Rules for Good Ontology Rules of thumb: represent ideals to be approximated to in practice often with trade-offs

The ontologist’s job is not to mimic or replace or usurp science not to discover statistical or functional laws it is to establish the categories involved in given domains of reality and the relations between them via: taxonomies and: partonomies and NORMATIVE ISSUES

Naturalness A good ontology should include in its basic category scheme only those categories which are instantiated by entities in reality (it should reflect nature at its joints)

A good first test: the categories in question should be reflected in TEE (for: Technically Extended English = English as extended by the various technical vocabularies of medical and scientific disciplines)

Basic categories reflected by morphologically simple terms: dog pain foot blood hunger hot red diabetes

No theoretical artifacts A good ontology should not include in its basic category scheme artifacts of logical, mathematical or philosophical theories (such as: transfinite cardinals, instantaneous rabbit-slices, non-existent golden mountains, functions across possible worlds, and the like).

A good category scheme should not be a mish-mash of natural and philosophical taxa (keep views separate: basic views, domain-specific views, theoretical-artefactual views)

Problem of Double-Counting in realm of substances foot, arm, nose; family, patient population fiat parts and aggregates on the same level of granularity should be explicitly marked as involving double-counting

Cheese-paring principle While a good ontology should use categories which reflect only TEE, it should also have the resources to do justice to the fact that the world can be sliced in many ways, including ways not reflected by TEE

Example of cheese-paring substance action (relational process) substance agent (substance plus role) patient (substance plus role) linked by mutual dependence

Always ask the question when is this proposition true? when does this entity exist? Two sorts of answers: at t (for SNAP entities) over time interval t ------------------------------------------- looking down on the order of time from the outside (for SPAN entities)

John lived in Kansas for 25 years when is this proposition true? when does the entity which makes it true exist?

Summing within SPAN and summing within SNAP are both acceptable John plus his role: Major John John plus his quality: hungry John The rest of the World Cup

Confess Double-Counting in realm of substances ear, nose, throat, arm family, clinical trial population fiat parts and aggregates on the same level of granularity should be explicitly marked as involving double-counting

SNAPshot ONTOLOGY

Confess Double-Counting in realm of processes beginning, end, first phase series of clinical trials, World Cup fiat parts and aggregates on the same level of granularity should be explicitly marked as involving double-counting

SPAN ONTOLOGY

SPAM ONTOLOGY

No Crossing Categories If C is a major category then an instance of C is always an instance of C whichever VIEW of C we take If C is a major category then an instance of C is always an instance of C whichever granularity we take

If x instances a category under any determinable, then it instances this category under all determinables John’s temperature is a SNAP entity The value of John’s temperature is 62 degrees (The value is changing all the time)

No ‘others’ All category labels should be positive

Respect Granularity spatial region substance quality parts of spatial regions are always spatial regions

Respect Granularity parts of substances are always substances spatial region substance quality parts of substances are always substances

Respect Granularity parts of qualities are always qualities spatial region substance quality parts of qualities are always qualities

Relations crossing the SNAP/SPAN border are not part-relations substance John John’s life sustaining in existence physiological processes

Rule for Crossing Granularities For x and y instances of basic categories If x is part of y, then x is of the same category as y (if x is substantial, then y is substantial) (if x is a quality, then y is a quality) (if x is a process, then y is process) (if x is a spatial region, then y is a spatial region) (if x is a spatial boundary, then y is a spatial boundary)

Rule for Crossing Granularities For x an instances of a basic category, x is always an instance of that category in every view or from every perspective (if x is substantial, then y is substantial) (if x is a quality, then y is a quality) (if x is a process, then y is process) (if x is a spatial region, then y is a spatial region) (if x is a spatial boundary, then y is a spatial boundary)

How to treat cross-categorial structures? which ontology do they belong to? How to treat higher-order attributions Universals have instances Universal A depends for its instantiation on the instantiation of universal B Roughly: these are meta-assertions (that they have special truthmakers of their own is an illusion of language)

Universals have instances is not an extra assertion rather it is something which shows itself via the syntax of a good ontological language (cf. Wittgenstein’s Tractatus)

Rules for good syntax in formalizing ontology entities of the same category should be represented in the language of ontology by means of symbols of the same type some symbols will not represent entities at all (⌐)

Tools are just tools If specific logical or mathematical or conceptual tools are needed, for example for semantic purposes, then these should be clearly recognized as tools and thus not be seen as having consequences for basic ontology. (Possible worlds …)

