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Examples of new ontologies using BFO

• Actionable Intelligence Retrieval System (AIRS)• US Transcom (Transportation Command)

Enterprise Ontology (http://www.securboration.com/)

• Mental Functioning Ontology (MFO), Emotion Ontology (MFO-EM)

• Financial Report Ontology: FRO– here BFO (and IAO) must be under the hood

http://www.securboration.com/

FMA: BFO under the hoodAnatomical Entity

Physical Anatomical Entity

Material Physical Anatomical Entity

-is a-

Non-material Physical Anatomical Entity

ConceptualAnatomical Entity

AnatomicalStructure

BodySubstance

BodyPart

HumanBody

OrganSystem

OrganCell

OrganPart

AnatomicalSpace

Anatomical Relationship

CellPart

Biological Macromolecule

Tissue

Non-Physical

Anatomical Entity



-is a-



AnatomicalStructure

BodySubstance

BodyPart

HumanBody

OrganSystem

OrganCell

OrganPart

AnatomicalSpace


CellPart


Tissue

Anatomical Entity



-is a-



AnatomicalStructure

BodySubstance

BodyPart

HumanBody

OrganSystem

OrganCell

OrganPart

AnatomicalSpace


CellPart


Tissue

Non-Physical

Blue Force Overwatch

The Plant Ontology

cROP: Common Reference Ontologies for Plants

Role of BFO in OBO Foundry

• OBO Foundry and related suites of ontologies will work only if their component ontologies are orthogonal

• Orthogonality can be established only if these ontologies are comparable

• BFO is at the core of the strategy to ensure compatibility

id: HP:0001943 ! Hypoglycemia = = decreased concentration of glucose in the blood

• intersection_of: PATO:0001163 ! decreased concentration• intersection_of: qualifier PATO:0000460 ! abnormal• intersection_of: towards CHEBI:17234 ! glucose• intersection_of: inheres_in FMA:9670 ! Portion of blood

Class: Hypoglycemia ≡ decreased concentration &towards some glucose & inheres_in some portion of blood & qualifier some 'abnormal‘

P. Robinson: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224779/http://www.ncbi.nlm.nih.gov/pubmed/23104991

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3224779/

http://www.ncbi.nlm.nih.gov/pubmed/23104991

http://www.ncbi.nlm.nih.gov/pubmed/23104991

HP:0001720 ! tachycardiaProcess: GO:0060048 cardiac muscle contractionQuality: PATO:0000912 increased rate

PATO:Rate =def. A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time

logically: rate(r,p) =def. p is a process & p consists of a sequence of similar sub-processes & these sub-processes repeat r times per unit time

Note that there is no reference to a quality or to inherence here

Tachycardi

• Thus Tachycardia only exists if there is the sort of cyclical repetition of cardiac muscle contraction that is involved in the heart's beating.Thus Tachycardia is not a rate of cardiac muscle contraction, but rather a rate of cardiac muscle contraction repetition.

Treatment of ‘process qualities’• ‘BFO:quality’ just means: a quality of an

independent continuant • PATO:process-quality uses 'quality' in a

different sense; providing this sense is well-defined, there is no objection to its use. Unfortunately most PATO:process-quality terms are currently poorly defined. The hope is that use of BFO 2.0 can help to bring improvements.

rate (rough version)

rate(r,p) =def. p is a process & p consists of a sequence of similar sub-processes & these sub-processes repeat r times per unit time

increased-rate(r,p) = def. p is such that r is greater than a certain normal threshold (defined for each particular kind of patient)

There are numbers here, and time units, and thresholds for numbers.

But there are no extra entities called ‘process qualities’

• If we observe that there are 3 apples in a bowl on Wednesday and 2 apples in the same bowl on Thursday, then we could express this by saying that the apples in the bowl had the quality of threeness on Wednesday and the quality of twoness on Thursday.

• People could talk like that if they wanted, butit would be ontologically much less adequate than just the assertion underlined above.

