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Lecture 3BFO: A Standard Upper
Level Ontology
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BFO als standard upper-level Ontologie
• Introduces Basic Formal Ontology (BFO)• Shows how BFO is extended by the
Information Artifact Ontology (controlled vocabulary for describing diagrams, images, documents, data, …)
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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 (= let’s look at the best scientific theory we have of this reality)
• Let’s 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
located near
LatrineWell
‘VT 334 569’
Distance Measurement
Result
Village Name
‘Khanabad Village’
Village
is_a
instance_of
Geopolitical Entity
Spatial Region
GeographicCoordinates
Setdesignates
instance_of
located in
instance_of
has location designates
has location
instance_of
instance_of
’16 meters’
instance_of
measurement_of
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Universals and Instances (from Bill Mandrick)
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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 ontologiesthe 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
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/ 10
Continuant
thing, quality …
Occurrent
process, event
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depends_on
Continuant Occurrent
process, eventIndependentContinuant
thing
DependentContinuant
quality
quality dependson bearer
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depends_on
Continuant Occurrent
process, eventIndependentContinuant
thing
DependentContinuant
quality, … event dependson participant
13
instance_of
Continuant Occurrent
process, eventIndependentContinuant
thing
DependentContinuant
quality
.... ..... .......
types
instances 14
depends_on
Continuant Occurrent
process
IndependentContinuant
thing
DependentContinuant
quality
.... ..... .......temperature dependson 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• Mary’s heart part_of Mary• Mary’s aorta connected_to Mary’s heart
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Clark et al., 2005
part_of
is_a
Definitions of relations
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Barry Smith, et al., “Relations in Biomedical Ontologies”, Genome Biology 2005, 6 (5), R46.
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)
IndependentContinuant
DependentContinuant
How to create an ontology from the top down
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Example: The Cell Ontology
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
United Nations Environment Programme
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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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– 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
OBO Open Biomedical Ontologies
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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) Foundry27
Blinding Flash of the Obvious
Continuant Occurrent(Process, Event)
IndependentContinuant
DependentContinuant
How to create an ontology from the top down
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Specifically Dependent Continuant
Red color of my skin
You Me
Accidens non migrat de subjecto in subjectum.
Accidents do not migrate from one substance to another
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Red color of your skin
depends_on depends_on
Continuant
IndependentContinuant
DependentContinuant
..... .....
Non-realizableDependentContinuant(quality)
Realizable DependentContinuant(function, role, disposition)
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Realizable dependent continuants
planfunctionroledispositioncapabilitytendency
continuants
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Their realizations
execution expression exercise realization applicationcourse
occurrents
32
Continuant
IndependentContinuant
DependentContinuant
..... .....
Non-realizableDependentContinuant(quality)
Realizable DependentContinuant(function, role, disposition)
33
realization depends_on realizable
Continuant Occurrent
IndependentContinuant
bearer
DependentContinuant
disposition
.... ..... .......Process of realization
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Specific Dependenceon 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.
35
depends_on
Continuant Occurrent
process, eventIndependentContinuant
thing
DependentContinuant
quality
.... ..... .......temperature dependson bearer
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The (Aristotelian) Ontological Sextet
Substances Quality entities Processes
UniversalsSubstance-universals
Quality-universals
Process-universals
ParticularsIndividual
Substances
Quality-instances (Tropes…)
Process-instances
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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the particular case of redness (of a particular fly eye)
the universal red
instantiates
an instance of an eye (in a particular fly)
the universal eye
instantiates
depends on
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the particular case of redness (of a particular fly eye)
red
instantiates
an instance of an eye (in a particular fly)
eye
instantiates
depends on
color anatomical structure
is_a is_a
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depends_on
Continuant Occurrent
process
IndependentContinuant
thing
DependentContinuant
quality
.... ..... .......temperature dependson bearer
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Specifically Dependent Continuants
SpecificallyDependentContinuant
