Werner CEUSTERS, MD

Guest Lecture for PHI 531 Problems in Ontology, class #23893 Referent Tracking:focus on particularsSeptember 10, 2012: 4-6PM – 141 Park Hall, UB North Campus, Buffalo NY Werner CEUSTERS, MD Center of Excellence in Bioinformatics and Life Sciences, Ontology Research Group and Department of Psychiatry University at Buffalo, NY, USA http://www.org.buffalo.edu/RTU

A digital copy of the world Ultimate goal of Referent Tracking

Two major representational components formulae representing ‘laws of nature’ symbols denoting what these ‘laws’ govern

Representations mimicking reality  The Time Lords’ Matrix on the planet Gallifrey (Dr. Who, 1976)

Requirements for this digital copy • R1: A faithful representation of reality • R2 … of everything that is digitally registered, what is generic scientific theories what is specific what individual entities exist and how they relate • R3: … throughout reality’s entire history, • R4 … which is computable in order to … … allow queries over the world’s past and present, … make predictions, … fill in gaps, … identify mistakes, ...

In fact … the ultimate crystal ball

Major problem: the ‘binding’ wall How to do it right ? gives you a cartoon of the world

Requirements for a digital copy of the world • R1: A faithful representation of reality • R2 … of everything that is digitally registered, what is generic scientific theories what is specific what individual entities exist and how they relate • R3: … throughout reality’s entire history, • R4 … which is computable in order to … … allow queries over the world’s past and present, … make predictions, … fill in gaps, … identify mistakes, ...

R1: A faithful representation of reality … … recognizes three levels: • The (first order) reality which exists ‘as it is’ prior to a cognitive agent’s perception thereof; • the cognitive representations of this reality embodied in observations and interpretations on the part of cognitive agents; • the publicly accessible concretizations constructed through cognitive insights as artifacts representing first order reality of which ontologies, terminologies and data repositories are examples. Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

Three levels of reality • The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

R Reality exist before any observation

R And also most structures in reality are there in advance. Reality exist before any observation • Humans had a brain well before they knew they had one. • Trees were green before humans started to use the word “green”.

Three levels of reality • The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; • Cognitive agents build up ‘in their minds’ cognitive representations of the world; Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

The ontology author acknowledges the existence of some Portion Of Reality (POR) B R

B Some portions of reality escape his attention. R

Three levels of reality • The world exists ‘as it is’ prior to a cognitive agent’s perception thereof; • Cognitive agents build up ‘in their minds’ cognitive representations of the world; • To make these representations publicly accessible in some enduring fashion, they create representational artifacts that are fixed in some medium. Smith B, Kusnierczyk W, Schober D, Ceusters W. Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain. Proceedings of KR-MED 2006, November 8, 2006, Baltimore MD, USA

He represents only what he considers relevant B RU1B1 • Both RU1B1 and RU1O1 are representational units referring to #1; • RU1O1 is NOT a representation of RU1B1; • RU1O1 is created through concretization of RU1B1 in some medium. RU1O1 O #1 R

B2 B1 O2 O1 R Another author might do it differently A methodology and tools are needed to do it in reproducible ways

Faithfulness through the right philosophy • Granular Partition Theory

2. Basic Formal Ontology (BFO) • An ontology which is • Realist: • Fallibilist: • Perspectivalist: • Adequatist: • There is only one reality and its constituents exist independently of our (linguistic, conceptual, theoretical, cultural) representations thereof, • theories and classifications can be subject to revision, • there exists a plurality of alternative, equally legitimate perspectives on that one reality these alternative views are not reducible to any single basic view.

Get down that wall Basic Formal Ontology: teaches us how to build an adequate grid. Granular Partition Theory: relates the copy to reality.

The BFO view of the world • The world consists of • entities that are • Either particulars or universals; • Either occurrents or continuants; • Either dependent or independent; and, • relationships between these entities of the form • <particular , universal> e.g. is-instance-of, • <particular , particular> e.g. is-part-of • <universal , universal> e.g. isa (is-subtype-of)

universals Ontology human being vertebrate air plane airport instance of… Enola Gay Barry Smith JFK George Bush particulars Inventory Particulars versus Universals

t meeting flying occurrents has-participant at time … Enola Gay Barry Smith JFK George Bush Continuants versus Occurents continuants

Instantiation for continuants universals child adult philosopher president t Barry Smith Instance-of at t George Bush Continuant particulars

Transformation-of isa Continuants undergo changes while keeping identity child adult president t Instance-at t Barry Smith George Bush particulars

General principle about relationships All universal level relationships are defined on the basis of particular level relationships Smith B, Ceusters W, Klagges B, Koehler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector A, Rosse C. Relations in biomedical ontologies, Genome Biology 2005, 6:R46.

Is_a is defined over instance-of For continuants • C is_a C1 = [definition] for allc, t, if c instance_of C at t then c instance_of C1 at t. For occurrents • P is_a P1 = [definition] for allp, if p instance_of P then p instance_of P1.

