ontology in buffalo august 27, 2012

Ontology in Buffalo

August 27, 2012

Barry Smith

Problems

How to find data

How to reason with data when you find it

How to integrate with other data

How to label the data you are collecting

Answer annotate your data with a common ontology

How to build a common ontology = an ontology that will integrate well with ontologies built for neighboring domains?

2

Science requires a common suite of ontologies covering all scientific domains

Science is global and seamlessScientific data is public

3

Ontologists in UB

• Barry Smith (Philosophy, Bioinformatics)• Werner Ceusters (Psychiatry, Bioinformatics)• Alan Ruttenberg (Director of UB Clinical and

Translational Data Exchange)• Alex Diehl (Neurology, Director of Ontology

Services for School of Medicine)

• Pain Ontology grant with NIDCR• Protein Ontology grant with NIGMS• Infectious Disease Ontology grant with NIAID• National Center for Biomedical Ontology grant with

NIHGR• Cell Ontology grant with NIHGR• SNOMED grant with NLM• ARGOS on EU/US cooperation in Health IT• VIVO / eagle-I collaboration

CollaborationsCenter for Brain and Behavior Informatics (http://cbbi.buffalo.edu)

Stroke Patient RegistryAlzheimers Patient RegistryDegenerative Disease Ontology Immunology Ontology

Roswell Park Cancer Institute (Malignancy Ontology)School of Dental Medicine (Pain Ontology, Picasso EHR)

http://cbbi.buffalo.edu/

Institute for Healthcare Informatics•http://ahc.buffalo.edu/ihi/Center of Excellence in Bioinformatics and Life Sciences•http://www.bioinformatics.buffalo.edu/

http://www.bioinformatics.buffalo.edu/

Ontologists in Buffalo

• Jason Corso (Computer Science – video analysis)

• Albert Goldfain (Blue Highway, Inc. – Infectious Disease Ontology, data exchange between devices)

• Dagobert Soergel (Information Studies – online advanced certificate program in ontology)

National Center for Biomedical Ontology (NCBO)

Stanford University Biomedical Research

Mayo Clinic

University at Buffalo

9

Uses of ‘ontology’ in PubMed abstracts

10

By far the most successful: GO (Gene Ontology)

11

GO provides a controlled system 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

12

US $200 mill. invested in literature and data curation using GO

over 11 million annotations relating gene products described in the UniProt, Ensembl and other databases to terms in the GOexperimental results reported in 52,000 scientific journal articles manually annoted by expert biologists using GO

13

GO is amazingly successful in overcoming the data balkanization problem

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, …

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)

Original OBO Foundry ontologies (Gene Ontology in yellow) 15

16

RELATION TO TIME

GRANULARITY



ORGAN ANDORGANISM

Organism(NCBI

Taxonomy)

Anatomical Entity(FMA, CARO)

OrganFunction

(FMP, CPRO) Phenotypic

Quality(PaTO)

Biological Process


COMPONENT

Cell(CL)

Cellular Compone

nt(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule



Molecular Process

(GO)

Environment Ontology

envi

ron

men

ts

are

her

e

17

RELATION TO TIME

GRANULARITY



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


COMPONENT

Cell(CL)

Cellular Componen

t(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule



Molecular Process

(GO)

http://obofoundry.org

Developers commit to working to ensure that, for each domain, there is community convergence on a single ontology

and agree in advance to collaborate with developers of ontologies in adjacent domains.

http://obofoundry.org

The OBO Foundry: a step-by-step, evidence-based approach to expand

the GO

18

OBO Foundry Principles

Common governance (coordinating editors)

Common training

Common architecture

• simple shared top level ontology

• shared Relation Ontology: www.obofoundry.org/ro

19

Open Biomedical Ontologies Foundry

Seeks to create high quality, validated terminology modules across all of the life sciences which will be

• non-redundant

• close to language use of experts

• evidence-based

• incorporate a strategy for motivating potential developers and users

• revisable as science advances20

The OBO Foundryis a collective experiment involving many biological and clinical communities attempting to create terminology resources which will support the goal of modularity

one ontology for each domain

No need for ‘mappings’

