Principles of Referent Tracking BMI 714 Course 24684

Principles of Referent Tracking BMI 714 Course 24684 – Spring 2018 Class 4 – February 20, 2018 Building Referent Tracking Systems Werner CEUSTERS

Essentials of Referent Tracking • • • Deciding what particulars should receive a universally unique identifier (IUI); Finding out whether or not a particular has already been assigned a IUI (each particular should receive maximally one IUI); Generating an IUI; Using IUIs in information systems, i. e. issues concerning the syntax and semantics of statements containing IUIs; Determining the truth values of statements in which IUIs are used; Correcting errors in the assignment of IUIs and in other assertions in tuples. .

Referent Tracking System Components Referent Tracking Software: Manipulation of assertions about particulars. Referent Tracking Datastore: • IUI repository: A collection of: • A-tuples, each one representing the assignment of a globally unique singular identifier to some particular. • N-tuples, each one providing a name for a particular • Referent Tracking Database: A collection of assertions in the form of tuples of various sorts about the particulars denoted through A-tuples 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.

Referent Tracking System Environment

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 labeling it with a UUID. ‘cognitive agent’: • A person; • An organization; • A device or software agent, e. g. • Bank note printer, • Image analysis software.

Assertion of assignments • IUI assignment is an act of which the execution has to be asserted in the IUI-repository: • A- tuple: • < IUIp, IUIa, tap> the assertion of the assignment • IUIp IUI of the particular • IUIa IUI of the author of the assertion • tap time of the assignment • tap does not give any information about when # IUIp started to exist ! That might be asserted in statements providing information about # IUIp.

Management of the IUI-repository • Adequate safety and security provisions are required for accessing N-tuples. • 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.

D-tuples: Validity and availability of information • < IUId, IUIT, td, E, C, S >, where: • IUId: is the IUI of the entity annotating IUIT by means of this D-tuple, • IUIT is the IUI of the tuple about which the D-tuple contains information, • E is either the symbol ‘P+1’ (for insertion) or any of the error type symbols as discussed further, • C is a symbol for the applicable reason for change as discussed further, • td is the time the tuple denoted by IUIT is inserted or ‘retired’, and • S is a list of IUIs denoting the tuples, if any, that replace the retired one. • A D-tuple is inserted: (1) to resolve mistakes in RTS, and (2) whenever a new tuple other than a D-tuple is inserted in the RTS. [1] Ceusters W. Dealing with Mistakes in a Referent Tracking System. In: Hornsby KS (eds. ) Proceedings of Ontology for the Intelligence Community 2007 (OIC-2007), Columbia MA, 28 -29 November 2007; : 5 -8.

Error types for representations in RTS reality configuration (1) OE (2) OR (3) representation authors' belief encoding BE BR IE TR (4) (5) (6) (7) ME (8) Reality: OE: Objective existence OR: Objective relevance Representation: BE: Author’s belief in existence BR: Author’s belief in relevance Seppãlã S, Smith B, Ceusters W. Applying the realism-based ontology versioning method for tracking changes in the Basic Formal Ontology in Information Systems. Proceedings of the Eight International Conference (FOIS 9 2014), Amsterdam: IOS Press, 2014; : 227 -240. IE: Author’s intended encoding TR: Type of reference ME: Magnitude of error

reality configuration 10 (1) P+1 A+2 A+3 A+4 P-1 P-2 P-3 P-4 P-5 P-6 P-7 P-8 P-9 P-10 P-11 P-12 A-1 A-2 A-3 A-4 A-5 OE (2) OR (3) representation authors' belief encoding BE BR IE TR (4) (5) (6) (7) Configuration types P: present in the ontology P+: justifiably present P–: unjustifiably present A: absent from the ontology A+: justifiably absent A–: unjustifiably absent ME (8)

reality configuration 11 (1) P+1 A+2 A+3 A+4 P-1 P-2 P-3 P-4 P-5 P-6 P-7 P-8 P-9 P-10 P-11 P-12 A-1 A-2 A-3 A-4 A-5 OE (2) OR (3) representation authors' belief encoding BE BR IE TR (4) (5) (6) (7) Configuration types 1+4+12+5=22 possible configurations based on (mis)matches between reality, beliefs, and encodings ME (8)

