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Biomedical subjects

R Baud

Publications and source records attributed to R Baud.

At least 19 recordsLinked to original sources
PubMed2002

A humanist's legacy in medical informatics: visions and accomplishments of Professor Jean-Raoul Scherrer.

OBJECTIVE: To report about the work of Prof. Jean-Raoul Scherrer, and show how his humanist vision, his medical skills and his scientific background have enabled and shaped the development of medical informatics over the last 30 years. RESULTS: Starting with the mainframe-based patient-centered hospital information system DIOGENE in the 70s, Prof. Scherrer developed, implemented and evolved innovative concepts of man-machine interfaces, distributed and federated environments, leading the way with information systems that obstinately focused on the support of care providers and patients. Through a rigorous design of terminologies and ontologies, the DIOGENE data would then serve as a basis for the development of clinical research, data mining, and lead to innovative natural language processing techniques. In parallel, Prof. Scherrer supported the development of medical image management, ranging from a distributed picture archiving and communication systems (PACS) to molecular imaging of protein electrophoreses. Recognizing the need for improving the quality and trustworthiness of medical information on the Web, Prof. Scherrer created the Health-On-the-Net (HON) foundation. CONCLUSIONS: These achievements, made possible thanks to his visionary mind, deep humanism, creativity, generosity and determination, have made of Prof. Scherrer a true pioneer and leader of the human-centered, patient-oriented application of information technology for improving healthcare.

History, 20th Century↗
PubMed2001

Comparing general and medical texts for information retrieval based on natural language processing: an inquiry into lexical disambiguation.

In this paper we compare two types of corpus, focusing on the lexical ambiguity of each of them. The first corpus consists mainly of general newspaper articles and literature excerpts, while the second belongs to the medical domain. To conduct the study, we have used two different disambiguation tools. First, each tool was validated in its respective application area. We then use these systems in order to assess and compare both the general ambiguity rate and the particularities of each domain. Quantitative results show that medical documents are lexically less ambiguous than unrestricted documents. Our conclusions emphasize the importance of the application area in the design of NLP tools.

Information Storage and Retrieval↗
PubMed2000

GALEN: a third generation terminology tool to support a multipurpose national coding system for surgical procedures.

Generalised architecture for languages, encyclopedia and nomenclatures in medicine (GALEN) has developed a new generation of terminology tools based on a language independent model describing the semantics and allowing computer processing and multiple reuses as well as natural language understanding systems applications to facilitate the sharing and maintaining of consistent medical knowledge. During the European Union 4 Th. framework program project GALEN-IN-USE and later on within two contracts with the national health authorities we applied the modelling and the tools to the development of a new multipurpose coding system for surgical procedures named CCAM in a minority language country, France. On one hand, we contributed to a language independent knowledge repository and multilingual semantic dictionaries for multicultural Europe. On the other hand, we support the traditional process for creating a new coding system in medicine which is very much labour consuming by artificial intelligence tools using a medically oriented recursive ontology and natural language processing. We used an integrated software named CLAW (for classification workbench) to process French professional medical language rubrics produced by the national colleges of surgeons domain experts into intermediate dissections and to the Grail reference ontology model representation. From this language independent concept model representation, on one hand, we generate with the LNAT natural language generator controlled French natural language to support the finalization of the linguistic labels (first generation) in relation with the meanings of the conceptual system structure. On the other hand, the Claw classification manager proves to be very powerful to retrieve the initial domain experts rubrics list with different categories of concepts (second generation) within a semantic structured representation (third generation) bridge to the electronic patient record detailed terminology.

Abstracting and Indexing↗
PubMed2000

Tagging medical texts: a rule-based experiment.

In this paper we describe the construction of a part-of-speech tagger for medical document retrieval purposes, therefore we have designed a specific architecture called minimal commitment. The system uses local grammatical rules for conducting the disambiguation task. Four evaluations are conducted, with and without taking unknown words into account. In between each evaluation the modules (lexicon, guesser, rules) of the system are incrementally improved.

Disease↗
PubMed1999

Happy birthday DIOGENE: a hospital information system born 20 years ago.

Since its birth in 1978, DIOGENE, the hospital information system of Geneva University Hospital has been constantly evolving, with a major change in 1995, when migrating from a centralized to an open distributed architecture. For a few years, the hospital had to face health policy revolution with both economical constraints and opening of the healthcare network. The hospital information system DIOGENE plays a significant role by integrating four axes of knowledge: medico-economical context for better understanding and influencing resources consumption; the whole set of patient reports and documents (reports, encoded summaries, clinical findings, images, lab data, etc.), patient-dependent knowledge, in a vision integrating time and space; external knowledge bases such as Medline (patient-independent knowledge); integration of these patient-dependent and independent knowledge in a case-based reasoning format, providing on the physician desktop all relevant information for helping him to take the most appropriate adequate decision.

Computer Systems↗
PubMed1999

The bridge between administrative and clinical information system.