Primitive instance-level relationships (RO) • c part_of c1 at t- a primitive relation between two continuant instances and a time at which the one is part of the other • p part_of p1, r part_of r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other) • c located_in r at t- a primitive relation between a continuant instance, a spatial region which it occupies, and a time • r adjacent_to r1 - a primitive relation of proximity between two disjoint continuants • t earlier t1 - a primitive relation between two times • c derives_from c1 - a primitive relation involving two distinct material continuants c and c1 • p has_participant c at t- a primitive relation between a process, a continuant, and a time • p has_agent c at t- a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process Smith B, Ceusters W, Klagges B, Koehler J, Kumar A, Lomax J, Mungall C, Neuhaus F, Rector A, Rosse C. Relations in biomedical ontologies, Genome Biology 2005, 6:R46.

Ontology Instance-of What is specific Referent Tracking A division of labor What is generic

Referent Tracking System Components • Referent Tracking Software Manipulation of statements about facts and beliefs • Referent Tracking Datastore: • IUI repository A collection of globally unique singular identifiers denoting particulars • Referent Tracking Database A collection of facts and beliefs about the particulars denoted in the IUI repository Manzoor S, Ceusters W, Rudnicki R. Implementation of a Referent Tracking System. International Journal of Healthcare Information Systems and Informatics 2007;2(4):41-58.

The reality: a digital copy of part of the world Applying the grid does not give a distorted representation of reality, but only an incomplete representation !!!

Key issue: keeping track of what the bits denote

Key issue: keeping track of what the bits denote • Images are no good: • Are too complex particulars in their own right that stand in another sort of relation to the part of reality that they depict. • Terms / names ? Middle-East Madagascar Katrina

Names are inadequate representational units • “JFK” “Enola Gay” • “Barry Smith” “George Bush”

denotes denotes denotes Relationship managed in the RTS IUI: Instance Unique Identifiers 5241 89023 109427

The IUI-repository • 17821 denotes Earth • 200896 Madagascar • 70567 Antananarivo • 9576 Hotel Sunny • 509579 the valiha-performance on August 7, 2006 in Hotel Sunny in Antananarivo • …

Key mechanism: IUI assignment • = an act carried out by the first ‘cognitive agent’ feeling the need to acknowledge the existence of a particular it has information about by labellingit with a universally unique singular identifier. • ‘cognitive agent’: • A person; • An organisation; • A device or software agent, e.g. • Bank note printer, • Image analysis software.

Criteria for IUI assignment (1) • The particular’s existence must be determined: • Easy for persons in front of you, tools, ... • Easy for ‘planned acts’: they do not exist before the plan is executed ! • Only the plan exists and possibly the statements made about the future execution of the plan • More difficult: a subject’s intensions, emotions • But the statements observers make about them do exist ! • However: • no need to know what the particular exactly is, i.e. which universal it instantiates • No need to be able to point to it precisely • A member of a specific organization • But: this is not a matter of choice, not ‘any’ out of ...

Criteria for IUI assignment (2) • The particular’s existence ‘may not already have been determined as the existence of something else’: • Morning star and evening star / Himalaya •  2 observers not knowing they observed the same thing • May not have already been assigned a IUI. • It must be relevant to do so: • Personal decision, (scientific) community guideline, ... • Possibilities offered by the annotation system • If a IUI has been assigned by somebody, everybody else making statements about the particular should use it

Assertion of assignments • IUI assignment is an act of which the execution has to be asserted in the IUI-repository: • <da, Ai, td> • da IUI of the registering agent • Ai the assertion of the assignment <pa, pp, tap> • pa IUI of the author of the assertion • pp IUI of the particular • tap time of the assignment • td time of registering Ai in the IUI-repository • Neither td or tap give any information about when #pp started to exist ! That might be asserted in statements providing information about #pp .

Relationships between particulars taken from a realism-based relation ontology Instantiation of a universal Annotation using terms from a non-realist terminology ‘Negative findings’ such as absences, missing parts, preventions, … Names for a particular Elementary RTS tuple types

Without ‘names’: pseudonymized database !

Management of the Data Store • Adequate safety and security provisions • Access authorisation, control, read/write, ... • Pseudonymisation • Deletionless but facilities for correcting mistakes. • Registration of assertion ASAP after IUI assignment • (virtual, e.g. LSID) central management with adequate search facilities.

Dealing with mistakes • This change involves RTS entries becoming assigned IUIs of their own which in the restructured D-template is symbolized by IUITi. • Di = <IUId, IUITi, t, E, C, S>. • IUId: the IUI of the entity annotating IUITi by means of the Di entry, • E: either the symbol ‘I’ (for insertion) or any of the error type symbols, • C: a symbol for the applicable reason for change • t: the time the tuple denoted by IUITi is inserted or ‘retired’, • S: a list of IUIs denoting the tuples, if any, that replace the retired one.

Eternal memory

Accept that everything may change: • changes in the underlying reality: • Particulars come, change and go • changes in our (scientific) understanding: • The planet Vulcan does not exist • reassessments of what is considered to be relevant for inclusion (notion of purpose). • encoding mistakes introduced during data entry or ontology development.

t U1 U2 Reality p3 Reality versus beliefs, both in evolution

Werner CEUSTERS, MD