21

OBO Foundry (example ontologies)GO Gene Ontology

CL Cell Ontology

SO Sequence Ontology

ChEBI Chemical Ontology

PATO Phenotype (Quality) Ontology

FMA Foundational Model of Anatomy Ontology

ChEBI Chemical Entities of Biological Interest

PRO Protein Ontology

Plant Ontology

Environment Ontology

Ontology for Biomedical Investigations

RNA Ontology

22

Introduction to Basic Formal Ontology

23

The central distinction

universal vs. instance

human being vs. Arnold Schwarzenegger

science text vs. diary

catalog vs. inventory

24

Ontologies arerepresentations of universals in reality

aka kinds, types, categories, species, genera, ...

25

A 515287 DC3300 Dust Collector Fan

B 521683 Gilmer Belt

C 521682 Motor Drive Belt

inventory

catalog26

A 515287 DC3300 Dust Collector Fan

B 521683 Gilmer Belt

C 521682 Motor Drive Belt

instances

universals27

siamese

mammal

cat

organism

object

animal

instances

frog

universals

28

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

29

An example of a simple rule:Each term in an ontology represents

exactly one universal

For this reason ontology terms should be singular nouns

organism

headache

drug administration

30

The Pre-History of BFO

• Aristotle (4th Century BC)

• Edmund Husserl’s Logical Investigations (1900-01)

• “Truthmaker” (1984)

• Patrick Hayes, “Naïve Physics Manifesto” (1985)

• Qualitative spatial reasoning (1990 – )

• DOLCE (1991 – )

• GO, FMA (2004 – )

31

Aristotle’s Ontological Square

Substantial Accidental

Second substance

man

cat

ox

Second accident

headache

sun-tan

dread

First substance

this man

this cat

this ox

First accident

this headache

this sun-tan

this dread

Uni

vers

alP

artic

ular

32

Edmund Husserl• Coined ‘formal ontology’• Introduced formal mereology• First formal account of dependence relations

33

Substantial Accidental

Independent continuant Second accident

this man

this ox

this man’s headache that man’s knowledge of Greek

Par

ticul

arU

nive

rsal

Truthmaker (1984)

Q: What is it in reality in virtue of which a true assertion such as

“John has a headache”

is true?

A: John’s current headache

34Kevin Mulligan, Peter M. Simons and Barry Smith, “Truth-Makers”, Philosophy and Phenomenological Research, 44 (1984), 287–321.

http://ontology.buffalo.edu/smith/articles/truthmakers/tm.html

John Searle

mind-to-world direction of fit – have truthmakers

Belief

Statement

Photograph

Scientific theory

world-to mind direction of fitPlan

Instruction

Request

Command

35

Hayes’ Naïve Physics Manifesto

BFO 1.n: How can we construct a formal ontology (= an ontology formalized using first-order predicate logic) that will represent the entities we experience in our everyday perception and action?

BFL 2.n: How can we do this in a way that will also be compatible with what we know from physics?

36

Qualitative spatial reasoning / mereotopology

• COSIT Conferences on Spatial Information Theory– http://www.cosit.info/

• Leeds Qualitative Spatial Reasoning Group – http://www.comp.leeds.ac.uk/qsr/

• Anthony Galton– http://empslocal.ex.ac.uk/people/staff/apgalton/

• Thomas Bittner– http://www.buffalo.edu/~bittner3

• Roberto Casati and Achille Varzi, Parts and Places (MIT Press, 1999)

37

The History of BFO

2004 BFO 1.0

2005 OBO Relation Ontology (RO)

2006 BFO 1.1

adds generically dependent continuants

2012 BFO 2.0

incorporates top-level relations from RO

addresses problem of process measurement data (e.g. heart rates)

38

BFO: A First Look

Continuant Occurrent(Process, Event)

IndependentContinuant

DependentContinuant

39

..... ..... .....universals

instances

Basic Formal Ontology

• a true upper level ontology

• no interference with domain ontologies

• no interference with issues of cognition

• no putative fictions

40

Main reason to use BFO

BFO has the largest body of users

(compare: This telephone network has the largest number of subscribers)