reality configuration 12 (1) P+1 A+2 A+3 A+4 P-1 P-2 P-3 P-4 P-5 P-6 P-7 P-8 P-9 P-10 P-11 P-12 A-1 A-2 A-3 A-4 A-5 OE (2) Y N Y Y N N Y Y Y Y N Y Y OR (3) Y na N N na na Y Y N N N Y na Y Y na N Y representation authors' belief encoding ME BE BR IE TR (4) (5) (6) (7) (8) Y Y Y R+ 0 N na na na 0 Y N OE/BEna 0 value pairsna NC na na na 0 Y/Y: correct assertion of the NC na na na 0 of a POR; ¬R Y Y existence Y 3 Y N Y/N: Y lack of awareness of a¬RPOR, 4 Y Y reflecting N an assertion. R– error; 5 Y Y N ¬R 1 N/N: correct assertion that some Y Y N R 2 does not. R+exist; 1 Y Y putative POR Y Y N ¬R 2 N/Y: Y the false belief that some Y Y N 3 putative POR exists; R– Y Y Y R++ 1 Y/NC: that some Y Y not considering Y R++ 2 Y Y POR exists; Y Ra 1 Y Y not considering Y Ra 4 N/NC: that some Y N na na 1 putative POR does not exist. N na na na 1 Y N na na 1 N na na na 1 NC na na na 1

representation authors' belief encoding configuration OE OR BE BR IE TR (1) (2) (3) (4) (5) (6) (7) P+1 Y Y Y R+ 2 A+1 N na na na A+2 Y N na na A+3 N NC na na na 1 Y A+4 N na NC na na na P-1 N na Y Y Y ¬R P-2 N na Y 3 Y N ¬R P-3 N na Y Y N R– P-4 Y Y N ¬R P-5 Y Y N RP-6 Y N Y Y Y R+ P-7 Y N Y Y N ¬R ‘na’ = not applicable P-8 Y N Y Y N R– 1. P-9 If there is no POR of a specific sort, relevance is not applicable. Y Y Y R++ 2. P-10 If an author does relevance is not Y not believe. Nin some POR, Y believed Y Y applicable. R++ 3. P-11 If an author did. Ynot consider. Y(‘nc’) existence of some. YPOR, believed is Y Y relevance Ra P-12 na Y Y Y Ra not applicable. N Y Y negative or. Y not applicable, N encoding nais not applicable. na 4. A-1 If believed relevance is either A-2 Y Y N na na na A-3 N na Y N na na A-4 Y N N na na na 13 A-5 Y Y NC na na na reality ME (8) 4 00 0 3 4 5 1 2 3 1 2 1 4 1 1 1

configuration 14 (1) P+1 A+2 A+3 A+4 P-1 P-2 P-3 P-4 P-5 P-6 P-7 P-8 P-9 P-10 P-11 P-12 A-1 A-2 A-3 A-4 A-5 representation authors' belief encoding OE OR BE BR IE TR (2) (3) (4) (5) (6) (7) Y Y Y R+ N na na na Y N NC na na na N Modes of nareference: NC na na na N na Y Y Y ¬R R+ na: faithful reference to Ycorrect referent N Y N ¬R N Y exist Y N R– ¬R na: no referent Y Y N ¬R R– Y: reference. Yto wrong referent Y Y N RY N Y Y Y R+ R++ : redundant reference Y N Y Y N ¬R Y Y reference. Y N R– Ra N: ambiguous Y Y Y R++ Y N Y Y Y R++ Y Y Y Ra N na Y Y Y Ra Y Y Y N na na na N na Y N na na Y N N na na na Y Y NC na na na reality ME (8) 0 0 0 3 4 5 1 2 3 1 2 1 4 1 1 1

reality configuration 15 (1) P+1 A+2 A+3 A+4 P-1 P-2 P-3 P-4 P-5 P-6 P-7 P-8 P-9 P-10 P-11 P-12 A-1 A-2 A-3 A-4 A-5 OE (2) Y N Y Y N N Y Y Y Y N Y Y OR (3) Y na N N na na Y Y N N N Y na Y Y na N Y representation authors' belief encoding BE BR IE TR (4) (5) (6) (7) Y Y Y R+ N na na na Y N na na NC na na na Y Y Y ¬R Y Y N R– Y Y N ¬R Y Y N RY Y Y R+ Y Y N ¬R Y Y N R– Y Y Y R++ Y Y Y Ra Y N na na na Y N na na Magnitude ofna error NC na na na ME (8) 0 0 0 3 4 5 1 2 3 1 2 1 4 1 1 1

Pto. P statements - particular to particular • ordered sextuples of the form Ri = <IUIa, ta, r, o, P, tr> IUIa is the IUI of the author of the statement, ta a reference to the time when the statement is made, r the particulars referred to in P, o a reference to the ontology from which r is taken, P ordered an IUIs referring of listparticulars the to between which r obtains, and, tr a reference to the time at which the relationship obtains. • P contains as much IUIs as required by the arity of r. In most cases, P will be an ordered pair such that r obtains between the particular represented by the first IUI and the one referred to by the second IUI. • As with A statements, these statements must also be accompanied by a meta -statement (D-tuple) capturing when the sextuple became available to the Ceusters W, Manzoor S. How to track absolutely everything? In: Obrst L, Janssen T, Ceusters W (eds. ) referent tracking system. Ontologies and Semantic Technologies for the Intelligence Community. Frontiers in Artificial Intelligence and Applications. IOS Press Amsterdam, 2010; : 13 -36.