Trade off between cheese-paring and sake-mongering We say “For Pierre’s sake …, for Heinrich’s sake …” But There are no sakes in this room This is so however we slice the cheese

Problems arise for partial ontologies only if they come along with the claim to be complete (reductionists are nearly always correct in what they hold to exist -- but incorrect when they hold that nothing else exists)

Even reductionists are right as far as they go (even their peculiar maps of reality, as consisting of processes, or of spacetime worms, are transparent to reality) The only problem with such maps is that they are not complete

Rules Governing Taxonomies Every (coherent, tested) ontology for a given domain at a given level of granularity should be representable as a tree in the mathematical sense

Natural scientific classifications are principled

Principled classifications satisfy the no-diamonds rule: A E F G B C D H Good Bad

Counterexample in the realm of artifacts ? urban structures buildings car parks multi-story car-parks

Eliminating counter-examples urban structures buildings parking areas multi-story car-parks “Ontoclean”

No ‘others’ A good taxonomy should contain no taxons labeled ‘others’

Representations A representation is never identical with the object which it is a representation of

Fallibilism Ontologists are seeking principles that are true of reality, but this does not mean that they have special powers for discovering the truth. Ontology is, like physics or chemistry, part of a piecemeal, on-going process of exploration, hypothesis-formation, testing and revision.

Fallibilism Ontological claims advanced as true today may well be rejected tomorrow in light of further discoveries or new and better arguments Ontology is like a small window on reality which, in fits and starts, gets bigger and more refined as we proceed

Adequatism A good ontology should be adequatist: its taxonomies and partonomies should comprehend the entities in reality at all levels of aggregation, from the microphysical to the cosmological, and including also the middle world (the mesocosmos) of human-scale entities in between. Adequatists: Aristotle, Ingarden, Chisholm

Nothing in life is certain except death and taxes Fictionalism is always wrong Either an entity exists, or it does not exist Either an entity type exists, or it does not exist

Quine is wrong There is no entity without identity We have no identity criteria for people taxes plans diseases

A good category scheme should not be a mish-mash of individuals and universals Universals are not extra types of entities Types of entities ARE universals Boxes in category diagrams represent universals The instances are what the boxes contain

SNAPshot ONTOLOGY

SNAPshot ONTOLOGY

Tree structure Higher nodes within the tree represent more general universals, lower nodes represent less general universals.

Branches connecting nodes represent the relations of inclusion of a lower category in a higher: man is included in mammal mammal is included in animal and so on.

An Ontology (Taxonomy) should be Principled Suppose that in counting off the cars passing beneath you on the highway, your checklist includes one box labeled red cars and another box labeled Chevrolets. The resultant inventory will be unprincipled; you will almost certainly be guilty of counting some cars twice. Unprincipled = the two modes of classification belong to two distinct classifications made for two distinct purposes

Tree structure implies: A good ontology should satisfy certain well-formedness rules

Well-formedness rule Each tree is unified in the sense that it has a single top-most or maximal node, representing the maximum category comprehending all the categories represented by the nodes lower down the tree

Why trees? A taxonomy (ontology) with two maximal nodes would be in need of completion by some extra, higher-level node representing the union of these two maxima. Otherwise it would not be one taxonomy at all, but rather two separate taxonomies (e.g. SNAP and SPAN)

‘Entity’ = label for the highest-level category of ontology. Everything which exists is an entity Alternative top-level terms favored by different ontologists: ‘thing,’ ‘object,’ ‘item,’ ‘element,’ ‘existent.’ Use of ‘entity’ is dangerous (see Frege)

Basis in minimal nodes (leaves) Leaves of the tree represent the lowest categories (infima species) = categories in which no sub-categories are included. ‘Has a basis in minimal nodes’ = the categories at the lowest level of the tree exhaust the maximum category

Exhaustiveness The chemical classification of the noble gases is exhausted by: Helium, Neon, Argon, Krypton, Xenon and Radon. …normally very hard to achieve

For a taxonomy with a basis in minimal nodes every intermediate node in the tree is identifiable as a combination of minimal nodes.

More well-formedness principles There should be a finite number of steps between the maximal category and each minimal category. There should be the same number of steps between the topmost node of the tree and all its lowest-level nodes.

Well-Formedness The taxonomy as a whole is thereby divided into homogeneous levels, each level represents a jointly exhaustive and pairwise disjoint partition of the corresponding domain of categories on the side of objects in the world.

