BMI714 Course 22630 Spring 2019 Class 2 February 5 2019 The Essence of Referent Tracking Werner CEUSTERS 1 Why RT started medical coding systems used naively preserve certain ambiguities ID: 1037346
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1. Principles of Referent TrackingBMI714Course 22630 – Spring 2019Class 2 – February 5, 2019The Essence of Referent TrackingWerner CEUSTERS1
2. Why RT started: medical coding systems used naively preserve certain ambiguities.557204/07/199026442006closed fracture of shaft of femur557204/07/199081134009Fracture, closed, spiral557212/07/199026442006closed fracture of shaft of femur557212/07/19909001224Accident in public building (supermarket)557204/07/199079001Essential hypertension093924/12/1991255174002benign polyp of biliary tract230921/03/199226442006closed fracture of shaft of femur230921/03/19929001224Accident in public building (supermarket)4780403/04/199358298795Other lesion on other specified region557217/05/199379001Essential hypertension29822/08/19932909872Closed fracture of radial head29822/08/19939001224Accident in public building (supermarket)557201/04/199726442006closed fracture of shaft of femur557201/04/199779001Essential hypertensionPtIDDateObsCodeNarrative093920/12/1998255087006malignant polyp of biliary tract2
3. Goal of Referent Tracking (RT)Faithfull representation of how particulars ‘of interest’ relate to other Portions of Reality (PoR) ‘of interest’.3
4. Particulars, representations, PoRportions of realityparticularsrepresentations4‘relate’
5. Particulars, representations, PoRportions of realityparticularsrepresentations5‘relate’
6. Reality Representationhttps://www.statnews.com/2016/03/24/appendix-cancer-treatment/
7. Reality Representationhttps://www.statnews.com/2016/03/24/appendix-cancer-treatment/
8. William Kent in ‘Data and Reality’p35, 3rd edition, 2012.
9. Representational components of RTInstance Unique Identifiers (IUI) within an RT-system: globally and singularly unique identifier for any referent in broad sense,for particulars in the original narrow sense.9
10. 557204/07/199026442006closed fracture of shaft of femur557204/07/199081134009Fracture, closed, spiral557212/07/199026442006closed fracture of shaft of femur557212/07/19909001224Accident in public building (supermarket)557204/07/199079001Essential hypertension093924/12/1991255174002benign polyp of biliary tract230921/03/199226442006closed fracture of shaft of femur230921/03/19929001224Accident in public building (supermarket)4780403/04/199358298795Other lesion on other specified region557217/05/199379001Essential hypertension29822/08/19932909872Closed fracture of radial head29822/08/19939001224Accident in public building (supermarket)557201/04/199726442006closed fracture of shaft of femur557201/04/199779001Essential hypertensionPtIDDateObsCodeNarrative093920/12/1998255087006malignant polyp of biliary tractIUI-001IUI-001IUI-001IUI-003IUI-004IUI-004IUI-005IUI-005IUI-005IUI-007IUI-007IUI-007IUI-002IUI-012IUI-0067 distinct disordersCodes for ‘types’ AND identifiers for instances … one of a few possibilities10
11. IUIs for 1st and 2nd order realityhttps://www.statnews.com/2016/03/24/appendix-cancer-treatment/this man‘this man’#1‘#1’
12. Key RT 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 labelling it with a universally unique singular identifier. ‘cognitive agent’:A person;An organization;A device or software agent, e.g.Bank note printer,Image analysis software.
13. Criteria for IUI assignmentThe particular’s existence must be determined:However: no need to know what the particular exactly is, i.e. which universal it instantiatesNo need to be able to point to it preciselyA member of a specific organizationBut: this is not a matter of choice, not ‘any’ out of ...The particular 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 systemIf a IUI has been assigned by somebody, everybody else making statements about the particular should use it
14. Identifiers and pseudo-identifiersRepresentationRealityID-aID-bEntity-1ID-cEntity-2ID-dEntity-3ID-eEntity-4ID-fEntity-5Pseudo-identifiers:ID-a: denotes nothingID-b: denotes ambiguouslySingularly unique identifier: ID-cNon-singularly unique identifiers: ID-f, ID-d, ID-e
15. Assertion of assignments: A-tuples.IUI assignment is an act of which the execution has to be asserted in an IUI-repository:<da, Ai, td> da IUI of the registering agentAi the assertion of the assignment <pa, pp, tap> pa IUI of the author of the assertionpp IUI of the particulartap time of the assignmenttd time of registering Ai in the IUI-repositoryNeither td or tap give any information about when #pp started to exist ! That might be asserted in statements providing information about #pp .
