28 research outputs found
Evaluation of natural language processing from emergency department computerized medical records for intra-hospital syndromic surveillance
<p>Abstract</p> <p>Background</p> <p>The identification of patients who pose an epidemic hazard when they are admitted to a health facility plays a role in preventing the risk of hospital acquired infection. An automated clinical decision support system to detect suspected cases, based on the principle of syndromic surveillance, is being developed at the University of Lyon's Hôpital de la Croix-Rousse. This tool will analyse structured data and narrative reports from computerized emergency department (ED) medical records. The first step consists of developing an application (UrgIndex) which automatically extracts and encodes information found in narrative reports. The purpose of the present article is to describe and evaluate this natural language processing system.</p> <p>Methods</p> <p>Narrative reports have to be pre-processed before utilizing the French-language medical multi-terminology indexer (ECMT) for standardized encoding. UrgIndex identifies and excludes syntagmas containing a negation and replaces non-standard terms (abbreviations, acronyms, spelling errors...). Then, the phrases are sent to the ECMT through an Internet connection. The indexer's reply, based on Extensible Markup Language, returns codes and literals corresponding to the concepts found in phrases. UrgIndex filters codes corresponding to suspected infections. Recall is defined as the number of relevant processed medical concepts divided by the number of concepts evaluated (coded manually by the medical epidemiologist). Precision is defined as the number of relevant processed concepts divided by the number of concepts proposed by UrgIndex. Recall and precision were assessed for respiratory and cutaneous syndromes.</p> <p>Results</p> <p>Evaluation of 1,674 processed medical concepts contained in 100 ED medical records (50 for respiratory syndromes and 50 for cutaneous syndromes) showed an overall recall of 85.8% (95% CI: 84.1-87.3). Recall varied from 84.5% for respiratory syndromes to 87.0% for cutaneous syndromes. The most frequent cause of lack of processing was non-recognition of the term by UrgIndex (9.7%). Overall precision was 79.1% (95% CI: 77.3-80.8). It varied from 81.4% for respiratory syndromes to 77.0% for cutaneous syndromes.</p> <p>Conclusions</p> <p>This study demonstrates the feasibility of and interest in developing an automated method for extracting and encoding medical concepts from ED narrative reports, the first step required for the detection of potentially infectious patients at epidemic risk.</p
Overview of BioASQ 2021-MESINESP track. Evaluation of advance hierarchical classification techniques for scientific literature, patents and clinical trials
CLEF 2021 – Conference and Labs of the Evaluation Forum, September 21–24, 2021, Bucharest, Romania,There is a pressing need to exploit recent advances in natural language processing technologies, in
particular language models and deep learning approaches, to enable improved retrieval, classification
and ultimately access to information contained in multiple, heterogeneous types of documents. This is
particularly true for the field of biomedicine and clinical research, where medical experts and scientists
need to carry out complex search queries against a variety of document collections, including literature,
patents, clinical trials or other kind of content like EHRs. Indexing documents with structured controlled
vocabularies used for semantic search engines and query expansion purposes is a critical task for enabling
sophisticated user queries and even cross-language retrieval. Due to the complexity of the medical domain
and the use of very large hierarchical indexing terminologies, implementing efficient automatic systems
to aid manual indexing is extremely difficult. This paper provides a summary of the MESINESP task
results on medical semantic indexing in Spanish (BioASQ/ CLEF 2021 Challenge). MESINESP was carried
out in direct collaboration with literature content databases and medical indexing experts using the DeCS
vocabulary, a similar resource as MeSH terms. Seven participating teams used advanced technologies
including extreme multilabel classification and deep language models to solve this challenge which can