Which rules satisfied by BFO?

Types of Formal Relation Intracategorial Mereological (part) Topological (connected, temporally precedes) Dependency Intercategorial Inherence (quality of) Location Participation (agent)

Relations can also hold across granularities Microbial processes in the human body sustain the human body in existence Neurophysiological processes in the brain cause and provide the substratum for cognitive processes

Trees of universals (species-genus hierarchies) capture the way the world is (realism) – they depict the invariant structures/patterns/regularities in reality

or: species-genus hierarchies may capture the way the world should be – by depicting the structures/patterns/regularities in the realm of standards, ideal cases, recipes (a hierarchy of medical therapies)

Anglocentric (Aristotelian) Realism The general terms of TEE (or many of them), including terms like ‘Coca Cola’, correspond to universals (species and genera, invariant patterns) in reality

Two distinct realms of being universals particulars general individual types tokens species instances essence fact

species, genera instances substance organism animal mammal cat frog siamese frog instances

common nouns proper names substance organism animal mammal cat pekinese mammal cat organism substance animal common nouns proper names Common nouns

types substance organism animal cat mammal siamese frog tokens

Accidents: Species and instances substance animal mammal human Irishman Accidents: Species and instances types this individual token man tokens

There are universals both among substances (man, mammal) and among qualities (hot, red) and among processes (run, movement) There are universals also among spatial regions (triangle, room, cockpit) and among spatio-temporal regions (orbit)

Substance universals pertain to what a thing is at all times at which it exists: cow man rock planet VW Golf

red hot suntanned spinning Quality universals pertain to how a thing is at some time at which it exists: red hot suntanned spinning Clintophobic Eurosceptic

Process universals reflect invariants in the spatiotemporal world taken as an atemporal whole football match course of disease exercise of function (course of) therapy

Processes and qualities, too, instantiate genera and species Thus process and quality universals form trees

Accidents: Species and instances quality color red scarlet R232, G54, B24 this individual accident of redness (this token redness – here, now)

- IS-WE-STATE-OF This is a link which relates a STATE of a PROPERTY to the element where this STATE inherence. Example: TEMPERATURE (is the property)                HIGH TEMPERATURE (is a state of the property TEMPERATURE)                HOT WATER   [HAS-WE-STATE]   HIGH TEMPERATURE (But at the level of the instance the reverse link can also be applied "high temperature 1" IS-WE-STATE-OF "hot water 1”)

  HAS-EXISTENT This link relates a process of existence to the entity that exists. Example: MEDICAL HISTORY (is considered an EXISTANCE IN THE PAST) and HAS-EXISTENT a HEALTHCARE PHENOMENOM So "history of diabetes" is (for us) an "existence of diabetes in the past" and "diabetes" is the entity which existed.

-         HAS-SAYING This is a link which relates a COMMUNICATIVE PROCESS (mental process) to the element which is communicated. Ex: MENTION OF ABSCESS [HAS-SAYING] ABSCESS  -        HAS- SENSOR Relates an INTERNAL MENTAL PROCESS ( thinking, observation...) to the person/animal who performs this action Ex: (at instance level) "John recognizes Mary." becomes "recognizing process 1" HAS-SENSOR "John 1"

-  HAS-PHENOMENON Also for  INTERNAL MENTAL PROCESS, but phenomenon is the entity which has been "perceived". (Mary in the example above) Ex: DETERMINATION OF PROGNOSIS [HAS-PHENOMENON] PROGNOSIS

-        HAS-SYSTEMIC-MEDIUM Relates a MATERIAL PROCESS to an entity which participates is the process in an active and passive way at the same time EX: ARM INFLAMMATION [HAS-SYSTEMIC-MEDIUM] ARM or CHANGE IN WEIGHT [HAS-SYSTEMIC-MEDIUM] WEIGHT

-       HAS-CEN-OCCURENCE-DURING Temporal link that indicates the event in question has happened (begun and ended) during the reference event. Ex: INFARCT DURING SURGERY [HAS-CEN-OCCURENCE-DURING] SURGICAL DOING

Perspectivalism Perspectivalism Different partitions may represent cuts through the same reality which are skew to each other

Ontology like cartography must work with maps at different scales and with maps picking out different dimensions of invariants

Varieties of granular partitions Partonomies: inventories of the parts of individual entities Maps: partonomies of space Taxonomies: inventories of the universals covering a given domain of reality