Snowballing network effects:

data annotated using BFO-conformant ontologies becomes more valuable

numbers of people with expertise in building BFO-conformant ontologies increases

41

How BFO is constructed and maintained

Simplicity

BFO has objects

BFO has qualities of objects

BFO has no qualities of qualities

Simplicity

BFO has particulars

BFO has universals

Only particulars instantiate universals

(no ‘meta-universals’)

42

How BFO is constructed and maintained

Perspectivalism:

Ontologies are windows on reality

There is a multiplicity of windows (perspectives), all equally veridical, i.e. transparent to reality

For example we can view an organism as a single object or as a collection of molecules (granular perspectives)

43

44

reality exists behind a transparent grid

= a veridical partition

Barry Smith, “Beyond Concepts, or: Ontology as Reality Representation”, (FOIS 2004), http://ontology.buffalo.edu/bfo/Beyond_Concepts.pdf

Ontological realism

45

Alberti‘s Grid

46

Common sense involves many verdical partitions

otherwise we would all be dead

The common sense partitions of folk physics, folk psychology, folk biology, are to a large degree transparent to realityIt is such common sense partitions that are involved, for instance, when someone takes your temperature in the hospital

Many veridical partitions

47

The fundamental thesis of ontological realism

that many of our natural-language and scientific partitions are transparent to reality

is in fact quite trivial

BFO 1.0

49

Three Fundamental Dichotomies

• Universal/Type vs. instance

• Continuant vs. occurrent

• Dependent vs. independent

http://ontology.buffalo.edu/bfo/ 50

Basic Formal Ontology



DependentContinuant

http://ifomis.uni-saarland.de/bfo/51

Blinding Flash of the Obvious



DependentContinuant

http://ifomis.uni-saarland.de/bfo/52

Continuant entities

- have continuous existence in time

- preserve their identity through change

- exist in toto if they exist at all

Occurrent entities

- have temporal parts

- unfold themselves phase by phase

- exist only in their phases/stages

53

You are a substance

Your life is a process

You are 3-dimensional

Your life is 4-dimensional

54

BFO: the very top

ContinuantOccurrent

(always dependent on one or more

independent continuants)


Specifically DependentContinuant

55

instance_of

Continuant Occurrent

process, eventIndependentContinuant

thing


quality

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

types

instances 56

Specifically dependent continuants

• ‘

Qualities • of whiteness of this cheese, of mass of

this banana, of rigidity of this stone

57

Continuant



..... .....

Non-realizableDependentContinuant(quality)

Realizable DependentContinuant(function, role, disposition)

58

Realizable dependent continuants

Role: nurse role, pathogen role, food role

Disposition: fragility, virulence, susceptibility, genetic disposition to disease X

Function: to pump (of the heart), to unlock (of the key)

59

realization specifically_depends_on realizable



bearer

SpecificallyDependentContinuant

disposition

.... ..... .......60

Process of realization

BFO

ContinuantOccurrent(Process)


(molecule, cell, organ,organism)

DependentContinuant

(quality, function,disease)

e.g. Functioning

e.g. Side-Effect, Stochastic Process, ...

..... ..... .... .....61

BFO partitions reality

all terms included in the ontology are intended to designate universals in reality, in conformity with the basic principle of science-based ontology

but this means that science-based ontologies are on the one hand windows on the universals in reality, but on the other hand windows on the instances in reality

62

Realizable dependent entities

role

disposition

functioncontinuants

63

Their realizations

execution

expression

exercise

application

course

occurrents

64




Quality Disposition

e.g. FunctioningFunctione.g. Disease

Role

Realizable DependentContinuant

65

BFO 1.1

66

Specifically Dependent Continuants

SpecificallyDependentContinuant

Quality, PatternRealizable Dependent Continuant

if any bearer ceases to exist, then the quality or function ceases to exist

the color of my skin

the function of my heart

67

Generically Dependent Continuants

GenericallyDependentContinuant

Information Object

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

68

Information objects

pdf file

poem

symphony

algorithm

symbol

sequence

molecular structure

69

Generically dependent continuants such as plans, laws …

are concretized in specifically dependent continuants

(the plan in your head, the protocol being realized by your research team, the law being implemented by this government agency)