Similarly,if we observe that there is a 63 bpm heart rate in a patient on Wednesday and 102 bpm heart rate in the same partient on Thursday, then we could express this by saying that the heart beat process of the patient had the quality of sixtythree-bpm-ness on Wednesday and ofonehundredandtwo-bpm-ness on Thursday. People could talk like that if they wanted, butit would be ontologically much less adequate than just the assertion underlined above/

•63bpm Wednesday and 102 bpm in the same patient on Thursday

i.e. more beats per minute on Thursday

What BFO is designed to do

• BFO is not intending to constrain what people say, merely to provide a formally coherent basis for definitions (for example in PATO).

• Given this basis, it should be possible to define all the terms one needs, including all the terms one needs from PATO.

Which general terms refer to universals?

For some general terms X we can formulate definitions of the following sort:

(C) Collection of X’s =def. collection of particulars of type X.

How do we determine whether for (C) holds of a given term ‘X’? This is the job of scientists, in an on-going process of terminology evolution through which those terms come to be selected for that are fit to serve in successive formulations of the corresponding scientific theory.

Which general terms refer to universals?

Each scientific theory as it exists at any given stage will likely be marked by (as yet unidentified) terminologically relevant errors, and these errors will accordingly be carried over into the corresponding ontology. Hence, we cannot embrace any one-one correspondence between scientific general terms and universals in reality. Rather, we should assume, for heuristic purposes only, that at any given stage the terms used by scientists in a given discipline refer to universals, knowing full well that this assumption may be false for any given term.

Qualities determinable and determinate

temperatureblood pressuremass...

are continuantsthey exist through time while undergoing changes

17

Qualitiestemperature / blood pressure /

mass ...are dimensions of variation within the structure of the entity; a quality is something which can change while its bearer remains one and the same

18

A Chart representing how John’s temperature

changes

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Qualities

temperature / blood pressure / mass ...are dimensions of variation within the structure of the entity; a quality is something which can change while its bearer remains one and the samehence only independent continuants may have qualities

20

John’s temperature

the temperature John has throughout his entire life, cycles through different determinate temperatures from one time to the next

John’s temperature is a physiology variable which, in thus changing, exerts an influence on other physiology variables through time

21

temperature


22

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

One issue

Chris Mungall:

BFO should have some documented position as to •determinables are still present when their value is zero •OR physics is such that no true determinable can take on a zero value.

a quality is something which can change while its bearer remains one and the samehence only independent continuants may have qualities for suppose q were a quality of a processthen q would have to be something which could change while the process, its bearer, would remain one and the same – and this is not possible

24

temperature course


25

increasing temperature

course

constant temperature

course

decreasing temperature

course

instantiates at t1

instantiates at t4

instantiates at t5

temperature


37.2º37.2ºCC

instantiates at t3

unit of measurement

ºC

measures

information artefact

measurement record

“John has temperature 37.2ºC at t3”

instantiates

about

uses

John

inheres_in

temperature


37.2ºCtemperature

instantiates at t3

unit of measurement

ºC

measures


measurement record

“37.2ºC at t3”

instantiates

about

uses

about

about

note re IAO aboutness

BFO: The Very Top

continuant

independentcontinuant

dependentcontinuant

quality

occurrent

temperature 28

Blinding Flash of the Obvious


dependentcontinuant

quality

temperature types

instances

organism

John John’s

temperature 29

Blinding Flash of the Obvious


dependentcontinuant

quality

temperature types

instances

organism

John John’s

temperature 30


dependentcontinuant

quality

temperature types

instances

organism

John John’s

temperature

31

Can sites have histories?Full process(p) =def. there is some spatiotemporal regions r & p is the sum of all processes occurring in r

A history is a full process

Participants of a history: independent continuant, site – but what if they coincide spatio-temporally

32

Process profiles

Full process(p) =def. there is some spatiotemporal regions r & p is the sum of all processes occurring in r

Example of full process: history

Process profile = a process that is less than a full process

33

Canonical example

• A spinning top is spinning• A spinning top is simultaneously

warming

The spinning and the warming are both proper parts of the full process (= all the processes taking place within the

