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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

FMA: BFO under the hood

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

BFO issues process qualities rate is a determinate specific rate is a determinable differences are clinically significant only defined down to a specific level of granularity

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

 HP:0001720 ! tachycardia Process: GO:0060048 cardiac muscle contraction Quality: 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, but it 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 of onehundredandtwo-bpm-ness on Thursday. People could talk like that if they wanted, but it 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 temperature blood pressure mass ... are continuants they exist through time while undergoing changes

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 same

A Chart representing how John’s temperature changes

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 same hence only independent continuants may have qualities

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

temperature John’s temperature 37ºC 37.1ºC 37.2ºC 37.3ºC 37.4ºC 37.5ºC instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John’s temperature

a quality is something which can change while its bearer remains one and the same hence only independent continuants may have qualities for suppose q were a quality of a process then 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

temperature course John’s temperature increasing temperature course constant temperature course decreasing temperature course instantiates at t1 instantiates at t4 instantiates at t5 John’s temperature

temperature John’s temperature information artefact unit of measurement 37.2ºC temperature measurement record measures Compare DOLCE version at http://forge.morfeo-project.org/wiki_en/index.php/Image:Quality-framework.png ºC instantiates instantiates at t3 uses John’s temperature “37.2ºC at t3” about

“John has temperature 37.2ºC at t3” information artefact temperature unit of measurement measures 37.2ºC measurement record instantiates at t3 Compare DOLCE version at http://forge.morfeo-project.org/wiki_en/index.php/Image:Quality-framework.png ºC John’s temperature instantiates uses inheres_in “John has temperature 37.2ºC at t3” John about

A Chart representing how John’s temperature changes

BFO: The Very Top continuant occurrent quality temperature independent

Blinding Flash of the Obvious independent continuant dependent continuant quality organism temperature types instances John John’s temperature

Blinding Flash of the Obvious independent continuant dependent continuant quality organism temperature types instances John John’s temperature

temperature John’s temperature 37ºC 37.1ºC 37.2ºC 37.3ºC 37.4ºC 37.5ºC instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John’s temperature

human John embryo fetus neonate infant child adult instantiates at t1

in nature, no sharp boundaries here human in nature, no sharp boundaries here embryo fetus neonate infant child adult instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John

portion of liquid water Phase transitions portion of water portion of ice portion of liquid water portion of gas instantiates at t1 instantiates at t2 instantiates at t3 this portion of H20

in nature, no sharp boundaries here temperature in nature, no sharp boundaries here in nature, no sharp boundaries here 37ºC 37.1ºC 37.2ºC 37.3ºC 37.4ºC 37.5ºC instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John’s temperature

http://books. google. co. uk/books http://books.google.co.uk/books?id=EqEa2hf7U2AC&pg=PA459&lpg=PA459&dq=a+heart+disease+that+comes+in+successive+phases&source=bl&ots=1pbSgZIa8u&sig=Zp0OwNJjeniJi-KbMOjQ5_v3w-o&hl=en&ei=vPx7S566EIv60wSg9eXYBQ&sa=X&oi=book_result&ct=result&resnum=4&ved=0CBMQ6AEwAw#v=snippet&q=late&f=false

heart function: to pump function with healthy heart function with early lesions and small fibrous plaques function with asymptomatic disease, silent infarction function with surface disruption of plaque function with unstable angina function with stable angina instantiates at t1 instantiates at t2 instantiates at t3 instantiates at t4 instantiates at t5 instantiates at t6 John’s heart function: to pump

physics plus control of the physics what the biological function does is to regulate the physics parameter: rate of cardiac contraction (with range of normality, and abnormality) mathematical function: to pump = mapping between input- and output-pressure the parameters are fixed dispositions are changing the parameter values,

heart function: to pump pumping function of heart after fatality instantiates at t7 John’s heart function: to pump

heart function: to pump material entity material entity pumping function of healthy heart portion of blood portion of blood instantiates at t1 instantiates at t1 instantiates at t1 this portion of deoxygenated blood 1 John’s heart function: to pump this portion of oxygenated blood has input has output

heart function: to pump material entity pumping function of healthy heart clot instantiates at t1 instantiates at t1 instantiates at t1 this clot 1 John’s heart function: to pump this clot has input has output

heart function: to pump material entity quality pumping function of healthy heart oxygenated portion of blood concentration of oxygen instantiates at t1 instantiates at t1 instantiates at t1 John’s heart function: to pump this portion of blood this concentration has output need to get time right

