Developing a Biomedical Ethics Ontology (BMEO) Robert Arp, Ph.D. Ontology Research Group (ORG) National Center for Biomedical Ontology (NCBO)

protection of human subjects includes: - articulation of civil and moral laws - development of IRBs and other committees - clarity and coherence of terms - disseminating review information

clarity and coherence of terms what exactly is:risk? autonomy? ethical duty?

disseminating review information making the results of numerous reviews available from US and world in a common, easily searchable form

clarity and coherence of terms disseminating review information

Benefits: - assistance to those seeking clarity or consensus about how to apply ethical principles in similar situations - fostering detection of inconsistencies in use of terminologies clarity and coherence of terms disseminating review information

Benefits: - generating standardized forms - standardized vocabulary for submissions to regulatory agencies - improving collection of data from past studies clarity and coherence of terms disseminating review information

How do we get these Benefits? clarity and coherence of terms disseminating review information

How do we get these Benefits? Biomedical Ethics Ontology (BMEO) clarity and coherence of terms disseminating review information One Way

Biomedical Ethics Ontology (BMEO) What is an ontology?

Ontology: - graph comprised of a backbone taxonomic tree whose leaves or nodes represent types of entities in reality - nodes are connected by branches or edges representing principally the is_a subtype relation

PORPHYRIAN TREE Thing Material Substance Animate (Living) Entity Living Entity with Sensation (Animal) Rational Animal (Human) Non- Rational Animal Living Entity without Sensation (Vegetation) Non-Animate Entity Immaterial Substance

PORPHYRIAN TREE Thing Material Substance Animate (Living) Entity Living Entity with Sensation (Animal) Rational Animal (Human) Non- Rational Animal Living Entity without Sensation (Vegetation) Non-Animate Entity Immaterial Substance is_a subtype relation only: e.g., Material Substance is_a Thing Taxonomy

Compare: Linnean Taxonomy or Periodic Table is_a relation only Taxonomy

Ontology: - also supplemented by other edges representing relations such as part_of, preceded_by, has_participant, inheres_in, and any number of other relations holding between these types of entities

Examples: cell nucleus= entity located_in= relation cell= entity - cell nucleus located_in cell - X-ray test has_participant patient - verdict preceded_by court trial - petroleum jelly transformation_of petroleum

entities relations

Beginning of an Ontology for MRI Tests

Thesaurus Ethics in the Life Sciences (TELS) German Reference Centre for Ethics in the Life Sciences (DRZE), University of Bonn: - string matching, at best e.g., find all string instances of the word: ‘risk’

TELS - no reasoning Ontology - some reasoning brain part_of nervous system, and nervous system part_of body, therefore brain part_of body. West Texas petroleum is_a petroleum, and petroleum is_a flammable liquid, therefore West Texas petroleum is_a flammable liquid. is_a and part_of are transitive

TELS - no reasoning Ontology - some reasoning brain part_of nervous system, and nervous system part_of body, therefore brain part_of body. West Texas petroleum is_a petroleum, and petroleum is_a flammable liquid, therefore West Texas petroleum is_a flammable liquid. is_a and part_of are transitive

TELS - no reasoning Ontology - some reasoning brain part_of nervous system, and nervous system part_of body, therefore brain part_of body. West Texas petroleum is_a petroleum, and petroleum is_a flammable liquid, therefore West Texas petroleum is_a flammable liquid. is_a and part_of are transitive

TELS - no reasoning Ontology - some reasoning brain part_of nervous system, and nervous system part_of body, therefore brain part_of body. West Texas petroleum is_a petroleum, and petroleum is_a flammable liquid, therefore West Texas petroleum is_a flammable liquid. is_a and part_of are transitive

TELS - no reasoning Ontology - some reasoning brain part_of nervous system, and nervous system part_of body, therefore brain part_of body. West Texas petroleum is_a petroleum, and petroleum is_a flammable liquid, therefore West Texas petroleum is_a flammable liquid. is_a and part_of are transitive

TELS Search= ‘animal’ Result= ‘animal x’, ‘animal y’

Ontology Search= ‘animal’ Result= ‘animal x’, ‘animal y’

Result = More Information - animal is_a eukaryote - cat is_a animal - animal brain located_in animal - adult animal transformation_of embryo animal - animal has_role test subject - animal participates_in experiment

Successful ontologies: - Gene Ontology (GO) - Foundational Model of Anatomy (FMA) - Ontology for Biomedical Investigations (OBI) - Protein Ontology (PO) - Open Biomedical Ontologies (OBO) Foundry at:

an ontology also provides a controlled, structured vocabulary that supports reasoning and which includes a standardized consensus- based list of terms for use by all of those working in a given community, above all when describing data to be entered into a computer

clarity and coherence of terms RECALL

Goals of ontology: - improve retrieval and dissemination of information - make the information more easily searchable by human beings and more efficiently and reliably processable by computers