34

Families of process profiles

• Quality process profiles• Measurement/assay process profiles• Scientific discipline demarcated

process profiles• Diseases• Speech, music, thinking, writing,

dancing …

35

Relative process profiles

36


dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

life of an organism

John’s life

37


dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

course of temperature

changes

John’s temperature history

38

process profile

quality process profile


dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

life of an organism

John’s life

39


dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

metabolism of an organism

John’s metabolism

40

process profile


dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

growth of an organism

John’s growth

41

process profile


dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

development of an organism

John’s development

42

process profile

temperature


43

37ºC37.1º

C37.5º

C37.2º

C37.3º

C37.4º

C

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

human

John

embryo

fetus adultneonat

einfant child

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

human

John

45

embryo

fetus adultneonat

einfant 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

portion of water

this portion of H20

46

portion of ice

portion of liquid water

portion of gas

instantiates at t1

instantiates at t2

instantiates at t3

Phase transitions

temperature


47

37ºC37.1º

C37.5º

C37.2º

C37.3º

C37.4º

C

instantiates at t1

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6



heart disease

John’s heart disease (continuant)

49

disease with asymptomatic disease, silent

infarction

disease with early lesions

and small fibrous plaques

disease with

stable angina

disease with surface disruption of plaque

disease with

unstable

angina

instantiates at t2

instantiates at t3

instantiates at t4

instantiates at t5

instantiates at t6

What is the course of John’s heart disease?

52


dependentcontinuant

disposition

heart disease

organism

John John’s

heart disease

occurrent

process

heart disease course

John’s heart disease course

53

process profile

heart function: to

pump

John’s heart function: to pump

55

pumping function of heart after

fatality

instantiates at t7

heart function: to

pump


56

pumping function of

healthy heart

instantiates at t1

this portion of deoxygenated blood

1

instantiates at t1

material entity

portion of blood

this portion of oxygenated blood

instantiates at t1

material entity

portion of blood

has input has output

heart function: to

pump


57

instantiates at t1

this clot1

instantiates at t1

this clot

instantiates at t1

material entity

clot

has input has output

pumping function of

healthy heart

heart function: to

pump


58

pumping function of

healthy heart

instantiates at t1

this portion of blood

instantiates at t1

material entity

oxygenated portion of blood

this concentration

instantiates at t1

quality

concentration of oxygen

has output need to get time right

Continuant Occurrent

IndependentContinuant

SpecificallyDependentContinuant

Quality

ProcessGenericallyDependentContinuant

Information Artifact

Sequence…

GDCs

• universals are unchangeable -- GDCs are always such that they are changeable (there are instances of the relevant universal which can change, e.g. successive editions of books)

• lower levels of types do not ‘carry identity’ in OntoClean terms

• are threshold divisions (hence we do not have sharp boundaries, and we have a certain degree of choice, e.g. in how many subtypes to distinguish, though not in their ordering)

61


dependentcontinuant

quality

temperature types

instances

organism

John John’s

temperature

62


dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

course of temperature

changes

John’s temperature history

63


dependentcontinuant

quality

temperature

organism

John John’s

temperature

occurrent

process

life of an organism

John’s life

64

temperature


37.2ºC temperatur

einstantiates at t3


measurement datum

“37.2ºC at t3”

instantiates

measurement assay

quality process

temperature assay at t3

instantiates

has outputJohn

has_input

about

BFO: The Very Top

continuant


dependentcontinuant

67

dependentcontinuant

quality realizable dependentcontinuant

68

role(optional)

disposition(has physical

basis)

dependentcontinuant

quality realizable

role(optional)

disposition(aka ‘ability’)

function(a disposition designed

or selected for)

:.

Role of some chemical compound: to serve as analyte in an experiment

of this human being: to serve as PI of this research project

70

:.

Role optional:exists because the bearer is in some special natural, social, or institutional set of circumstances in which the bearer does not have to be

71

:.

Rolesoften form systems of mutual dependence

husband / wife first in queue / last in queuedoctor / patient

host / pathogen

72

:.

Function - of liver: to store glycogen- of birth canal: to enable transport- of eye: to see- of mitochondrion: to produce ATP

reflection of physical makeup of bearer 73

:.