Quality, Pattern
Realizable 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 weight43
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) Foundry44
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)
rationale of OBO Foundry coverage
GRANULARITY
RELATION TO TIME
45
Continuant
IndependentContinuant
Specifically DependentContinuant
..... .....Quality
Realizable DependentContinuant(function, role, disposition)
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Specific Dependenceon 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
GenericallyDependentContinuant
Information Object
Gene 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 48
Continuant
IndependentContinuant
Specifically DependentContinuant
..... .....Quality
Realizable DependentContinuant(function, role, disposition)
49
Realizable dependent continuants
plan
function
role
disposition
capability
tendency
continuants
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Their realizations
execution
expression
exercise
realization
application
course
occurrents
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Continuant Occurrent
IndependentContinuant
SpecificallyDependentContinuant
Quality
Disposition
Functioning
Function
GenericallyDependentContinuant
Realizable
Role
Information Artifact
Sequence…
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
IAO-Intel
• IAO-Intel – an extension of IAO and incorporating features of the AIRS Information Ontology – to provide common resources for the consistent description of information artifacts of relevance to the intelligence community
IAO: Report / IAO-Intel: Intelligence Report
IAO-Intel terms are defined by using terms from the ontologies in the yellow box via relations such as:•is-about•created-by•derives-from and so forth
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
top level
mid-level
domain level
Information Artifact Ontology
(IAO)
Ontology for Biomedical
Investigations(OBI)
Spatial Ontology
(BSPO)
Basic Formal Ontology (BFO)
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Information Artifactsartifact =def. an entity created through some deliberate act or acts by one or more human beings and which endures through time
information artifact: an artifact that can be the bearer of information
(a) information artifact (IA) – a hard drive, a passport, a piece of paper with a drawing of a map(b) information content entity (ICE) – an entity which is about something and which can potentially exist in multiple (for example digital or printed) copies – a jpg file, a pdf file
Types and tokens
Copyable information artifacts can exist both as tokensPeirce and as typesPeirce
Token = the particular information artifact of interest, tied to some particular physical information bearer: the photographic image on this piece of paper retrieved from this enemy combatantType = The copyable information content that is carried by the artifact in question. The same photographic image type may be printed out in multiple paper tokensWarning: this is not the same as the instance-class distinction
IAO is designed to address the need for metadata standards, not by
replacing existing standards,• but rather by providing a single, consistent
framework for tagging (‘semantic enhancement’) of existing data stores
• Its purpose is to provide a uniform, non-redundant, algorithmically processable and easily extendible consensus system of tags
Core of IAOType Definition IAO
Information Content Entity (ICE)
a generically dependent continuant that stands in the relation of aboutness to some entity
ICE
Information Structure Entity (ISE)
a generically dependent continuant that is not an ICE but which is complemented or complementable by one or more ICEs to create another ICE (example: cell in a spreadsheet, hard line break, space between words, semi-colon)
(new)
Information Quality Entity (IQE)
a quality that concretizes some ICE or ISE. (Comment: Typically an IQE will be a complex pattern made up of multiple qualities joined together spatially)
Information Carrier
Artifact a Material Entity that was created or modified or selected by some Agent to realize a certain function or to fulfill a certain role (Example: a screwdriver, a hard drive, a traffic sign)
(new)
Information Artifact (IA)
an artifact whose function is to bear an IQE.(Examples: a hard drive, a blank sheet of paper, a passport, a currency note)
(new)
Plan added as primitive (new)61
Attributes of IAs
• Information artifacts have attributes along a number of distinct dimensions, treated in low-level ontology modules
• Terms in these modules will be applied to explicate information relating to IAs of different sorts, and to annotate data pertaining to IA instances
• Attributes of IAs vs. Attributes of subject-matters, targets, topics, …
Attributes of IAs (cont.)
• Some dimensions of IA attributes are common to all areas, both military and non-military – Purpose– Life cycle Stage (draft, finished version, revision)– Language,– Format– Provenance– Source (person, organization)
Generic Attributes of IAs (for IAO)• Purpose
– Descriptive purpose: scientific paper, newspaper article, after-action report
– Prescriptive purpose: legal code, license, statement of rules of engagement
– Directive purpose (of specifying a plan or method for achieving something): instruction, manual, protocol
– Designative purpose: a registry of members of an organization, a phone book, a database linking proper names of persons with their social security numbers
• Purposes specific to IAO-Intel– Inform ing the commander,– Providing targeting support– Intelligence preparation of the battlefield.
