Biomedical subjects

Paul Fabry

Publications and source records attributed to Paul Fabry.

8 recordsLinked to original sources

PubMed2005

Methodology to ease the construction of a terminology of problems.

INTRODUCTION: Problem lists summarize an aspect of the patient's medical history and provide an important way to implement entry points for clinical pathways and guideline-oriented care. However, in order to automate processes based on problem lists, the use of controlled vocabularies is required. We developed a methodology to extract a collection of standardized problem-related terms from medical documents entered in free text by physicians. METHODS: We extracted a corpus of sentences describing problems from a randomized selection of admission notes collected at the University Hospitals of Geneva. Theses sentences underwent manual and automatic normalization processes, and a statistical clustering, in order to build a set of terms. RESULTS: We obtained 17,805 sentences from 5000 admission notes. We refined them into 1546 terms, 88.6% of which could be related to a relevant problem statement. DISCUSSION: A clinically relevant problems terminology was derived from clinical admission notes in free-text using a few methodical steps with a reasonable investment of human resources. Such an approach will ease the development and the use of problem lists better suited to user needs.

Medical Records, Problem-Oriented↗

PubMed2005

Amplification of Terminologia anatomica by French language terms using Latin terms matching algorithm: a prototype for other language.

OBJECTIVE: Terminologia anatomica is the new standard in anatomical terminology. This terminology is available only in Latin and English and its worldwide adoption is subject to the addition of terms from others languages. On the other hand, Nomina anatomica, the previous standard, has been widely translated. Aim of this work was to append foreign terms to Terminologia by using similarity-matching algorithm between its Latin terms and those from Nomina. METHODS: A semi-automatic matching of Latin terms from Terminologia with those of Nomina was performed using a string-to-string distance algorithm and manual assessment. We used a French-Latin version of Nomina together with Terminologia and we suggested French terms for Terminologia. Coverage was evaluated by the number of exact and approximate matches. A target of 78% was set due to the higher number of terms in Terminologia compared to Nomina. Relevance was estimated by manually comparing the meanings of the English and French terms related to the same Latin term. The question was whether they refer to the same anatomical structure. RESULTS: Exact or approximate matches were found for 5982 terms (76.5%) of Terminologia. Our results indicated that more than 75% of the terms from Terminologia came from Nomina, most of them were left unchanged and all were used with the same meaning. CONCLUSION: This method produces relevant results, reaching our 78% target. The method is based only on Latin terms and can be used for other languages. We consider this work as a starting point for adding terms to other knowledge sources, such as the foundational model of anatomy or the Unified Medical Language System (UMLS).

Algorithms↗

PubMed2005

Desiderata for representing anatomical knowledge.

The general problem of knowledge representation for gross anatomy supporting both computers and human is rarely globally solved. Partial solutions are flourishing, but the actual and potential users are left with a lack of satisfaction and uncomfortable feeling of incompleteness. Moreover, these solutions are not ready for a sound evolution and are at risk to disappear at any moment by default of adequate maintenance. In addition, the problem is complicated by the fact that any solutions should be relevant for Natural Language Processing applications in a multilingual environment.This paper tackles with this problem and defines the basic steps for a proper knowledge representation scheme. Taking the subdomain of gross anatomy, it shows how each step has been solved and what performances and benefits are expected by such a solution. A discussion is done on the way to interface from a common source for both computers and humans.

Anatomy↗

PubMed2005

Towards a multilingual version of terminologia anatomica.

OBJECTIVE: Terminologia Anatomica (TA) is the new standard in anatomical terminology. This terminology is available only in Latin and English and its worldwide adoption is subdued to the addition of terms from others languages. On the other hand Nomina Anatomica (NA), the previous standard, has been widely translated. Aim of this work was to append foreign terms to TA by using similarity matching algorithm between its Latin terms and those from NA. METHODS: A semi-automatic matching of Latin terms from TA with those of NA was performed using a string-to-string distance algorithm and manual assessment. We used a French - Latin version of NA together with TA and we suggested French terms for TA. Coverage was evaluated by the number of exact and approximate matches. A target of 80% was set due to the superior number of terms in TA compared to NA. Relevance was estimated by manually comparing the meanings of the English and French terms related to the same Latin term. The question was whether they refer to the same anatomical structure. RESULTS: Exact or approximate matches were found for 5,982 terms (76.5%) of TA. Our results outlined that more than 75% of the terms from TA came from NA, most of them were left unchanged and all were used with the same meaning. CONCLUSION: This method produces relevant results, reaching our 80% target. The method is based only on Latin terms and can be used for other languages and for others terminologies including Latin terms.