Qualities are categorical features of reality – you just have them

Functions, roles and dispositions are potential featires of reality: they are realizable dependent continuants, realized in certain associated processes

74


dependentcontinuant

role

drug role

portion of chemical compound

this portion of aspirin

role of this portion of aspirin

occurrent

process

process of drug

adminstration

John’s taking this portion of aspirin

75


dependentcontinuant

role

drug role

portion of chemical compound

this portion of aspirin

role of this portion of aspirin

occurrent

process

process of drug

adminstration

John’s taking this portion of aspirin

76

inheres_in

realized_in

• The Road to Convergence

All ontologies for each given domain (anatomy, chemistry…) should be part of a single suite of interoperable ontologies

should use a common top-level corefor subdomains with many variants, should

follow the strategy of canonical ontologies with extensions

should require acceptance of common, tested guidelines on all subscribing ontology developers

77

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)

initial OBO Foundry coverage, ontologies automatically semantically coupled

GRANULARITY

RELATION TO TIME

78

Disposition (Internally-Grounded Realizable

Entity)disposition =def.

a realizable entity which if it ceases to exist, then its bearer is physically changed, and whose realization occurs when this bearer is in some special physical circumstances, in virtue of the bearer’s physical make-up

79

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*) OBO Foundry Modular Organization

top level

mid-level

domain level

Information Artifact Ontology

(IAO)

Ontology for Biomedical

Investigations(OBI)

Spatial Ontology(BSPO)

Basic Formal Ontology (BFO)

80

Relations

instance-instance (primitives allow definitions)instance-typetype-type

RO 2.0 type-type – All-some rule holdsadd causes dependence includes mutual dependence among

roles, functions

Keep RO 2.0 small

‘depends_on’ is short for ‘specifically_depends_on’

‘generically_depends_on’ is written out in full

life ofhas physical basis

address relations between

• site,• located_in• contained_in

RO 2.0 lists simple relations (such as depends_on);

there are many complex defined relations (such as inheres_in,

is_quality_of)

A inheres_of B =def. A depends_on B and A is_a dependent continuant and B is_a independent

continuantA is_quality_of B =def. A depends_on B and A is_a

quality and B is_a independent continuant

starting point is here (Work of Chris Mungall)

• http://www.fruitfly.org/~cjm/ro/ro.html

Generic Dependence

• Specific Dependence • Duration of

Get versioning right

• CL is a standard version

keep ‘derives from’

• change examples• recommend biologists use ‘develops from’• location involves site?• vaccine, clinical outcome, effectiveness

prevention, diagnosis, treatment, clinical registry ogms

The Relation Ontology

• immanent relations in BFO– specific dependence– generic dependence– realization

89

How to use the RO all–some form

• LMO2 molecules interact with ELF2 molecules false

• LMO2 molecules have the disposition to interact with ELF2 molecules true

Axioms

• ALL Occurrent depends_on SOME Continuant• ALL DependentContinuant depends_on SOME

IndependentContinuant• ALL IndependentContinuant occupies SOME

3D SpatialRegion• ALL Site occupies SOME 3D SpatialRegion• ALL BoundaryOfObject occupies SOME 0, 1 or

2D SpatialRegion

91

Axioms

• ALL BoundaryOfObject is_part_of SOME Object

• ALL Object has_part SOME BoundaryOfObject• ALL ProcessualEntity occurs_in SOME

SpatiotemporalRegion• ALL ProcessualEntity has_participant SOME

IndependentConinuant

92

Only something that holds of all As will be an assertion that holds of the type A

Hence the All-Some ruleOr analogous rules for n-ary relations

(where n > 2)

93

Definitions of type-level relations presuppose underlying instance-level relations

A is_a B presupposes instance_ofAll instances of A are instances of B

A part_of B presupposes instance-level-part-ofEvery instance of A are instance-level-parts-of

some instance of B

Rules for including relations in RO

To avoid forking, keep RO as small as possibleIf we have a relation, say, adjacent_to in RO, then we should not add lists of easily defined relations of the form

adjacent_to_organ: adjacent_to_cytoplasm:adjacent_to_neuron:

In general: include a relation only if it is lexicalized

•

95


In every case we need to check, before we add a relation A R B, that, for some set of A and B terms we have data about the As and data about the Bs which is such that

all the instances of A stand in instance-level R to some B

e.g. all the instances of cell membrane stand in instance-level part_of to cell

96


Some_some relations are important not to ontology but to the treatment of empirical data e.g. relating to exceptions to proposed general hypotheses

However, in developing RO, we will need to keep track of instance-level relations in any case, and then corresponding some-some relations (and also various kinds of probabilistic relations) come for free

•

97

Thus for example

Instead of:•

results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of

use just the relations:•

results_in, is_aand the types:

reception_of_stimulus, conversion_into_molecular_signal

98

Or in other words:

A results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of B=Def.