On one side, physicians are asked to record administrative information, such as activity measurement, case-mix of their specialty, billing, for statistical, legal or reimbursement purposes; and on the other side, they need to gather detailed information about their own patients in terms of clinical evolution, for the day-to-day care of the patients or for clinical research purposes. Many other actors are also involved with these processes, both on the administrative side, such as registration officers, administrators and on the clinical side, nurses and other care providers. Applications have been developed within hospital information systems for capturing and disseminating information according to these specific actors and dedicated purposes. But more and more appears the need to integrate these data for insuring the coherence of information and avoiding redundancy of data capture. How to conciliate these objectives? We describe the Geneva's approach for integrating the administrative and the clinical systems.

Data Collection↗
PubMed1999

Document versus data centred approach to the EPR.

This paper presents the document centred Electronic Patient Record (EPR) as currently in production in a large university hospital and subject to multiple additional developments in the coming years. A number of basic hypothesis have been developed in order to reach the best medical practice and the success of this application. In addition, the alternative approach of data centred EPR is compared, and different benefits and pitfalls are highlighted. It is not easy to evaluate the consequences of such an initial trend, but changing one's mind after having a system in daily production is anyway costly and difficult. Therefore, the selection of the right orientation in a given hospital necessitates a scientific debate.

Data Collection↗
PubMed1999

Galen: a third generation terminology tool to support a multipurpose national coding system for surgical procedures.

GALEN has developed a new generation of terminology tools based on a language independent concept reference model using a compositional formalism allowing computer processing and multiple reuses. During the 4th framework program project Galen-In-Use we applied the modelling and the tools to the development of a new multipurpose coding system for surgical procedures (CCAM) in France. On one hand we contributed to a language independent knowledge repository for multicultural Europe. On the other hand we support the traditional process for creating a new coding system in medicine which is very much labour consuming by artificial intelligence tools using a medically oriented recursive ontology and natural language processing. We used an integrated software named CLAW to process French professional medical language rubrics produced by the national colleges of surgeons into intermediate dissections and to the Grail reference ontology model representation. From this language independent concept model representation on one hand we generate controlled French natural language to support the finalization of the linguistic labels in relation with the meanings of the conceptual system structure. On the other hand the classification manager of third generation proves to be very powerful to retrieve the initial professional rubrics with different categories of concepts within a semantic network.

Abstracting and Indexing↗
PubMed1998

Reconciling users' needs and formal requirements: issues in developing a reusable ontology for medicine.

A common language, or terminology, for representing what clinicians have said and done is an important requirement for individual clinical systems, and it is a pre-requisite for integrating disparate applications in a distributed telematic healthcare environment. Formal representations based on description logics or closely related formalisms are increasingly used for representing medical terminologies. GALEN's experience in using one such formalism raises two major issues, as follows: how to make ontologies based on description logics easy to use and understand for both clinicians and applications developers; what features are required of the ontology and description logic if they are to achieve their aims. Based on our experience we put forward four contentions: two relating to each of these two issues, as follows: that natural language generation is essential to make a description logic based ontology accessible to users; that the description logic based ontology should be treated as an "assembly language" and accessed via "intermediate representations" oriented to users and "perspectives" adapting it to specific applications; that independence and reuse are best supported by partitioning the subsumption hierarchy of elementary concepts into orthogonal taxonomies, each of which forms a pure tree in which the branches at each level are disjoint but nonexhaustive subconcepts of the parent concept; that the expressivity of the description logic must include support for transitive relations despite the computational cost, and that this computational cost is acceptable in practice. The authors argue that these features will be necessary, though by no means sufficient, for the development of any large reusable ontology for medicine.

Clinical Medicine↗
PubMed1998

Integrated computerized patient records: the DIOGENE 2 distributed architecture paradigm with special emphasis on its middleware design.

DIOGENE 2 is a full-scale distributed/open hospital information system that by June 1995 had already achieved its migration from a former mainframe system. Thanks to that architecture there is an obvious need for a common "glue" devoted to tightening up scattered applications into a middleware-based network of interoperability. After this the design of open/distributed Electronic Patient Records (EPRs) became feasible. A brief historical sketch of DIOGENE is presented from its initial to its present phase. A working prototype of these distributed EPRs is discussed showing current achievements during its first stage of production in the clinics of the University Hospitals of Geneva. On-going expansion to other public hospitals, as well as to general practioners (GPs) in the Geneva area, are partly described.

Computer Communication Networks↗
PubMed1998

Full text multilingual automatic morphosemantems for stand-alone or Internet based applications.

The authors present an automatic tool able to provide real-time morphosemantic decomposition of natural language sentences in French, German and English. This tool demonstrates the feasibility of Natural Language Processing on standard PC computers and the technology involved has been successfully implemented in daily used applications in several European hospitals. It considerably alleviates the burden of coding with various international classification and enhances the quality of the final results. This tool, delivered on PC platforms, is highly convivial and provides a versatile interface to any existing applications based on the Microsoft Windows standards. Moreover, all high levels functions have been encapsulated in Object Oriented Components and can therefore be reused using the Common Object Model standards to develop stand-alone or Internet applications.