16. IUIs for 1st and 2nd order realityhttps://www.statnews.com/2016/03/24/appendix-cancer-treatment/this man‘this man’#1‘#1’this picture part#2isAbout at t
17. Reality and representationthis heart‘this heart’#12‘#12’this picture part#245isAbout at t
18. ConventionThrough ‘this heart’ one sees this heart.Through picture part #245 one sees this heart.Through #245 one sees picture part #245.Through #12 one sees this heart.
19. OGMS: ‘Findings’ / ‘observations’On the side of the patientBodily featuresSymptomsSignsObserved through physical examinationObserved through lab testRepresentationsFindingsAnamnestic findingsClinical findingsLaboratory findingsScheuermann R, Ceusters W, Smith B. Toward an Ontological Treatment of Disease and Diagnosis. 2009 AMIA Summit on Translational Bioinformatics, San Francisco, California, March 15-17, 2009;: 116-120.
20. OGMS: ‘Findings’ / ‘observations’On the side of the patientBodily featuresSymptomsSignsObserved through physical examinationObserved through lab testClinical phenotypeRepresentationsFindingsAnamnestic findingsClinical findingsLaboratory findingsClinical pictureisAbout at t
21. Particulars, representations, PoRportions of realityparticularsrepresentations21‘relate’
22. Representational components of RTInstance Unique Identifiers (IUI) within an RT-system: globally and singularly unique identifier for any referent in broad sense,for particulars in the original narrow sense.RT-tuples: representations of Relationships involving formal relations involving a particular,…22
23. ‘Relations’(mainstream view)Relations:‘entities that glue together other entities’Formal relations:‘hold between two or more entities directly, without any further intervening individual’.Material relations:‘have material structure on their own’.Guizzardi & Wagner. What’s in a Relationship: An Ontological Analysis. In: Qing Li, Stefano Spaccapietra, Eric Yu, Antoni Olivé (Eds.), Conceptual Modeling - ER 2008. Lecture Notes in Computer Science, Vol. 5231, 83-97, 2008 https://doi.org/10.1007/978-3-540-87877-3_8↗
24. Material relation‘John is in a relation with Mary’24JohnMaryJM Romantic relationshipisAbout at t
25. Material relation‘John is in a relation with Mary’25JohnMaryJM Romantic relationshipBFO:ObjectBFO:Relational QualityinstanceOf at tisAbout at t
26. Material relation‘John is in a relation with Mary’26JohnMaryJM Romantic relationshipBFO:ObjectBFO:Relational QualityinstanceOf at tisAbout at tinheresIn at tinheresIn at t
27. Material relation‘John is in a relation with Mary’27JohnMaryJM Romantic relationshipBFO:ObjectBFO:Relational QualityinstanceOf at tisAbout at tinheresIn at tinheresIn at t
28. Material relation‘John is in a relation with Mary’28JohnMaryJM Romantic relationshipBFO:ObjectBFO:Relational QualityinstanceOf at tisAbout at tinheresIn at tinheresIn at t
29. Material relations‘have material structure on their own’Are entities in their own rightRelate other entities to each other by means of formal relationsExamples: what might by some be denoted by‘patient’‘treatment’‘driver’Example in BFO: relational qualitiesHave a plurality of independent continuants as their bearers.29
30. Formal relations‘John is in a relation with Mary’30JohnMaryJM Romantic relationshipBFO:ObjectBFO:Relational QualityinstanceOf at tisAbout at tinheresIn at tinheresIn at t
31. Formal relations‘hold between two or more entities directly, without any further intervening individual’Basic formal relations:existential dependence, inherence, subtype-of, part-of, subset-of, instantiation, …Domain formal relations:‘relations that exhibit similar characteristics, i.e., those relations of comparison such as is taller than, is older than, knows more Greek than’.31Guizzardi & Wagner. What’s in a Relationship: An Ontological Analysis. In: Qing Li, Stefano Spaccapietra, Eric Yu, Antoni Olivé (Eds.), Conceptual Modeling - ER 2008. Lecture Notes in Computer Science, Vol. 5231, 83-97, 2008 https://doi.org/10.1007/978-3-540-87877-3_8↗
32. Most basic form of RT-tuples#245 BFO:instanceOf XYZ:Image at t1.#12 BFO:instanceOf FMA:heart at t2#245 IAO:isAbout #12 at t3#245 BFO:continuantPartOf #260 at t4…#260