A results_in B & B is_a reception_of_stimulus& B is_a conversion_into_molecular_signal

99

Consequences of including only all-some relations in RO

All relations will be evaluable as1. Transitive2. Symmetric3. Reflexive4. Anti-Symmetric

All relations will support reasoningis_somehow_related_to

is the worst kind of relation to create100

True Path Rule

the pathway from a child term all the way up to its top-level parent(s) must always be true (Gene Ontology Consortium, 2001)

= both is_a and part_of are transitive

LacksInstance-type level

p lacks U with respect to r at time t =def. there is no instance u of U such that p stands in r to u at t.

Type-type level C1 lacks C2 with respect to r =def. for all c,t, if c instance of C1 at t then c lacks C2 with respect to r at time t.

Need a way to state on top of this: that C1s normally stand in r to some C2

To be added to the Relation OntologyRO Core (examples)

• dependent_on (between a dependent entity and its carrier or bearer)

• quality_of (between a dependent and an independent continuant)

• functioning_of (between a process and an independent continuant)

To be added to the Relation OntologyRO IL (instance-level relations) (examples)

• lacks (between an instance and a type, e.g. this pig lacks tail)




• process has_site a = process has_participant b and b part_of a

process has_site alveolar membrane = process has_participant hemoglobin and hemoglobin part_of alvealor membrane

process:injection has_site jugular vein = process has participant (some dose of compound in the form of liquid with role drug) and (some dose of compound in the form of liquid with role drug) part_of jugular vein .

Why going for such convolution ? What is the gain here ?What is the cost of adding a primitive (when there is a valid case for it)

All this is declared at instance level but surely all instances of intrajugular injection must take place in some jugular vein(I am of course talking of canonical injection, not those performed by trainees )

disposition =def.

a realizable entity which if it ceases to exist, then its bearer is physically changed, and whose realization occurs when this bearer is in some special physical circumstances, in virtue of the bearer’s physical make-up

107

function =def.

a disposition thatis such that the physical make-up of its bearer is something the bearer possesses because it came into being, either through natural [‘positive’?] selection (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain kind.

Relation Ontology 2.0

ROhttp://obofoundry.org/ro/

is_apart_of

has_partlocated_in

contained_inadjacent_to

transformation_ofderives_frompreceded_by

has_participanthas_agent

Multiple defined relationsplus: instance_of, instance-level relations

http://obofoundry.org/ro/

Strategy

Small number of relations to be added to this listThe whole list to be incorporated into BFO 2.0Other relations

New Proposed Relations

specific dependence (between SDC and bearer)generic dependence (between GDC and bearer)concretization of (between SDC and GDC)boundary_ofrealizesis_aboutlacksprojects_onto (region)

LacksInstance-type level

p lacks U with respect to r at time t =def. there is no instance u of U such that p stands in r to u at t.

Type-type level C1 lacks C2 with respect to r =def. for all c,t, if c instance of C1 at t then c lacks C2 with respect to r at time t.

Defined relations in RO 2.0

• a inheres_in b=def. a is specifically dependent on b (a and b are continuants)

• quality_of =def. a inheres_in b and a is a quality


To be added to the Relation OntologyRO IL (instance-level relations) (examples)

• lacks (between an instance and a type, e.g. this pig lacks tail)




How to deal with shapes?

Shapes seem to be qualities of spatial regions as well as of independent continuants, but BFO says all qualities are qualities of independent continuants

The spatial subdivisions used e.g. in sampling experiments

to be dealt with as fiat parts of sites.

Clarifications needed

• Time, duration, time point• Spatial extent, distance, gap quality, spatial

coordinate: length as quality vs. length of spatial interval

switch on webex. examples of new ontologies using bfo actionable intelligence retrieval system...

Documents

process p

processquality uses

hood slide

compatibility slide

webex slide

processquality terms

plant ontology slide

quality of threeness