New Foundations for Social Ontology

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

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We will be able to use ontologies to help us share data

are ontologically coherent (created under adult supervision)

and logically coherent

and computationally tractable

and work well together – evolve together

– created according to the tested rules

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A new approach

prospective standardization based on objective measures of what works

bring together selected groups to agree on and commit to good terminology / annotation habits (traffic laws) preemptively

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Compare science1. scientific theories must be common

resources (cannot be bought or sold)

2. they must use open publishing venues

3. they must constantly evolve to reflect results of scientific experiments (“evidence-based”)

4. must be synchronized– use common SI system of units– common mathematical theories (built by adults)

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for science

create an evolutionary path towards improvement, of the sort we find in science

a collaborative, community effort to ensure buy-in

with rewards for participation

good versioning principles to ensure legacy annotation efforts not wasted

Requirements

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for scienceCreate a consensus core of

interoperable domain ontologies

starting with low hanging fruit and working outwards from there

built and validated by trained experts

backed by persons of influence in different communities

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This solution is already being implemented in the domain of

biomedicine

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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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a family of interoperable gold standard biomedical reference ontologies, based on the Gene Ontology

http://obofoundry.org

The OBO FoundryThe OBO Foundry

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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)

The Open Biomedical Ontologies (OBO) Foundry11

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)

OBO Foundry ontology modules

GRANULARITY

RELATION TO TIME

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Central principle of the OBO Foundry: ontological modularity

• division of labor• division of expertise• division of authority• no mapping problem• additivity of annotations• no silo effect – always one ontology for

every need• creates tested guidelines (traffic laws) for

those with new ontology needs13

Obstacles to the realization of ontology modularity based on

coherent traffic laws of the sort we find in science

• Computer scientists are teaching

people ontology tools• Computer engineers have an interest in

multiple new ontologies• Every Tuesday a new ontology of wheat

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The result:

Paris has_temperature 62o

Mohammed is_a string

Amount of money is_a integer

Currency has_unit $

Nuclear weapon is_a concept

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ontologies for ‘agent’

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SUMO

Contract = def. Attribute that applies to Propositions where something is promised in return, i.e. a reciprocal promise.

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Cyc

Contract =def. a collection of agreements

[whereby] each sentence is a legal

agreement in which two or more agreeing

agents promise to do (or not to do)

something. There are legal consequences

to breaking the promises made in a

contract

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Legal Ontology of Contract Formation

http://www.dit.unitn.it/~pavel/cando/Pictures/Posters/Mullen.pdf

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Legal Ontology of Contract Formation

http://www.dit.unitn.it/~pavel/cando/Pictures/Posters/Mullen.pdf

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What we need 1 (adults)

a thoroughly tested, mandated, common top-level ontology to enable minimal ontology interoperability

thoroughly tested, mandated domain ontologies built and maintained recognized by domain experts

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What we need 2 (training)

Professional training for ontologists

to teach people to CREATE ONTOLOGY CONTENT

to teach people to USE ONTOLOGY CONTENT

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What we need 3 (institutions)

institutions for ontology standardization

– counterparts of the authority structure maintained by Linux or by the SI System of Units or the IUPAC chemical nomenclature organization

(W3C does not see what is needed for advancement of ontology towards coherence and consistency)

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What we need 4 (standards)

Standards governing

rules for ontology development, versioning, modularity

ensuring interoperability

Authorities able to apply these rules, and ensure

filling in of gaps by experts

sustainability

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What we need 6 (Darwinian struggle for survival)

ontology evaluation with teeth

if ontology (science) is to be born, ontologies must die

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Ontology needs to become more like a science

basis in evidence

established results – authoritative ontologies*

expert peer review

credit for good ontology work

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Peer review evaluation process

Required where the quality of inputs cannot be evaluated mechanically

-- journal articles

-- research proposals

-- people (for career promotion in universities …)

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Treat ontologies like publications

This is happening already with databases:Nature Signaling

Nature Pathway Interactions

Nature Ontologies ?

