Bioinformatics and Technology Applications in Medication Management. Ontology: background and application to Medication Management Buffalo, NY, USA, June 13th, 2008

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Bioinformatics and Technology Applications
inMedication Management.Ontology background
and application to Medication Management
Buffalo, NY, USA, June 13th, 2008

• Werner CEUSTERS, MD
• Center of Excellence in Bioinformatics and Life
  Sciences, and
• National Center for Biomedical Ontology,
  University at Buffalo, NY, USA

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Ontology is popular
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Ontology one word, two meanings

• In philosophy
• Ontology (no plural) is the study of what
  entities exist and how they relate to each other
• In computer science and (biomedical informatics)
  applications
• An ontology (plural ontologies) is a shared and
  agreed upon conceptualization of a domain
• Our realist view within the Ontology Research
  Group combines the two
• We use realism, a specific theory of ontology, as
  the basis for building high quality ontologies,
  using reality as benchmark.

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Realism-based ontology

• Basic assumptions
• reality exists objectively in itself, i.e.
  independent of the perceptions or beliefs of
  cognitive beings
• reality, including its structure, is accessible
  to us, and can be discovered through (scientific)
  research
• the quality of an ontology is at least determined
  by the accuracy with which its structure mimics
  the pre-existing structure of reality.

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Three major views on reality

• Basic questions
• What does a general term such as tree refer
  to?
• Do generic things exist?

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Dominant view in computer science is conceptualism

• Basic questions
• What does a general term such as tree refer
  to?
• Do generic things exist?

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Dominant view in computer science is conceptualism
Realism
Conceptualism
Nominalism
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Terminology one word, two meanings

• Terminology is the study of identifying and
  labelling concepts pertaining to a subject
  field.
• Terminology related activities
• analysing the concepts and concept structures,
• identifying the terms assigned to the concepts,
• establishing correspondences between terms,
  possibly in various languages,
• compiling a terminology, on paper or in
  databases,
• managing terminology databases,
• creating new terms, as required.

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Why this interest in biomedical terminologies?

• Nuances in the English language can be both
  challenging and amusing, however, when variants
  in language impact treatment, safety and billing,
  it is all challenge and no humor.
• Although English contains a reasonable degree of
  conformity, divergence in phrasing and meaning
  can compound comprehension problems and impact
  patient safety. These language "woes" can be
  minimized through the use of sophisticated
  healthcare IT systems with terminology management
  services.

Schwend GT. The language of healthcare. Variance
in the English language is harming patients and
hospitals' bottom lines. Is healthcare IT the
solution? Health Manag Technol. 2008
Feb29(2)14, 16, 18
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An example of a terminology RxNorm

• What a standardized nomenclature for the
  smooth exchange of information
  between and within
  organizations
• Goal to allow various systems using
  different drug nomenclatures to
  share data efficiently at the
  appropriate level of abstraction
• Method a standard format in the naming of
  clinical drugs reflecting the active
  ingredients, strengths, and dose form
  comprising that drug. When any of these elements
  vary, a new name is created as a
  separate concept. An RxNorm name should
  exist for every strength and dose of every
  available combination of clinically
  significant ingredients.

http//www.nlm.nih.gov/research/umls/rxnorm/overvi
ew.html
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RxNorm for expressing similarities in medications

• Orajel Mouth Sore Rinse 150 MG/ML Mucous Membrane
  Topical Solution
• Perimax Perio Rinse 15 MG/ML Mucous Membrane
  Topical Solution
• Peroxyl 0.015 MG/MG Oral Gel
• Peroxyl 15 MG/ML Mucous Membrane Topical Solution
• Proxacol 30 MG/ML Topical Solution
• Superoxol 350 MG/ML Topical Solution

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Method standardized name composition
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RxNorm through RxNav
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However

• Terminology
• solves certain issues related to language use,
  i.e. with respect to how we talk about entities
  in reality (if any)
• Relations between terms / concepts
• does not provide an adequate means to represent
  independent of use what we talk about, i.e. how
  reality is structured
• Women, Fire and Dangerous Things (Lakoff).
• Ontology (of the right sort)
• Language and perception neutral view on reality.
• Relations between entities in first-order reality

