Developing a Biomedical Ethics Ontology (BMEO)

Developing a Biomedical Ethics Ontology (BMEO) Robert Arp, Ph.D. Ontology Research Group (ORG) http://org.buffalo.edu/ National Center for Biomedical Ontology (NCBO) http://bioontology.org/

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

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) 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_asubtype relation

PORPHYRIAN TREE

Taxonomy PORPHYRIAN TREE is_a subtype relation only: e.g., Material Substance is_aThing

Taxonomy Compare: LinneanTaxonomy or Periodic Table is_a relation only

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_participantpatient • verdict preceded_by court trial • petroleum jelly transformation_ofpetroleum

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: http://www.drze.de/BELIT/thesaurus/ - string matching, at best e.g., find all string instances of the word: ‘risk’

TELS- no reasoningOntology- some reasoningbrain part_of nervous system, andnervous system part_of body, thereforebrain part_of body.West Texas petroleum is_a petroleum, andpetroleum is_a flammable liquid, thereforeWest Texas petroleum is_a flammable liquid. is_aand part_ofare transitive

TELSSearch= ‘animal’ Result= ‘animal x’, ‘animal y’

OntologySearch= ‘animal’ Result= ‘animal x’, ‘animal y’

OntologySearch= ‘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: http://obofoundry.org/.

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 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 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

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)

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

Developing a Biomedical Ethics Ontology (BMEO)