Ontology peer review methodology being tested within the OBO Foundry

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Peer review assessment tasks

Is the ontology consistent with the rules (on modularity, …) ?

Does the ontology provide adequate coverage of its defined domain?

To what level is inferencing supported in the ontology relations structure?

Does the ontology interoperate with other ontologies in the system

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Is the ontology being developed collaboratively through the engagement and participation of relevant domain stakeholders and developers of neighboring ontologies?

Does the ontology have a tracker for submissions of new terms and notification of errors?

Does the ontology have a help desk which has prompt response times?

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Is the ontology syntactical correct

Is a URI assigned to each term of the ontology?

Does the URI point to required metadata for this term (including natural language and formal definitions).

Are all identifiers and preferred terms unique 

Are all asserted subclass relations correct in light of the intended interpretation

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Perhaps the ontology of law needs silos?

But if we are to use ontologies as a rigorous means of comparing and integrating legal systems and associated data, then we need a robust common ontology framework

-- a common top-level ontology

-- a common set of ontology relations

-- common (mid-level) domain ontologies

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http://code.google.com/p/information-artifact-ontology/

Information Artifact Ontology

One domain ontology with which an ontology of legal entities must cohere:

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Basic Formal Ontology (BFO)

Continuant Occurrent

processIndependentContinuant

thing

DependentContinuant

quality, role, function …

.... ..... .......38

Blinding Flash of the Obvious

Continuant Occurrent

processIndependentContinuant

thing

DependentContinuant

quality

.... ..... .......quality dependson bearer

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Information entities are relative to provenance and to processors in a way in which types are not

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What is a datum?

Continuant Occurrent

processIndependentContinuant

laptop, book

DependentContinuant

quality

.... ..... .......datum: a pattern in some medium with a certain kind of provenance

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Continuant Occurrent

IndependentContinuant

DependentContinuant

.... ..... .......

InformationEntity

Action

creating a datum

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Generically Dependent Continuants

GenericallyDependentContinuant

Information Entity

Sequence

if one bearer ceases to exist, then the entity can survive, because there are other bearers (copyability)

the pdf file on this laptop

the DNA (sequence) in that chromosome

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Generically Dependent Continuants

GenericallyDependentContinuant

Information Artifact

Gene Sequence

.pdf file .doc file

instances 44

Transcriptomics (MIAME Working Group)

Proteomics (Proteomics Standards Initiative)

Metabolomics (Metabolomics Standards Initiative)

Genomics and Metagenomics (Genomic Standards Consortium)

In Situ Hybridization and Immunohistochemistry (MISFISHIE Working Group)

Phylogenetics (Phylogenetics Community)

RNA Interference (RNAi Community)

Toxicogenomics (Toxicogenomics WG)

Environmental Genomics (Environmental Genomics WG)

Nutrigenomics (Nutrigenomics WG)

Flow Cytometry (Flow Cytometry Community)

IAO adopted, and being violently tested, inter alia, by:

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Information Entity (science)

‘information’ – mass noun (Shannon and Weaver)

‘information entity’ – count noun (Information Ontology)

Information entities are, roughly: artifacts in the realm of qualities (patterns)

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Information Entity (science)

protocoldatabasetheoryontology gene listpublicationresult...

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Information Entity (labeling)

serial numberbatch numbergrant numberperson numbernameaddressemail addressURL...

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Type or instance

ContinuantOccurrent(Process)

IndependentContinuant

human being,protocol document

DependentContinuant

pattern of ink marks

Applying the protocol

Side-Effect …

... .. ..... .... .....49

Continuant Occurrent

IndependentContinuant

DependentContinuant

.... ..... .......