70

Generically dependent continuants

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

72

Universal or instance

ContinuantOccurrent(Process)


human being,protocol document

DependentContinuant

pattern of ink marks

Applying the protocol

Side-Effect …

... .. ..... .... .....73

Generically Dependent Continuants

GenericallyDependentContinuant

Information Entity

Sequence

.pdf file .doc file

instances 74

BFO 2.0

75

not a sum of objects, but something like a set:

a certain part of material reality, picked out by a certain granular partition

BFO:object_aggregate

76

The Beatles

77

The Beatles

78

We use the

partition to pick out a certain object aggregate in this particular portion of material reality, then

we mask all other portions of reality, from external (the water) and internal (the cells and

molecules)

79

John Paul George Ringo

is a veridical partition. The

Beatles truly do (did) exist

80

John Paul George Ringo

81

king rook queen pawn knight bishop

chess pieces table topsurrounding

space

molecules

all these partitions are verdical

which can however change its members over time

(e.g. the aggregate of members of the International Association for Ontology and Its Applications)

examples: populations, families, tribes, species, planetary systems – anything associated with a count, a registry, an inventory, a census

BFO:object_aggregate

82

inventory

83

member_part_of

a member_part_of b at t =Def. a is an object at t

& there is at t a mutually exhaustive and pairwise disjoint partition of b into objects x1, …, xn with a = xi for some natural number i.

Use this as basis for a theory of groups, organizations and other social objects

84

human

John85

embryo fetus adultneonate infant child

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

in nature, no sharp boundaries here

Non-rigid universals = universals which (may) hold of a continuant

only for a certain time in the life of the continuant

portion of water

this portion of H20

86

portion of ice

portion of liquid water

portion of gas

instantiates at t1

instantiates at t2

instantiates at t3

Phase transitions

temperature

John’s temperature endures through time87

37ºC 37.1ºC 37.5ºC37.2ºC 37.3ºC 37.4ºC

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

When we measure temperatures we impose a quantitative partition on a portion of reality

temperature

John’s temperature (a quality instance) 88

37ºC 37.1ºC 37.5ºC37.2ºC 37.3ºC 37.4ºC

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

rigid

Determinable and determinate qualities

non-rigid

temperature

John’s temperature 89

37ºC 37.1ºC 37.5ºC37.2ºC 37.3ºC 37.4ºC

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6



Determinable and determinate qualities

Recall how we deal with phase sortals

John instance_of nurse at t =Def.

John instance_of human being at t

& for some x, x instance_of nurse role

& x inheres_in John at t

90

Role universals are rigid universals

Nurse role is_a role

(Role universals are rigid universals)

If x instance_of role at t, then x instance_of role at all times at which x exists.

Quality, disposition, region, material entity – these too are rigid universals

Is object a rigid universal?

91

Full processes

p is a full process =Def. for some spatiotemporal region s,

p occupies s

& every process q which occupies some part of s is part of p

All full processes occupying any given spatiotemporal region are identical

92

History

history of a material entity m = the full process which is the sum of processes taking place in the spatiotemporal region occupied by m

93

HistoryThe relation between a material entity and its

history is one-to-one:

for any material entity a, there is exactly one process which is the history of a,

for every history h, there is exactly one material entity which h is the history of.

Histories are additive. Thus for any two material entities a and b, the history of the sum of a and b is the sum of their histories.

94

Lives (for OGMS)

The life of an organism is the history of the corresponding OGMS:extended organism

95

Partial processes

p is a partial process = p is a process & p is not a full process

96

A spinning top is simultaneously getting warmer

Two distinguishable (indeed separately measurable process profiles) in a single region of spacetime

97

Typically, processes are very complicated

a single running process p might be an instance of multiple universals such as

– 3.12 m/s motion process, – 9.2 calories per minute energy burning process,– 30.12 liters per kilometer oxygen utilizing process, – cardiovascular exercise process of type #16and so on.