be viewed as a multi-label classification problem. MESINESP resources, we have released a Gold Standard
collection of 243,000 documents with a total of 2179 manual annotations divided in train, development
and test subsets covering literature, patents as well as clinical trial summaries, under a cross-genre
training and data labeling scenario. Manual indexing of the evaluation subsets was carried out by three
independent experts using a specially developed indexing interface called ASIT. Additionally, we have
published a collection of large-scale automatic semantic annotations based on NER systems of these
documents with mentions of drugs/medications (170,000), symptoms (137,000), diseases (840,000) and
clinical procedures (415,000). In addition to a summary of the used technologies by the teams, this paperS
SIFR BioPortal : Un portail ouvert et générique d’ontologies et de terminologies biomédicales françaises au service de l’annotation sémantique
National audienceContexte – Le volume de données en biomédecine ne cesse de croître. En dépit d'une large adoption de l'anglais, une quantité significative de ces données est en français. Dans le do-maine de l’intégration de données, les terminologies et les ontologies jouent un rôle central pour structurer les données biomédicales et les rendre interopérables. Cependant, outre l'existence de nombreuses ressources en anglais, il y a beaucoup moins d'ontologies en français et il manque crucialement d'outils et de services pour les exploiter. Cette lacune contraste avec le montant considérable de données biomédicales produites en français, par-ticulièrement dans le monde clinique (e.g., dossiers médicaux électroniques). Methode & Résultats – Dans cet article, nous présentons certains résultats du projet In-dexation sémantique de ressources biomédicales francophones (SIFR), en particulier le SIFR BioPortal, une plateforme ouverte et générique pour l’hébergement d’ontologies et de terminologies biomédicales françaises, basée sur la technologie du National Center for Biomedical Ontology. Le portail facilite l’usage et la diffusion des ontologies du domaine en offrant un ensemble de services (recherche, alignements, métadonnées, versionnement, vi-sualisation, recommandation) y inclus pour l’annotation sémantique. En effet, le SIFR An-notator est un outil d’annotation basé sur les ontologies pour traiter des données textuelles en français. Une évaluation préliminaire, montre que le service web obtient des résultats équivalents à ceux reportés précedement, tout en étant public, fonctionnel et tourné vers les standards du web sémantique. Nous présentons également de nouvelles fonctionnalités pour les services à base d’ontologies pour l’anglais et le français
Foundation, Implementation and Evaluation of the MorphoSaurus System: Subword Indexing, Lexical Learning and Word Sense Disambiguation for Medical Cross-Language Information Retrieval
Im medizinischen Alltag, zu welchem viel Dokumentations- und Recherchearbeit gehört, ist mittlerweile der überwiegende Teil textuell kodierter Information elektronisch verfügbar. Hiermit kommt der Entwicklung leistungsfähiger Methoden zur effizienten Recherche eine vorrangige Bedeutung zu.
Bewertet man die Nützlichkeit gängiger Textretrievalsysteme aus dem Blickwinkel der medizinischen Fachsprache, dann mangelt es ihnen an morphologischer Funktionalität (Flexion, Derivation und Komposition), lexikalisch-semantischer Funktionalität und der Fähigkeit zu einer sprachübergreifenden Analyse großer Dokumentenbestände.
In der vorliegenden Promotionsschrift werden die theoretischen Grundlagen des MorphoSaurus-Systems (ein Akronym für Morphem-Thesaurus) behandelt. Dessen methodischer Kern stellt ein um Morpheme der medizinischen Fach- und Laiensprache gruppierter Thesaurus dar, dessen Einträge mittels semantischer Relationen sprachübergreifend verknüpft sind. Darauf aufbauend wird ein Verfahren vorgestellt, welches (komplexe) Wörter in Morpheme segmentiert, die durch sprachunabhängige, konzeptklassenartige Symbole ersetzt werden. Die resultierende Repräsentation ist die Basis für das sprachübergreifende, morphemorientierte Textretrieval.
Neben der Kerntechnologie wird eine Methode zur automatischen Akquise von Lexikoneinträgen vorgestellt, wodurch bestehende Morphemlexika um weitere Sprachen ergänzt werden. Die Berücksichtigung sprachübergreifender Phänomene führt im Anschluss zu einem neuartigen Verfahren zur Auflösung von semantischen Ambiguitäten.