InformationEntity

Action

creating a datum

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type: human beingInstance: Leon Tolstoy

type: novelInstance: War and Peace

type: bookInstance: this copy of War and Peace

Types and instances

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Is the Coca-Cola trademark a type or an instance?If the Coca-Cola trademark were a type, and the copies on my laptop and on your laptop instances, then there would be many Coca-Cola trademarks

Hence the Coca-Cola trademark is an instance

What is a trademark?

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Is War and Peace a type or an instance?If War and Peace were a type, and the copies of War and Peace in my library and in your library were instances, then

• there would be many War(s) and Peaces.

Hence War and Peace is an instance.

What is a work of literature?

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There can be two copies of the US Declaration of Independence

There cannot be two US Declarations of Independence

There cannot be subtypes of the US Declaration of Independence

There are not two Declarations of Independence

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Rule for types

Their names are pluralizable

There can be three peopleThere cannot be three Condoleezza Rices

Information Entities = entities which can exist in many perfect copies

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Specific dependence

Continuant Occurrent

process

IndependentContinuant

thing

DependentContinuant

quality

.... ..... .......headache dependson human being

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Generically Dependent Continuants

GenericallyDependentContinuant

Information Entity

Sequence

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

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are realized through being concretized in specifically dependent continuants(the plan in your head, the protocol being realized by your research team)

Generically dependent continuants

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they have a different kind of provenance

◦Aspirin as product of Bayer GmbH◦aspirin as molecular structure

Generically dependent continuants are distinct from types

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Generically Dependent Continuants

GenericallyDependentContinuant

Information Entity

Sequence

.pdf file .doc file

instances 61

are concretized in specifically dependent continuants

Beethoven’s 9th Symphony is concretized in the pattern of ink marks which make up this score in my hand

Generically dependent continuants

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do not require specific media (paper, silicon, neuron …)

Generically dependent continuants

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Realizable Dependent Continuants

SpecificallyDependentContinuant

Quality, PatternRealizable Dependent Continuant

inert ert

Occurrent

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Examplesperformance of a symphonyprojection of a filmutterance of a sentenceapplication of a therapycourse of a diseaseincrease of temperature

OccurrentRealizable Dependent Continuant

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ContinuantOccurrent

IndependentContinuant

Specifically DependentContinuant

Quality Disposition

Realization

Role

Realizable DependentContinuant

GenericallyDependentContinuant

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A violinist reads the score of Beethoven’s 9th Symphony and a concretization of the Symphony is created in his mind (something like a plan)

In playing he realizes this plan, thereby generating a performance of the Symphony

Realizable Dependent Continuants are always specifically dependent

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Nature Protocols

vs.

The protocol McDoe has been following in this project since March

Realizable Dependent Continuants are always specifically dependent

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McDoe reads the protocol as published and a concretization of the protocol is created in his mind (something like a plan)

In his laboratory work he realizes this plan, thereby generating an experiment

Realizable Dependent Continuants are always specifically dependent

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Informational Entity (law)

licensepermissioncontractregulation

...

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Open Source Licenses

Open source licenses define the privileges and restrictions a licensor must follow in order to use, modify or redistribute the open source software.

Examples include Apache License, BSD license, GNU General Public License, ...

The proliferation of open source licenses is one of the few negative aspects of the open source movement because it is often difficult to understand the legal implications of the differences between licenses.

(Wikipedia)71

By following the strategy of the Gene Ontology

Examine the instances in reality – laptops, labels, actions of signing contracts – and their interrelations

Distinguish license template from license (correctly filled-in)

How to create a common representation of the entities in the domain of

contracts and licensing?

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All terms in an ontology must have instances in realityOntologies must be anchored to reality through these instancesWe anchor the ontology of information entities through human acts of using language, through documents, through acts of entering data into a registry ...

Basic rule of evidence-based ontology

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Open Source Licenses

Open source license as generically dependent continuant (compare: protocol in Nature Protocols)

The license signed by John and Jim, a specifically dependent continuant whose bearer is (say) a specific piece of paper

The former is a concretization of the latter

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