Petr Kolesa | PubMed Health

PubMed2006

Tools for Czech biomedical ontologies creation.

The paper describes procedures and a tool we have developed to simplify and speed up creating of Czech biomedical ontologies. Our method is based on searching for concepts in a corpus of medical texts and binding those concepts to an established international ontology. The new ontology will have two major advantages: it will be compatible with the international ontology and it will possibly cover all concepts used in the Czech healthcare. The tool supports an author of ontology by mechanizing some routine tasks that occurs in the process of an ontology creation. It tries to learn how to identify concepts in texts and how to bind them to the ontology. The tool then displays the suggestions to a user, who can correct them and add some new ones. Based on this feedback the tool adjusts rules for concept finding and binding. To accomplish such behaviour we have employed some natural language processing methods and information extraction tools.

Czech Republic↗

PubMed2005

Obstacles to Implementing an Execution Engine for Clinical Guidelines Formalized in GLIF.

This article is on obstacles we faced when developing an executable representation of guidelines formalized the Guideline Interchange Format (GLIF). The GLIF does not fully specify the representation of guidelines at the implementation level as it is focused mainly on the description of guideline's logical structure. Our effort was to develop an executable representation of guidelines formalized in GLIF and to implement a pilot engine, which will be able to process such guidelines. The engine has been designed as a component of the MUltimedia Distributed Record system version 2 (MUDR(2)). When developing executable representation of guidelines we paid special attention to utilisation of existing technologies to achieve the highest reusability.Main implementation areas, which are not fully covered by GLIF, are a data model and an execution language. Concerning the data model we have decided to use MUDR(2)'s native data model for this moment and to keep watching the standardisation of a virtual medical record to implement it in execution engine in the near future. When developing the execution language, first of all we have specified necessities, which the execution language ought to meet. Then we have considered some of the most suitable candidates: Guideline Execution Language (GEL), GELLO, Java and Python. Finally we have chosen GELLO although it does not completely cover all required areas. The main GELLO's advantage is that it is a proposed HL7 standard. In this paper we show some of the most important disadvantages of GELLO as an executable language and how we have solved them.

Decision Making, Computer-Assisted↗