Classification↗
PubMed1998

Automatic extraction of linguistic knowledge from an international classification.

Automatic extraction of knowledge from large corpus of texts is an essential step toward linguistic knowledge acquisition in the medical domain. The current situation shows a lack of computer-readable large medical lexicons, with a partial exception for the English language. Moreover, multilingual lexicons with versatility for multiple languages applications are far from reach as long as only manual extraction is considered. Computer-assisted linguistic knowledge acquisition is a must. A multilingual lexicon differs from a monolingual one by the necessity to bridge the words in different languages. A kind of interlingua has to be built under the form of concepts to which the specific entries are attached. In the present approach, the authors have developed an intelligent rule-based tool in order to focus on a multilingual source of medical knowledge, like the International Classification of Disease (ICD) which contains a vocabulary of some 20,000 words, translated in numerous languages.

Disease↗
PubMed1998

Galen-In-Use: using artificial intelligence terminology tools to improve the linguistic coherence of a national coding system for surgical procedures.

GALEN has developed a language independent common reference model based on a medically oriented ontology and practical tools and techniques for managing healthcare terminology including natural language processing. GALEN-IN-USE is the current phase which applied the modelling and the tools to the development or the updating of coding systems for surgical procedures in different national coding centers co-operating within the European Federation of Coding Centre (EFCC) to create a language independent knowledge repository for multicultural Europe. We used an integrated set of artificial intelligence terminology tools named CLAssification Manager workbench to process French professional medical language rubrics into intermediate dissections and to the Grail reference ontology model representation. From this language independent concept model representation we generate controlled French natural language. The French national coding centre is then able to retrieve the initial professional rubrics with different categories of concepts, to compare the professional language proposed by expert clinicians to the French generated controlled vocabulary and to finalize the linguistic labels of the coding system in relation with the meanings of the conceptual system structure.

Artificial Intelligence↗
PubMed1997

Galen-In-Use: an EU Project applied to the development of a new national coding system for surgical procedures: NCAM.

GALEN has developed a language independent common reference model based on a medically oriented ontology and practical tools and techniques for managing healthcare terminology including natural language processing. GALEN-IN-USE is the current phase which applied the modelling and the tools to the development or the updating of coding systems for surgical procedures in different national coding centre co-operating within the European Federation of Coding Centre (EFCC) to create a multilingual knowledge repository for multicultural Europe. NCAM (Nomenclature Commune des Actes Médicaux) is the new French multipurpose coding system for surgical procedures. The labels are processed from the intermediate dissections to the Grail representation and the natural language generation by the electronically related Medical Informatics research centres network of Saint Etienne, Manchester, Geneva and Nijmegen. The national coding centre is able to retrieve the initial labels with different categories of concepts, to compare the professional language proposed by expert clinicians to the French generated controlled vocabulary and to finalize the linguistic labels of the coding system in relation with the meanings of the conceptual system structure.

Electronic Data Processing↗
PubMed1996

Integrated computerized patient records: a two-year Geneva experience.

The UNIDOC system of computer-based medical records that was developed and made operational within the DIOGENE-2 Hospital Information System (HIS), is based upon a fully standardized and distributed open systems architecture. It should also be emphasized that UNIDOC illustrates a feasible marriage of the two technologies, UNIX and MS-DOS, is in many respects successful enough to be recommended as a sound general solution to medical office integration into a HIS.

Abstracting and Indexing↗
PubMed1995

Toward a medical linguistic knowledge base.

This paper presents the design of a Medical Linguistic Knowledge Base (MLKB). This MLKB is intended to be the multilingual recipient for all the declarative knowledge about languages. It includes words, their syntax and their conceptual representation, typology of concepts of the domain, rules for semantic analysis and conceptual schemata. For that purpose, Sowa's conceptual graphs are considered as an adequate knowledge representation. The MLKB will be an enormous body of information, and the difficulty to feed it and to validate it appears immediately. Therefore, it is necessary to start an international initiative to merge efforts from different groups.

Language↗
PubMed1995

Word segmentation processing: a way to exponentially extend medical dictionaries.

One of the most critical problems of automatic natural language processing (NLP) is the size of the medical lexicons. The set of compound medical words and the continual creation of new terms renders medical lexicons exhaustive beyond question. The structure of such dictionaries usually consists of two parts: 1) the morphological and sometimes syntactical information necessary to identify, on a grapheme level, a given word in a sentence, and 2) the part often devoted to conceptual knowledge associated with the recognized word. It is only when these two prerequisites are fulfilled that an attempt to understand the meaning of a whole expression is possible. The approach developed in this paper is a pragmatic way to rapidly increase the lexico-semantic part of medical dictionaries. We developed a semi-automatic tool, as a prototype to demonstrate the feasibility of this approach. This tool is able to translate almost any diagnosis expressed in French into its equivalent in the ICD-9CM coding scheme.

Dictionaries, Medical as Topic↗