Goals of ontology: - ensure that the different bodies of information collected by different researchers in the same domain should all be represented in the same way, which assists interoperability and shareability of that information

disseminating review information RECALL

CONSIDER CLINICAL TRIAL REVIEWS

“It’s a huge paperwork mess.” —Randy Juhl, University of Pittsburgh Vice Chancellor for Research Conduct and Compliance (University of Pittsburgh, University Times: The Faculty and Staff Newspaper, 36 (21), 2004) CONSIDER CLINICAL TRIAL REVIEWS

Biomedical Ethics Ontology (BMEO)

- detect inconsistencies in use of terminologies Recall Benefits

Biomedical Ethics Ontology (BMEO) - detect inconsistencies in use of terminologies - provides a standardized vocabulary for submissions to regulatory agencies

Biomedical Ethics Ontology (BMEO) - detect inconsistencies in use of terminologies - provides a standardized vocabulary for submissions to regulatory agencies - assistance to those seeking clarity or consensus about how to apply ethical principles in similar situations

Biomedical Ethics Ontology (BMEO) - improving the collection of data from past studies

Biomedical Ethics Ontology (BMEO) - improving the collection of data from past studies - generating standardized forms, in a compatible way, across investigations

TEST CASE: IRBs and Clinical Trial Review

STEP ONE: list the terms that correspond to the entities, and provide clear and coherent definitions See Handout

Aristotelian definitions: an A is a B that/which is C (or Cs) - a board (A) is a group of persons (B) that is organized to monitor, assess, and evaluate some activity (C) - a review board (A) is a board (B) that participates in some review (C) - an institutional review board (A) is a review board (B) that participates in a clinical trial review (C)

Aristotelian definitions: an A is a B that/which is C (or Cs) - a board (A) is a group of persons (B) that is organized to monitor, assess, and evaluate some activity (C) - a review board (A) is a board (B) that participates in some review (C) - an institutional review board (A) is a review board (B) that participates in a clinical trial review (C)

Aristotelian definitions: an A is a B that/which is C (or Cs) - a board (A) is a group of persons (B) that is organized to monitor, assess, and evaluate some activity (C) - a review board (A) is a board (B) that participates in some review (C) - an institutional review board (A) is a review board (B) that participates in a clinical trial review (C)

Aristotelian definitions: an A is a B that/which is C (or Cs) - a review is a process in which persons participate that involves the understanding, assessing, and evaluating of some idea or project - a clinical trial review is a review that is performed by an IRB of a proposed clinical trial (an investigation… human subjects) - an expedited clinical trial review is a clinical trial review that is conducted by the institutional review board chairperson because the proposed clinical trial involves minimal risk

Aristotelian definitions: an A is a B that/which is C (or Cs) - a review is a process in which persons participate that involves the understanding, assessing, and evaluating of some idea or project - a clinical trial review is a review that is performed by an IRB of a proposed clinical trial (an investigation… human subjects) - an expedited clinical trial review is a clinical trial review that is conducted by the institutional review board chairperson because the proposed clinical trial involves minimal risk

Aristotelian definitions: an A is a B that/which is C (or Cs) - a review is a process in which persons participate that involves the understanding, assessing, and evaluating of some idea or project - a clinical trial review is a review that is performed by an IRB of a proposed clinical trial (an investigation… human subjects) - an expedited clinical trial review is a clinical trial review that is conducted by the institutional review board chairperson because the proposed clinical trial involves minimal risk

board review board national review board IRB finance board board of directors review animal experiment review clinical trial review (CTR) expedited CTR full CTR

board review board national review board IRB finance board board of directors review animal experiment review clinical trial review (CTR) expedited CTR full CTR

Less-complicated terms (?): - institutional review board - clinical trial - clinical trial review More-complicated terms (?): - ethical duty - risk - role

TEST CASE: IRBs and Clinical Trial Review STEP TWO: list the terms that correspond to the relations, and provide clear and coherent definitions See Handout

is_owed: Def.=a relationship between persons whereby the person owed has a claim against those who fail to abide by some duty owes_a: Def.=a relationship between persons whereby the person owing has a duty to perform some action or intended action to the person owed

- ensure logical coherence and accuracy of information ALSO, make sure to: Work with ethicians, clinicians, doctors, biomedical researchers

- seek optimal interoperability by using an upper level ontology such as Basic Formal Ontology: Common entities, relations, and vocabulary across ontologies ALSO:

- concretize the BMEO in a computer tractable representational artifact like Protégé: ALSO:

- apply the BMEO, and test the results in a computing context in communities of researchers ALSO: BMEO Wiki Page at: dokuwiki/hslwiki/doku.php?id =bioethics_ontology

This work was funded by the National Institutes of Health through the NIH Roadmap for Biomedical Research, Grant 1 U 54 HG Information on the National Centers for Biomedical Computing can be found at: Thank You

Thanks to Barry Smith, David Koepsell, and Andrea Ott for their work in our paper titled: Creating a Controlled Vocabulary for the Ethics of Human Research: Toward a Biomedical Ethics Ontology (BMEO) Thank You