33. Referent tracking assertionsWhen x or y is a continuant(-like portion of reality):Through: x relation y at tOne sees: x relation y at tWhen x or y is an occurrent(-like portion of reality):Through: x relation y One sees: x relation y
34. Examples of Referent Tracking assertions #1 participantOf #2 at t1 #2 instanceOf DiagnosticProcess #1 participantOf #3 at t2 #3 instanceOf Life #1 participantOf #4 at t3 #4 instanceOf SurgicalProcedure #4 precededBy #2 #4 partOf #3 t3 partOf t2
35. ‘#n’: (globally) singularly unique identifiers #1 participantOf #2 at t1 #2 instanceOf DiagnosticProcess #1 participantOf #3 at t2 #3 instanceOf Life #1 participantOf #4 at t3 #4 instanceOf SurgicalProcedure #4 precededBy #2 #4 part of #3 t3 partOf t2
36. To be precise …This yellow 4-character string #1:is an instance of BFO:Independent continuant,it has the quality of being yellow,It has another quality of being of such width, … .I use it today to denote myself and I assigned it the status of Instance Unique Identifier (IUI), and therefor:it has another quality which is an Information Quality Entity (IQE =def. a quality that is the concretization of some information content entity)that quality is about me,that quality is the concretization of an instance of IUI, a subtype of ICE, which is also about me.
37. ‘tn’: (globally) unique identifiers #1 participantOf #2 at t1 #2 instanceOf DiagnosticProcess #1 participantOf #3 at t2 #3 instanceOf Life #1 participantOf #4 at t3 #4 instanceOf SurgicalProcedure #4 precededBy #2 #4 part of #3 t3 partOf t2
38. Configurations through Referent TrackingWhen x or y is a continuant: x relation {y} at tOtherwise: x relation {y} Where:x is a particular,relation (at) is a relation between x, y (and t),y is a particular or a type,t is a BFO:temporal_region,x relation y at t is a configuration,x relation y is a configuration.portions of reality
39. Non-ternary relationsTypical case: ternary relationsx relation {y} at tRelation between x, y and tBinary relations:e.g.: x does-not-denote at tQuaternary relations:e.g.: x between {y,z} at t{y,z, …} order of relata must be specified in tuple type syntax description.
40. Representational components of RTInstance Unique Identifiers (IUI) within an RT-system: globally and singularly unique identifier for any referent in broad sense,for particulars in the original narrow sense.RT-tuples: representations of Relationships involving formal relations involving a particular,‘shortcut’ relations between certain portions of realities. 40
41. Shortcut relational assertion#245 IAO:isAbout #12 at t3#245 BFO:continuantPartOf #260 at t4…#260 XYZ:containsReprOf #12 at t3#260
42. Shortcut relations must be describeda XYZ:containsReprOf b at t means:a BFO:instanceOf Representation at t b BFO:existAt t1t1 <some time relation> tc BFO:instanceOf Representation at tc BFO:continuantPartOf a at tc IAO:isAbout b at t42
43. Commitments in Referent Trackingportions of realitycontinuantsoccurrentsparticularstypesconfigurationsrelations??representationsparticipationme participating in my lifeorganismmemy lifeuniversals43relationships
44. Continuants versus Occurrents:differences for temporal indexingContinuantOccurrente.g. pathological processIndependentContinuante.g. organismDependentContinuante.g. patientrole .... ..... .......universalsparticularshas_participantinheres_ininstance_ofis_ais_ainstance_of at t44
45. Representational components of RTInstance Unique Identifiers (IUI) within an RT-system: globally and singularly unique identifier for any referent in broad sense,for particulars in the original narrow sense.RT-tuples: representations of Relationships involving formal relations involving a particular‘shortcut’ relations between certain portions of realities.Temporal region identifiersDifferent from IUIs since often unique denotation cannot be ascertained.45
46. Most basic form of RT-tuples#245 BFO:instanceOf XYZ:Image at t1.#12 BFO:instanceOf FMA:heart at t2#245 IAO:isAbout #12 at t3#245 BFO:continuantPartOf #260 at t4…#260
47. 47