Descriptive purpose=def. the purpose of describing some portion of
realityExamples: scientific paper, newspaper article,
diary, experimenter log notebookPrescriptive purpose=def. the purpose of prescribing or permitting or
allowing some activityExamples: a legal code, a license
Purpose of an Information Artifact
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Directive purpose=def. the purpose of specifying a plan or method for
achieving somethingExamples: instruction, manual, recipe, protocolDesignative purpose=def. the purpose of uniquely designating some
entity or the members of some class of entitiesExamples: a registry of members of an organization,
a phone book, a database linking proper names of persons with their social security numbers.
Purpose of an Information Artifact
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Examples of Generic Attributes of IAs
• Purpose• Lifecycle Stage (draft, finished version, revision)• Language• Format• Provenance• Source (person, organization)
These terms will be included in IAOEach corresponds to a specific low level ontology
Other IAO-Intel Attribute Dimensions• Classification
– Unclassified, open source– Secret– Top Secret
• Level– Strategic– Operational– Tactical
• Encryption Status• Encryption Strength
Strategy for Building IAO-Intel• Incremental expansion; the ontology is planned to
include artifacts spanning the entire range of IAs, from authoritative data sources to unprocessed reports
• Identify orthogonal dimensions of IA attributes and create Low-Level Ontology modules (LLOs)– Small, shallow, and structured following the principle
of single inheritance– Used to
• Construct more complex terms and define IAO terms• Explicate the meanings of terms standardly used by
different agencies• Annotate instance data
IAO and BFO
BFO: Generically Dependent Continuant
BFO: Independent Continuant
BFO: Specifically Dependent Continuant
Information Content
Entity (ICE)
Information Quality Entity
(Pattern) (IQE)
Information Structure
Entity (ISE)
Information Artifact (IA)
Generically Dependent Continuant
GenericallyDependentContinuant
pdf filejpg file
Gene 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
71
Information artifacts
pdf file
poem
symphony
algorithm
symbol
– can migrate from one information artifact to another
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Continuant
IndependentContinuant
Specifically DependentContinuant
Quality
Disposition
Information Artifact
Role
Realizable DependentContinuant
73
GenericallyDependentContinuant
Gene Sequence
Continuant
IndependentContinuant
Specifically DependentContinuant
Quality Information Artifact
74
GenericallyDependentContinuant
Gene Sequence
Material Entity
Information Bearing
Entity
Continuant
IndependentContinuant
Specifically DependentContinuant
QualityInformation
Artifact
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GenericallyDependentContinuant
Material Entity
Information Bearing
Entity (yourhard drive
Information Quality Entity (pattern on
your hard drive)depends_on
Continuant
IndependentContinuant
Specifically DependentContinuant
Quality Information Artifact
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GenericallyDependentContinuant
Material Entity
Information Bearing
Entity
Information QualityEntity
depends_on concretized_by
IAO: information content entity=def. an entity that is generically dependent on some artifact and stands in the relation of aboutness to some entity
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IA IBE ISE ICE
MS Word file (.doc, .docx)
Hard drive (magnetized sector)
MS Word format Varies
KML file Hard drive (magnetized sector)
KML Map overlay
JPEG file (.jpg)Hard drive (magnetized sector)
JPEG format Image
Email fileHard drive (magnetized sector)
Internet Message Format (e.g., RFC 5322 compliant) Message
USMTF Message file
A specific government network
USMTF Format Message
PassportPaper document; (may include photographs, RFID tags)
ID formats, security marking formats …
Name, Personal data, Passport number, Visas
Title Deed Official paper document Varies Varies
Report Varies Varies Varies
Overlay Sheet( e.g. Map Overlay Sheet)
Acetate sheetMIL-STD-2525 Symbols; FM 101-1-5 Operational Terms and Graphics
Map overlay
IAO and BFO
BFO: Generically Dependent Continuant
BFO: Independent Continuant
BFO: Specifically Dependent Continuant
Information Content
Entity (ICE)
Information Quality Entity
(Pattern) (IQE)
Information Structure
Entity (ISE)
Information Artifact (IA)
IAO and BFO (cont.)
• BFO relations between ICEs, ISEs, IQEs and IBEs can be set forth as follows:– ICE generically-depends-on IBE– ISE generically-depends-on IBE– IQE specifically-depends-on IBE– ICE concretized-by IQE– ISE concretized-by IQE
• IAO contains in addition relations which allow to formulate metadata concerning attributes of IAs such as author, creation date, classification status, and so forth