Automatic ontology oriented clinical concept extraction from free-text reports for CSI (Computer Semantic Interoperability)

Presenters

David Mendes (PhD Student at Universidade de vora) Irene Rodrigues Departamento de Informtica da Universidade de vora
CENTRIA Centre for Artificial Intelligence of UNL

Agenda

The research activities framed Issues faced Proposal Availability of tools & techniques/technologies Conclusions

Background

Problem Faced

Clinical Practice ontologies dont exist so far with appropriate characteristics for adequate reasoning and alignment with Well Founded Standards Automatic acquisition (population) is compulsory given that the size of the available data residing in EHRs renders manual curating impossible Automatic clinical concept acquisition tools have come of age to enable the automatic population of a suitable ontology for Clinical Practice The characteristics of the target Ontology is a matter not handled in the present work but is a research line issue by itself.

Conclusions

CPR vs OGMS as target

Both Computer Based Patient Record ontology (CPR) and Ontology for General Medical Science (OGMS) are ontologies of entities existing during clinical encounters. Include very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', symptom, 'diagnosis', 'patient', and 'healthcare provider'. Both use the Basic Formal Ontology (BFO) as an upper-level ontology as support for Ontological Realism. Both provide a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL. CPR is W3C Standard since 2009. OGMS is still very seminal .

Acquiring controlled vocabularies

TMM Tooling

Local

Create seminal TM, refine using customized MT (1) Manual translation of their jargon for the translator tutoring, (2) PDF to raw text, or to structured (XML). (3) NER (Named Entity Recognition), (4) WSD (Word Sense Disambiguation) according to the previously acquired concepts in our controlled vocabulary, (5) EAV (Extraction of Attributes and Values) is the final pure, single language, task that has to be performed and in which we need the tools that this paper refers to filter the concepts from the annotated text to extract concept instances, (6) Semantic annotation using the Web interface.

Remote

SAM SOAP Corpus

SOAP report depicts a clinical encounter in a semistructured way in a datable point of time. The Subjective, Objective, Assessment, Plan (SOAP) framework is a well-known, canonical structure in the medical domain.

Ontology population

Subjective, the symptoms section S where we extract directly into a cpr:symptom Objective, the O section where are sign records that we take as generator for cpr:clinical-findings or cpr:sign-finding Assessment, the analysis section A which are the clinical investigation acts cpr:clinical-investigation-act

Can be clinical-analisys-act, diagnostic-procedure or laboratory-test

Plan, the P section where the cpr:therapeutic-acts can be extracted

Can be medical-therapy, physical-therapy, psychological-therapy or therapeutic-procedure

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The Software Architecture

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Acquisition Flowchart

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CSI with QA

Our team is two-headed:

Knowledge representation and acquisition team in vora Discourse controller team for smart QuestionAnswering in Coimbra Currently only controlled cardiology environment is being developed. Generalization being the most challenging issue.
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Current on-going controlled results

Q: What is the patients personal history? A: Hypertension for 15 years; Diabetes Mellitus type 2 for 10 years; Cholecystectomy 2 years ago; Diabetic father; Obese BMI 26,5; Abdominal perimeter 106 cm. Q: What is the suggested diagnosis? A: Labratory routines: lipid profile; HgA1c; Rx thorax; ECG in rest; Ecochardiogram; Effort test (Effort proof or Chardiac scintigraphy); Q: What is the immediate recommended therapy assuming that AHT and Diabetes are not controlled ? A: Rich fiber and vegetable diet; polifraccionate and hiposaline; IECA or ARA II; Calcium Antagonist; Metformine; Estatine;
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Conclusion

Automatic clinical concept acquisition tools have come of age to enable the automatic population of a suitable ontology for Clinical Practice The development of an Ontology based layer to represent the acquired medical knowledge allows for CSI at a conceptual level
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Thank you very much !!

Questions ?
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