Die Leistungsfähigkeit des morphemorientierten Textretrievals wird im Rahmen umfangreicher, standardisierter Evaluationen empirisch getestet und gängigen Herangehensweisen gegenübergestellt
Towards a system of concepts for Family Medicine. Multilingual indexing in General Practice/ Family Medicine in the era of Semantic Web
UNIVERSITY OF LIÈGE, BELGIUM
Executive Summary
Faculty of Medicine
Département Universitaire de Médecine Générale.
Unité de recherche Soins Primaires et Santé
Doctor in biomedical sciences
Towards a system of concepts for Family Medicine.
Multilingual indexing in General Practice/ Family Medicine in the era
of SemanticWeb
by Dr. Marc JAMOULLE
Introduction
This thesis is about giving visibility to the often overlooked work of family
physicians and consequently, is about grey literature in General Practice
and Family Medicine (GP/FM). It often seems that conference organizers
do not think of GP/FM as a knowledge-producing discipline that deserves
active dissemination. A conference is organized, but not much is done with
the knowledge shared at these meetings. In turn, the knowledge cannot be
reused or reapplied. This these is also about indexing. To find knowledge
back, indexing is mandatory. We must prepare tools that will automatically
index the thousands of abstracts that family doctors produce each year in
various languages. And finally this work is about semantics1. It is an introduction
to health terminologies, ontologies, semantic data, and linked
open data. All are expressions of the next step: Semantic Web for health
care data. Concepts, units of thought expressed by terms, will be our target
and must have the ability to be expressed in multiple languages. In turn,
three areas of knowledge are at stake in this study: (i) Family Medicine as a
pillar of primary health care, (ii) computational linguistics, and (iii) health
information systems.
Aim
• To identify knowledge produced by General practitioners (GPs) by
improving annotation of grey literature in Primary Health Care
• To propose an experimental indexing system, acting as draft for a
standardized table of content of GP/GM
• To improve the searchability of repositories for grey literature in GP/GM.
1For specific terms, see the Glossary page 257
x
Methods
The first step aimed to design the taxonomy by identifying relevant concepts
in a compiled corpus of GP/FM texts. We have studied the concepts
identified in nearly two thousand communications of GPs during
conferences. The relevant concepts belong to the fields that are focusing
on GP/FM activities (e.g. teaching, ethics, management or environmental
hazard issues).
The second step was the development of an on-line, multilingual, terminological
resource for each category of the resulting taxonomy, named
Q-Codes. We have designed this terminology in the form of a lightweight
ontology, accessible on-line for readers and ready for use by computers of
the semantic web. It is also fit for the Linked Open Data universe.
Results
We propose 182 Q-Codes in an on-line multilingual database (10 languages)
(www.hetop.eu/Q) acting each as a filter for Medline. Q-Codes are also available
under the form of Unique Resource Identifiers (URIs) and are exportable
in Web Ontology Language (OWL). The International Classification of Primary
Care (ICPC) is linked to Q-Codes in order to form the Core Content
Classification in General Practice/Family Medicine (3CGP). So far, 3CGP is
in use by humans in pedagogy, in bibliographic studies, in indexing congresses,
master theses and other forms of grey literature in GP/FM. Use by
computers is experimented in automatic classifiers, annotators and natural
language processing.
Discussion
To the best of our knowledge, this is the first attempt to expand the ICPC
coding system with an extension for family physician contextual issues,
thus covering non-clinical content of practice. It remains to be proven that
our proposed terminology will help in dealing with more complex systems,
such as MeSH, to support information storage and retrieval activities.
However, this exercise is proposed as a first step in the creation of an ontology
of GP/FM and as an opening to the complex world of Semantic Web
technologies.
Conclusion
We expect that the creation of this terminological resource for indexing abstracts
and for facilitating Medline searches for general practitioners, researchers
and students in medicine will reduce loss of knowledge in the
domain of GP/FM. In addition, through better indexing of the grey literature
(congress abstracts, master’s and doctoral theses), we hope to enhance
the accessibility of research results and give visibility to the invisible work
of family physicians