Continuant Occurrent Independent Continuant Specifically Dependent Continuant Generically Dependent Continuant Process Quality 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)

types instances quality temperature independent continuant dependent organism temperature types instances John John’s temperature

course of temperature changes independent continuant dependent continuant occurrent process quality organism course of temperature changes temperature John John’s temperature John’s temperature history

process quality life of an organism temperature independent continuant occurrent process quality organism life of an organism temperature John John’s temperature John’s life

quality process information artefact temperature measurement assay measurement datum 37.2ºC temperature instantiates instantiates instantiates at t3 John’s temperature Compare DOLCE version at http://forge.morfeo-project.org/wiki_en/index.php/Image:Quality-framework.png about temperature assay at t3 John “37.2ºC at t3” has_input has output

BFO: The Very Top continuant independent continuant dependent

dependent continuant realizable quality dependent continuant role (optional) disposition (has physical basis) with thanks to Robert Arp

(a disposition designed dependent continuant quality realizable role (optional) disposition (aka ‘ability’) with thanks to Robert Arp 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

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

Roles often form systems of mutual dependence. husband / wife Roles often form systems of mutual dependence husband / wife first in queue / last in queue doctor / patient host / pathogen

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

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

process of drug adminstration drug role independent continuant dependent continuant occurrent process role portion of chemical compound process of drug adminstration drug role this portion of aspirin role of this portion of aspirin John’s taking this portion of aspirin

process of drug adminstration drug role independent continuant dependent continuant occurrent role process inheres_in portion of chemical compound process of drug adminstration drug role realized_in this portion of aspirin role of this portion of aspirin John’s taking this portion of aspirin

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 core for 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

Organism-Level Process CONTINUANT OCCURRENT INDEPENDENT DEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Organism-Level Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function Cellular Process MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function Molecular Process RELATION TO TIME GRANULARITY initial OBO Foundry coverage, ontologies automatically semantically coupled

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

OBO Foundry Modular Organization Basic Formal Ontology (BFO) top level mid-level domain level Information Artifact Ontology (IAO) Ontology for Biomedical Investigations (OBI) Spatial Ontology (BSPO) Anatomy Ontology (FMA*, CARO) Environment Ontology (EnvO) Infectious Disease Ontology (IDO*) Biological Process Ontology (GO*) Cell Ontology (CL)* Cellular Component (FMA*, GO*) Phenotypic Quality Ontology (PaTO) Subcellular Anatomy Ontology (SAO) Sequence Ontology (SO*) Molecular Function (GO*) Protein Ontology (PRO*) * = dedicated NIH funding OBO Foundry Modular Organization

Relations instance-instance (primitives allow definitions) instance-type type-type RO 2.0 type-type – All-some rule holds add 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 of has 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 continuant A 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

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

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

Hence the All-Some rule Or analogous rules for n-ary relations Only something that holds of all As will be an assertion that holds of the type A Hence the All-Some rule Or analogous rules for n-ary relations (where n > 2)

Definitions of type-level relations presuppose underlying instance-level relations A is_a B presupposes instance_of All instances of A are instances of B A part_of B presupposes instance-level-part-of Every 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 possible If 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

Rules for including relations in RO 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

Rules for including relations in RO 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

Thus for example Instead of: use just the relations: results_in, is_a results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of use just the relations: results_in, is_a and the types: reception_of_stimulus, conversion_into_molecular_signal

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

Consequences of including only all-some relations in RO All relations will be evaluable as Transitive Symmetric Reflexive Anti-Symmetric All relations will support reasoning is_somehow_related_to is the worst kind of relation to create

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

Lacks Instance-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 Ontology RO 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 Ontology RO 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 Ontology RO IL (instance-level relations) (examples) lacks (between an instance and a type, e.g. this pig lacks tail) 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)

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

function =def. a disposition that is 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

RO http://obofoundry.org/ro/ is_a part_of has_part located_in contained_in adjacent_to transformation_of derives_from preceded_by has_participant has_agent Multiple defined relations plus: instance_of, instance-level relations

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

New Proposed Relations specific dependence (between SDC and bearer) generic dependence (between GDC and bearer) concretization of (between SDC and GDC) boundary_of realizes is_about lacks projects_onto (region)

Lacks Instance-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 functioning_of (between a process and an independent continuant)

To be added to the Relation Ontology RO IL (instance-level relations) (examples) lacks (between an instance and a type, e.g. this pig lacks tail) 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)

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