Each of these corresponds to a partial process within p.

Solution

• focus not on ‘thick’ processes, such as runnings or hearts’ beating

• but on ‘thin’ structural parts of processes

–called ‘process profiles’• (event patterns, …)

• a process of the sort that can be represented by a chart plotting quality measurement results on a single dimension against a time axis

• a quality process profile is a truthmaker for a time series graph of this sort

Single quality process profile

Examples of single quality process profiles

Examples of 1.the course of Jim’s temperature2.the course of Jim’s weight3.the course of Jim’s height4.the course of Jim’s fortuneEach is depictable by means of a time series graph

Process profile that which the output of a correct device would

represent

= that which a correct time-series graph would represent

Temperature

Call the process represented by this graph a (temperature) quality process profile

The graph picks out just one dimension of qualitative change within a much larger

conglomerate of processes

Hence ‘quality process profile’

What did your temperature do over the last month, Jim?

a target of a certain sort of cognitive selection, or cognitive profiling

Cardiac Cycle, Left Ventricle

http://en.wikipedia.org/wiki/Cardiac_cycle

Some processes can incorporate multiple quality process profiles



…corresponding to the multiple different sorts of partition of the same reality involved during measurement



multi-quality process profile



Compare perception of polyphonic music

• Cognitive selection of the cello part when you listen to a string quartet

• Picking out a certain process profile within a larger body of vibrations

• Ignoring sneezes, coughs, …• (sometimes focusing on sneezes and coughs

for diagnostic purposes)

110

simultaneous causality

specifically_depends_on


process


thing

DependentContinuant

quality

.... ..... .......temperature dependson bearer

112

The Beatles

114

115

... red orange yellow green ...

... crimson reddeep red

blood red

...

Quality partitions

116

Example: a chess game

W: Pawn to King4

B: Pawn to Queen’s Bishop 3

W. Pawn to Queen 3

...

Two directions of fit

world-to-mind and mind-to-world

what begins as a plan, ends as a record (with truthmaker – if it is a true record – the journey you took)

117

118

Example: An airline ticket

7:00am LH 465 Vienna

arrive London Heathrow 8:15am

9:45am LH 05 London Heathrow

arrive New York (JFK) 3:45pm

5:50pm UA 1492 New York (JFK)

arrive Columbus, OH 7:05pm

119








120








121








122








123








When you understood the airline ticket,

when you understood the reality of the corresponding portion of spacetime at the level of granularity dictated by the airline ticket,

you were directed towards a process profile called a journey

the journey is the truthmaker for the ticket

124




125

Process profiles and the role of standardized notations

music

chess

choreography

ship stow planning

military manoeuvres

language

traffic law

127

Process profiles and linguistics

Phonetics deals with the production of speech sounds by humans, often without prior knowledge of the language being spoken.

Phonology is about patterns of sounds in all spoken languages

128

Protocol#1 protocol (GDC) instance_of OBI: type plan

specification.

#1 concretized_in #2 (= plan in mind of leader of research team, a realizable SDC to carry out some experiment.

realization of #2 starts with the creation of a series of sub-protocols, which are plan specifications for each team member.

The experiment itself is the sum of the realizations of these plans, having outputs further GDCs such as publications, databases …

129

MusicBeethoven’s 9th Symphony, a certain abstract pattern

(generically dependent continuant), which we shall call #9

#9 instance_of symphony

symphony is_a musical work.

#9 instance_of musical work

#9 concretized_in specifically dependent continuant pattern of ink marks borne by this printed copy of the score #10

#9 concretized_in specifically dependent continuant pattern of grooves in this vinyl disk.

130

Music

#10 instance_of generically dependent continuant type OBI:plan specification

#10 specifies how to create performance of #9.

#10 is concretized_in this network of subplan (complex realizable SDC) distributed across the minds of the conductor and members of this orchestra #11

#11 realized_in this performance #12

#12 “copied” in what you hear (a process inside your head)

131




133

Are mental processes process profiles?

134

ontology in buffalo august 27, 2012

Documents