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An Ontology of Therapies. Claudio Eccher - eHealth Research Unit, FBK, Trento Antonella Ferro - Medical Oncology Unit, S. Chiara Hospital, Trento Domenico Pisanelli – Laboratory for Applied Ontology, CNR, Rome. eHealth 2009– Istanbul, 24th September 2009. Background.
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An OntologyofTherapies Claudio Eccher - eHealth Research Unit, FBK, Trento Antonella Ferro - Medical Oncology Unit, S. Chiara Hospital, Trento DomenicoPisanelli – Laboratory for Applied Ontology, CNR, Rome eHealth 2009– Istanbul, 24th September 2009
Background • Medicine is a very complex domain from the point of view of modeling and representing intended meaning: • different activity domains, scientific granularities, and user requirements for the same service; • ambiguous terminology (polysemy). • Ontologies are nowadays considered as the basic infrastructure for achieving semantic interoperability between information systems. • Semantic interoperability hinges on shared vocabularies whose semantics is described by ontologies in an unambiguous and machine-processable form.
The Oncocure Project • The Oncocure project, started in 2007, aims to: • design, and develop a prescriptive DSS based on breast cancer protocol encoded in Asbru; • integrate the DSS with a legacy oncological web-based EPR in use in the Medical Oncology Unit (MOU) of the S.Chiara Hospital of Trento (Northern Italy), in order to provide automatic support at the point of care. • One of the most challenging tasks in building a DSS and integrating it into the clinical workflow is to bridge the gap between the EPR and the DSS. • Cancer protocol require temporal and taxonomic abstractions, especially regarding therapies (e.g., anthracyclines in adjuvant).
AIM • Starting from the necessities of unambiguously define therapy-related concepts in the Oncocure project, we designed an axiomatic ontology for medical therapies, focused especially on oncologic therapies. • Axiomatic ontologies allow the explicit representation of ontological commitments related to terms to: • Facilitate meaning negotiation among agents; • Clarify and model the negotiation process itself.
Formal Ontologies classes, istances, roles Domain-independent Ontologies objects, events, processes, parts Reference Ontologies medicine, agriculture, law Domain Ontologies biomedical instruments, drugs, oncology therapies WhichOntologiesare wetalkingabout? • Rome • DOLCE • Ontologyoftherapies
The NCI Thesaurus • One of the most comprehensive vocabularies in the cancer domain, defined by its authors as: • “a biomedical vocabulary that provides consistent, unambiguous codes and definitions for concepts used in cancer research” • “exhibits ontology like properties in its construction and use” • NCIT is available in OWL (over 1.200.000 triples); • Although a valuable resource as reference terminology, as regards therapy concepts NCIT is merely a taxonomy (only IS_A relations) and suffers of some classification problems.
ExampleofProblemswith NCIT • Adjuvant_Therapy and Neo_Adjuvant_Therapy (treatments in different care phases) siblings of Hormone_Therapy and Chemotherapy (different drug kinds) and of Breast_Cancer_Treatment (treatment for a specific cancer); • Dose, Dose_Rate and Dose_Modification direct subclasses of Treatment_Regimen (is_a relation); • Protocol_Treatment_Arm (protocol in a clinical trial) sibling of Second_Line_Treament (treatment given after the first line failure); • Palliative_Surgery and Curative_Surgery (goal) siblings of Ambulatory_Surgical_Procedure (place).
Ontology Design Principles • Created in OWL (DL), • Based upon the top-level ontology DOLCE. • Endurants are distinguished in physical (resources) andnon physicalendurants (information entities). • Qualities: entities (weight, color, etc.) that characterize the features of the different items. • Endurants: entities wholly present at any time. • Perdurants: entities that extend in time by accumulating temporal parts.
The OntologyDeveloped • Medical therapies are represented by the therapy_description class (information entity). The enactment of a therapy is a perdurant.
Useof the Ontology • Our axiomatic ontology constitutes a model for labeling (temporally annotated) EPR data with higher level abstraction information for: • Modeling guidelines and interfacing automatic DSS with an EPR: guidelines often requires abstractions related to therapy history (e.g., Taxanes in adjuvant). • Enabling automatic data analysis: the identification and classification of therapies related to specific care delivery ‘phases’ facilitates visual representation for an immediate comprehension of the care process. • Controlling the medical errors: a physician can be automatically alerted if possible incongruities in data are found.
An Experiment • From the axioms defining the therapy_role_by_phase subclasses in the ontology we defined the rules to label oncological therapies in the EPR as neoadjuvant, adjuvant and metastatic. • Ex: Therapy takes place after surgery, ends before a progression, is administered to a patient with M0 tumor at diagnosis Adjuvant Therapy • Using the rules, we retrieved and labelled the set of breast cancer hormone and chemo-therapies administered in three years (2006-2008). • We compared our results with the therapy roles registered by the oncologist who planned the treatment (available since 2006).
results • 961 therapies (474 patients) with valid data (82 MX); • 868 (90.3 %) correctly classified; • 18 not classified (all MX). • 93 “incongruities”: • 4 adjuvant classified as metastatic (3 M1, 2 MX), 6 as neoadjuvant (2MX) • 6 neoadjuvant classified as adjuvant (5 M0, 1 MX), 2 as metastatic (1 M1, 1 M0) • 21 ‘palliative’ (metastatic) classified as adjuvant (1MX), 21 as neoadjuvant (11 M0, 10 MX). • 33 curative classified as metastatic (9 M0, 20 M1, 4 MX)
Conclusions • The relevant role of ontologies in the design and implementation of health care information systems is widely acknowledged. • Our axiomatic ontology, developed according to good design principles and based on a foundational ontology (DOLCE), allows to assign precise meanings to concepts and remove ambiguities. • Without an ontological grounding like this the same information may shift its sense according to the context and the human agent tacit knowledge.
The OntologyDeveloped • Medical therapies are represented by the therapy_description class (information entity). The enactment of a therapy is a perdurant. • With the help of an oncologist, therapies were classified according to their qualities: method (e.g., radiant, surgery), involved pathology, role (e.g., curative/palliative, primary/non primary), etc. • To describe a therapy, rather than establishing IS_A links, we add existential restrictions. • We can attach several qualities to the same therapy avoiding the entanglement of multiple hierarchies.
Ontology Design Principles • Basedupon the top-levelontology DOLCE. • Itinherits the basicdistinctionbetweenEndurants(entitieswhollypresent at anytime ) and Perdurants(entitiesthatextend in timebyaccumulatingtemporalparts). • Endurants are distinguishedbetweenphysical (resources) and non physicalentities (information entities) • Definitionofqualities: entities (pharmacological, radiant, etc.) thatcharacterize the featuresof the differentitems.