

EXAMPLE: The sets of 10m lines that are diameters of 10m circles is an example of <dimension_of_shape>


I think this means:

Circles have diameters.


The principle of non-subjective definitions

When formulating definitions avoid the use of phrases like ‘which may ...’, ‘that indicates …’, ‘… characterize …’, ‘an aspect of …’, ‘may have ...’, which invite subjective interpretation.

DEFINITION: A <feature_whole_part> is an <arrangement_of_individual> that indicates that the part is a non-separable, contiguous part of the whole.

DEFINITION: A <class_of_relationship_with_signature> is a <class_of_relationship> that may have a <role_and_domain> specified for each end’.


The ISO 15926 tiny theory of physics

DEFINITION: A <class_of_sub_atomic_particle> is a <class_of_arranged_ individual> whose members are constituent particles of atoms.

EXAMPLE: Proton, electron, meson, neutron, positron, muon, quark, and neutrino can be represented by instances of <class_of_sub_atomic_particle>

DEFINITION: An <arranged_individual> is a <possible_individual> that has parts that play distinct roles with respect to the whole. The qualities of an <arranged_individual> are distinct from the qualities of its parts.

What are the parts of a neutrino? What distinct roles do they play?


The principle of non-redundant definitions

do not include clauses in definitions which contribute nothing to the application of the definition.

DEFINITION: An <event> is a <possible_individual> with zero extent in time. An <event> is the temporal boundary of one or more <possible_individual>s, although there may be no knowledge of these <possible_individual>s.


Problems with ISO Standardization

Adoption by ISO does not guarantee that an artifact satisfies all the requirements which might reasonably be placed on an international standard.*

*See “Wüsteria”, Stud Health Technol Inform, 2005;116:647–652.


ISO standardization may bring costs

– harder to correct errors*– often involves less than ideal compromises (since

adoption by ISO requires compatibility with prior ISO standards)

*Some good news on this front re Lifecycle Integration Schema:

http://www.tc184-sc4.org/wg3ndocs/wg3n1328/lifecycle_integration_schema.html(not corrected since 2003)

http://www.tc184-sc4.org/wg3ndocs/wg3n1328/lifecycle_integration_schema.html

http://www.tc184-sc4.org/wg3ndocs/wg3n1328/lifecycle_integration_schema.html


More good news: Norwegian Truth

http://projects.dnv.com/reference_data/RD7Browser/

RD 7 Browser Version 2007/1




class_of_arranged_individual

DNV: A class of individuals that are arranged from parts

Lifecycle Integration Schema: A <class_of_arranged_individual> is a <class_of_individual> whose members are an arrangement of components.


but also problems:

DNV: Class of Individual =Def. A Class of Individual that is the part (component) in an assembly

DNV: Individual =Def. A Role used in ST 3451 and 3601 to designate the object that has the given status or material type, respectively


Perhaps I am entirely mistaken

Perhaps ISO 15926-2 is an excellent artifact of its kind – a ‘data model’; I do not know

But it is not an excellent ontology


What the oil and gas industry tells me

The ‘upper ontology’ of ISO 15926 is hardly used

The lower branches of ISO 15926 are useful as a controlled vocabulary (because what came before was so bad) – these lower levels deal

with pump, flange, valve,


What the oil and gas industry needs

rules governing prospective standards for controlled vocabularies for annotations of data which will support not only search but also interoperability of and reasoning with this data

‘interoperability’ here means not only between machines but also between people who need to build and use an ontology

National Center for Ontological Research (http://ncor.us) in conjunction with various organizations, including the GO consortium and NIST, is attempting to formulate, test and disseminate such rules

http://ncor.us/

http://ontologist.com1 the art of building useful ontologies barry smith

Documents

mammals cell ontology

com2 slide

core http

cell cell types

obo foundry slide

cellular component cell

alternative approach

kind of organism