48. Continuants versus Occurrents:differences for temporal indexingType – Type relations: never temporal indexing;when only occurrent types are involved: time is outside the realm.when a continuant type is involved: time factored out by the definition, e.g.:A part_of B (for universals) is defined as:Given any instance a and any time t, if a is an instance of the universal A at t, then there is some instance b of the universal B at t such that a is an instance-level part_of b at t.Particular – Type relations: only temporal indexing when a continuant is involved.Particular – Particular relations:only temporal indexing when a continuant is involved.48
49. Importance of being clearThe International Classification of Headache Disorders has‘Persistent idiopathic facial pain (PIFP)’ = ‘persistent facial pain with varying presentations …’Imagine three patients: all three have continuously pain,the first one has always pain which presents itself in the same way,the second one has also always pain which presents itself in the same way, but in a different way than the first one,the third one’s pain presents itself sometimes like the first one, sometimes like the second one, and sometimes different from those.Which patients satisfy the definition for PIFP ?49
50. Talking about particulars or types?‘Persistent idiopathic facial pain (PIFP)’ = ‘persistent facial pain with varying presentations …’t1t2t3t1t2t3t1t2t3t1t2t3t1t2t3t1t2t3persistentfacial painpresentation type1presentation type3presentation type2typesmy painhis painher painparti-culars50
51. ‘Persistent idiopathic facial pain (PIFP)’ = ‘persistent facial pain with varying presentations …’if the description is about types, then the three particular pains fall under PIFP.if the description is about (arbitrary) particulars, then only her pain falls under PIFP.Talking about particulars or types?51
52. Example from CPO (1)CognitiveRepresentation =def. MentalQuality AND is_about SOME Entityshould be:For all cr, t, if cr instance_of CognitiveRepresentation at t, then cr instance_of MentalQuality at t, and there is some e such that cr is_about e at t52
53. Example from CPO (1)What about ‘Entity’?Interpretation for BFO is unclear: ‘anything at all that exists in any way at all’ (Arp. et.al. 2015, p87)Everything what is committed to in RT ?Strictly BFO, thus only particulars, so that ‘entity’ is shortcut reference for ‘continuant or occurrent’ but does not have a universal on its own ?The OWL interpretation which ignores temporal indexing ?53
54. RT follows BFO and original RO principlesIn RT, assertions are primarily made about particulars:Particular to Particular relational assertions,Particular to Type relational assertions.Within the realm of particulars and universals, RT follows BFO principles, f.i. that within a BFO compatible ontology, all terms ought to be defined on the basis of particulars following the all/some schema.This does not work for CPO’s‘Act of Intelligence Gathering has_subclass Act of Intelligence Analysis’For all aig instance_of Act of Intelligence Gathering, there is some … ?54Smith 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.
55. Referent tracking assertions are realThrough: #1 partOf #2 at t1One sees: #1 partOf #2 at t1Thus we can assign identifiers to these assertions:#3 stands proxy for #1 partOf #2 at t1And we can write:#3 isAbout #1 at t3,#3 isAbout #2 at t3, …This is important for referent tracking systems which keep track of the faithfulness over time of: databases, orA RT system’s own representations.
56. The (very beginning of the) nitty grittyGender of patient XDenotes patient X’s age in yearsDenotes provider Y’s unique ID for patient XIUI assignments required: L1- : #1-1 (patient X), #1-2 (provider Y), #1-3 (patient X’s life), #1-4 (patient X’s gender)L3: #3-1 (the instance of ICE of which there is a concretization in cell A2, #3-2 (idem for B2), #3-3 (idem for C2)Assignment of temporal regions: in a similar repository as the IUI-repository but no requirement for singular uniqueness:t1 and t2 may denote the same temporal regionNo t# may be used for more than one temporal region.
57. Assignment57