This is the terminology / ontology divide
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The semantic triangle revisited
concepts
terms
objects
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Terminology Realist Ontology
Representation and Reference
terms
concepts
about
objects
First Order Reality
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Terminology Realist Ontology
Representation and Reference
terms
representational units
concepts
about
objects
universals
particulars
First Order Reality
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Terminology Realist Ontology
Representation and Reference
representational units
terms
concepts
cognitive units
communicative units
about
objects
universals
particulars
First Order Reality
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Terminology Realist Ontology
Three levels of reality in Realist Ontology
Representation and Reference
representational units
cognitive units
communicative units
universals
particulars
First Order Reality
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The three levels applied to medication management
Generic
Specific
3. Representation
2. Beliefs (knowledge)
1. First-order reality
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Places for ontology in medication management
Medication Management Detailed Use Case June
18th, 2007. (www.hhs.gov/healthit/documents/Us
eCaseMM.pdf)
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Terminology is too reductionist
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Terminology is too reductionist
What concepts do we need? How do we name concepts
properly?
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Terminological versus Ontological approach

• The terminologist defines
• a clinical drug is a pharmaceutical product
  given to (or taken by) a patient with a
  therapeutic or diagnostic intent. (RxNorm)
• The ontologist thinks
• Does given includes prescribed?
• Is manufactured with the intent to not
  sufficient?
• Are newly marketed products available in the
  pharmacy, but not yet prescribed not clinical
  drugs?
• Are products stolen from a pharmacy not clinical
  drugs?
• What about such products taken by persons that
  are not patients?
• e.g. children mistaking tablets for candies.

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RxNorm from an ontological perspective
http//www.nlm.nih.gov/research/umls/rxnorm/overvi
ew.html
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Why is this important ?

• Not as much for humans
• Our minds are very good in resolving
  ambiguities, even at unconscious levels.
• But for machines (computers, software)
• They cant deal with imprecise, vague or
  ambiguous statements.

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Standards for ePrescribing under Medicare Part D

• Formulary and benefits information
• NCPDP Formulary and Benefits Standard 1.0.
• Identification of providers
• National Provider Identifier (NPI)
• Medication history
• Medication History Standard in NCPDP SCRIPT 8.1
• Fill status notification
• RxFill in NCPDP SCRIPT 8.1

42 CFR Part 423. Federal Register / Vol. 73, No.
67 18917-42/ Monday, April 7, 2008 / Rules and
Regulations
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A realist ontological view on data standards
CSC. Record Locator Service Prototype.
Medications History Implementation Guide. V0.4.
2005-11-15.
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A realist ontological view on data standards
Inconsistent representation is E.g. part of
the drug name? Where is the strength and dosage?
CSC. Record Locator Service Prototype.
Medications History Implementation Guide. V0.4.
2005-11-15.
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A realist ontological view on data standards
Vocabularies with ontologically unclear
semantics 10 tablet 15 soluble tablet
11 enteric coated tablet 150 tablet,
effervescent 12 sustained release tablet
151 tablet, extended release 13 buccal or
sublingual tablet 16 tablet unspecified
14 chewable tablet 23 tablet 21 day supply
147 tablet, chewable 24 tablet 28 day supply
148 tablet, coated particles 72 vaginal
tablet 149 tablet, disintegrating
CSC. Record Locator Service Prototype.
Medications History Implementation Guide. V0.4.
2005-11-15.
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A realist ontological view on data standards
Mixing types and instances there is only one NDC
(particular), there are many manufacturers
(defined class)
CSC. Record Locator Service Prototype.
Medications History Implementation Guide. V0.4.
2005-11-15.
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The cost of ignoring the type/instance distinction
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Codes for types AND identifiers for instances
7 distinct disorders
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The power of realism in ontology design

• Reality as benchmark !

1. Is the scientific state of the
art consistent with biomedical reality ?
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The power of realism in ontology design

• Reality as benchmark !

2. Is my doctors knowledge up to date?
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The power of realism in ontology design

• Reality as benchmark !

3. Does my doctor have an accurate assessment of
my health status?
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The power of realism in ontology design

• Reality as benchmark !

4. How can we use case studies better to advance
the state of the art?
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The power of realism in ontology design

• Reality as benchmark !

5. Is our terminology rich enough to communicate
about all three levels?
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In summary

• Medication management involves many actors and IT
  systems semantic interoperability is thus a key
  issue.
• Ontologies (of the right sort) provide a deep
  level of semantic interoperability between IT
  systems, thereby keeping track
• of what is the case
• of what is known by some actor(s)
• of what has been and still needs to be done.
• Realism-based ontology, as a discipline, helps in
  creating ontologies of the right sort.