Algorithms↗

PubMed2004

Coping with the variability of medical terms.

OBJECTIVES: To cope with medical terms, which present a high variability of expression through a single natural language, in the sense that any term may be reformulated in hundred of different ways. METHODS: A typology of term variants is presented as a systematic approach in order to favour the implementation of an exhaustive solution. Then, an algorithm able to handle all variants is designed. RESULTS: Using MetaMap, single terms are analyzed with a success rate varying between 68 and 88 %; the algorithm presented in this paper improves this situation. CONCLUSIONS: This experience shows that a semantic driven method, based on a thesaurus, provides a satisfactory solution to the problem of variability of a single term. The presented typology is representative of most variants in a language.

Algorithms↗

PubMed2004

User acceptance of clinical information systems: a methodological approach to identify the key dimensions allowing a reliable evaluation framework.

The introduction of Computerized Information Systems (CIS) in clinical settings encountered difficulties. These difficulties highlight the lack of understanding of factors and mechanisms influencing user acceptance. The existing tools and research obtained contradictory results that point out the existence of neglected aspects, such as impacts of CIS, in computer science developments in complex settings. This paper proposes to identify key dimensions which make up user acceptance in clinical settings through the union of three methods. They define five main dimensions which require a concrete evaluation to validate the underlying proposed framework and to complete the description of the acceptance phenomenon. Identifying key dimensions opens the gate to comparative evaluation of many CIS and adds new indicators to evaluate the highlighted dimensions. A long-term aim is the development of longitudinal studies and to state priorities and guidelines for new CIS designs.

Attitude to Computers↗

PubMed2003

A frame-based representation of ICD-10.

UNLABELLED: Physicians are required to code information concerning a patient's stay in order to measure the medical activity in hospitals. They use the International Statistical Classification of Diseases and Related Health Problems, Tenth Revision (ICD-10). Coding is usually performed manually and computerized tools may be useful in speeding up and facilitating the tedious task of coding patient information. The aim of this work is to build a surface semantic model of ICD-10 in order to ameliorate a coding help system. METHODS: This work was focused on chapter XI of the ICD-10, Diseases of the Digestive System. Each term from both analytical and alphabetical indexes about this chapter were submitted to a morphological analysis in order to extract the medical concepts within. After a statistical analysis of these concepts and the way they connect themselves, a semantic model based on a "semantic frame" approach was built. RESULTS: Although this model could represent a reasonable amount of medical knowledge within chapter XI of the ICD-10 in a quite satisfactory way, it shows lack of efficiency for some other chapters. CONCLUSION: Difficulties have to be overcome when modelling a classification meant for manual utilisation, and a lot of work still has to be done to obtain an effective coding help system using the ICD-10.

Forms and Records Control↗

PubMed2003

Clinical documents: attribute-values entity representation,context, page layout and communication.

This paper presents how acquisition, storage and communication of clinical documents is implemented at the University Hospitals of Geneva. Careful attention has been given to user-interfaces, in order to support complex layouts, spell checking, and templates management with automatic prefilling. A dual architecture has been developed for storage using an entity-attribute-value unified database and a consolidated, patient-centered, layout-respectful file-based storage, providing both representation power and speed of access. This architecture allows a great flexibility for storing a continuum of data types, ranging from simple typed values to complex clinical reports. Finally, communication is entirely based on HTTP-XML internally, and a HL-7 CDA interface V2 is currently studied for external communication. Some of the problems encountered, mostly related to the typology of documents and the ontology of clinical attributes are evoked.

Computer Systems↗