Pto. U statements – particular to universal Ui = <IUIa, ta, inst, o, IUIp, u, tr> IUIa is the IUI of the author of the statement, ta made, inst obtaining between p and cl, eference o a u are taken, IUIthe inst p IUI referring to the particular whose relationship with u is asserted, u relationship, and, tr a reference to the time at which the relationship

Pto. N-statements (1) Ni=< IUIa, ta, ntj, ni, IUIp, tr, IUIc> • The person referred to by IUIa asserts at time ta that ni is the name of the nametype ntj that designates in the context IUIC in the real world the particular referred to by IUIp at tr. This template will further be referred to as Pto. N template. • Requires: • an ontology of name types, • Identification of communities within which the names are accepted. Ceusters W, Manzoor S. How to track absolutely everything? In: Obrst L, Janssen T, Ceusters W (eds. ) Ontologies and Semantic Technologies for the Intelligence Community. Frontiers in Artificial Intelligence and Applications. IOS Press Amsterdam, 2010; : 13 -36.

Pto. N-statements (2) < IUIa, ta, nt, n, IUIp, tr , IUIc > • IUIa is the IUI of the author asserting that n is a name of type nt used by IUIc to denote IUIp; • ta is a time-stamp indicating when the assertion was made; • IUIc is the IUI for the particular that uses the name n (this can be a person, a community of persons, an organization, an information system, . . . ); • IUIp is the IUI referring to the particular which the author associates with n; • n is the name which the author associates with IUIp; • nt is the nametype (examples being first name, last name, nick name, medical record number, and so forth); and • tr is a time-stamp representing a time at which the author considers the association appropriate.

U--tuples: “negative findings” U i = <IUIa, ta, r, o, IUIp, u, tr> The particular referred to by IUIa asserts at time ta that the relation r of ontology o does not obtain at time tr between the particular referred to by IUIp and any of the instances of the universal u at time tr For saying that a particular is not an instance of some universal, ‘r’ should denote the identity-relation in ontology o. Do not confuse with retiring erroneous statements. Ceusters W, Elkin P, Smith B. Negative Findings in Electronic Health Records and Biomedical Ontologies: A Realist Approach. International Journal of Medical Informatics 2007; 76: 326 -333

a Pto. CO statements: particular to concept code Coi = <IUIa, ta, cbs, IUIp, co, tr> IUIa is the IUI of the author of the statement, ta made, cbs is taken, IUIp the IUI referring to the particular which the author associates with co, co associates with p, and, Ceusters W, Manzoor S. How to track absolutely everything? In: Obrst L, Janssen T, Ceusters W (eds. ) Ontologies and Semantic Technologies for the Intelligence Community. Frontiers in Artificial Intelligence and Applications. IOS Press Amsterdam, 2010; : 13 -36.

Interpretation of Pto. CO statements • must be interpreted as simple indexes to terms in a dictionary. • All that such a statement tells us, is that within the linguistic and scientific community in which cbs is used, the terms associated with co may - i. e. are acceptable to be used to denote p in their determinative version.

A SNOMED-CT example <IUI-0945, 18/04/2005, SNOMED-CT v 0301, IUI-1921, 367720001, forever> • #IUI-0945: author of the statement • #IUI-1921: the left testicle of patient #IUI-78127 • 367720001: the SNOMED concept-code to which “left testis” is (in SNOMED) attached as term So we can denote #IUI-1921 by means of • that left testis • that entire left testis • that testicle, that male gonad, that testis • that genital structure • that physical anatomical entity • BUT NOT: that SNOMED-CT concept

Specifying times in RT tuples • General format: <temporal operator, temporal region> • E. g. : ‘at IUIt’ where IUIt is the IUI denoting the temporal region • Temporal operators come from ISO/DIS 12381(en)

Use of the CEN Time Standard for HIT ISO/DIS 12381(en) Health informatics — Time standards for healthcare specific problems

Specifying times in RT tuples • General format: <temporal operator, temporal region> • E. g. : ‘at IUIt’ where IUIt is the IUI denoting the specific instance of BFO: temporal-region. • Temporal operators come from ISO/DIS 12381(en). • Temporal specification of temporal regions through: • Relationship to other temporal regions using the temporal operators as relationships in Pto. P tuples where the relata are temporal regions or temporal boundaries, • Pto. N-tuples using a time notation standard (e. g. GMT).