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1.
J Biomed Inform ; 140: 104325, 2023 04.
Artigo em Inglês | MEDLINE | ID: mdl-36870586

RESUMO

Monoclonal antibodies (MAs) are increasingly used in the therapeutic arsenal. Clinical Data Warehouses (CDWs) offer unprecedented opportunities for research on real-word data. The objective of this work is to develop a knowledge organization system on MAs for therapeutic use (MATUs) applicable in Europe to query CDWs from a multi-terminology server (HeTOP). After expert consensus, three main health thesauri were selected: the MeSH thesaurus, the National Cancer Institute thesaurus (NCIt) and the SNOMED CT. These thesauri contain 1,723 MAs concepts, but only 99 (5.7 %) are identified as MATUs. The knowledge organisation system proposed in this article is a six-level hierarchical system according to their main therapeutic target. It includes 193 different concepts organised in a cross lingual terminology server, which will allow the inclusion of semantic extensions. Ninety nine (51.3 %) MATUs concepts and 94 (48.7 %) hierarchical concepts composed the knowledge organisation system. Two separates groups (an expert group and a validation group) carried out the selection, creation and validation processes. Queries identify, for unstructured data, 83 out of 99 (83.8 %) MATUs corresponding to 45,262 patients, 347,035 hospital stays and 427,544 health documents, and for structured data, 61 out of 99 (61.6 %) MATUs corresponding to 9,218 patients, 59,643 hospital stays and 104,737 hospital prescriptions. The volume of data in the CDW demonstrated the potential for using these data in clinical research, although not all MATUs are present in the CDW (16 missing for unstructured data and 38 for structured data). The knowledge organisation system proposed here improves the understanding of MATUs, the quality of queries and helps clinical researchers retrieve relevant medical information. The use of this model in CDW allows for the rapid identification of a large number of patients and health documents, either directly by a MATU of interest (e.g. Rituximab) but also by searching for parent concepts (e.g. Anti-CD20 Monoclonal Antibody).


Assuntos
Anticorpos Monoclonais , Vocabulário Controlado , Humanos , Anticorpos Monoclonais/uso terapêutico , Systematized Nomenclature of Medicine , Data Warehousing , Europa (Continente)
2.
BMC Med Inform Decis Mak ; 22(1): 34, 2022 02 08.
Artigo em Inglês | MEDLINE | ID: mdl-35135538

RESUMO

BACKGROUND: Unstructured data from electronic health records represent a wealth of information. Doc'EDS is a pre-screening tool based on textual and semantic analysis. The Doc'EDS system provides a graphic user interface to search documents in French. The aim of this study was to present the Doc'EDS tool and to provide a formal evaluation of its semantic features. METHODS: Doc'EDS is a search tool built on top of the clinical data warehouse developed at Rouen University Hospital. This tool is a multilevel search engine combining structured and unstructured data. It also provides basic analytical features and semantic utilities. A formal evaluation was conducted to measure the impact of Natural Language Processing algorithms. RESULTS: Approximately 18.1 million narrative documents are stored in Doc'EDS. The formal evaluation was conducted in 5000 clinical concepts that were manually collected. The F-measures of negative concepts and hypothetical concepts were respectively 0.89 and 0.57. CONCLUSION: In this formal evaluation, we have shown that Doc'EDS is able to deal with language subtleties to enhance an advanced full text search in French health documents. The Doc'EDS tool is currently used on a daily basis to help researchers to identify patient cohorts thanks to unstructured data.


Assuntos
Data Warehousing , Semântica , Registros Eletrônicos de Saúde , Humanos , Processamento de Linguagem Natural , Ferramenta de Busca
3.
Health Info Libr J ; 38(2): 113-124, 2021 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31837099

RESUMO

BACKGROUND: PubMed is one of the most important basic tools to access medical literature. Semantic query expansion using synonyms can improve retrieval efficacy. OBJECTIVE: The objective was to evaluate the performance of three semantic query expansion strategies. METHODS: Queries were built for forty MeSH descriptors using three semantic expansion strategies (MeSH synonyms, UMLS mappings, and mappings created by the CISMeF team), then sent to PubMed. To evaluate expansion performances for each query, the first twenty citations were selected, and their relevance were judged by three independent evaluators based on the title and abstract. RESULTS: Queries built with the UMLS expansion provided new citations with a slightly higher mean precision (74.19%) than with the CISMeF expansion (70.28%), although the difference was not significant. Inter-rater agreement was 0.28. Results varied greatly depending on the descriptor selected. DISCUSSION: The number of citations retrieved by the three strategies and their precision varied greatly according to the descriptor. This heterogeneity could be explained by the quality of the synonyms. Optimal use of these different expansions would be through various combinations of UMLS and CISMeF intersections or unions. CONCLUSION: Information retrieval tools should propose different semantic expansions depending on the descriptor and the search objectives.


Assuntos
Comportamento Apetitivo , PubMed/normas , Humanos , Armazenamento e Recuperação da Informação/métodos , Avaliação de Programas e Projetos de Saúde/métodos , PubMed/tendências , Semântica
5.
BMC Med Inform Decis Mak ; 17(1): 94, 2017 Jul 03.
Artigo em Inglês | MEDLINE | ID: mdl-28673304

RESUMO

BACKGROUND: MEDLINE is the most widely used medical bibliographic database in the world. Most of its citations are in English and this can be an obstacle for some researchers to access the information the database contains. We created a multilingual query builder to facilitate access to the PubMed subset using a language other than English. The aim of our study was to assess the impact of this multilingual query builder on the quality of PubMed queries for non-native English speaking physicians and medical researchers. METHODS: A randomised controlled study was conducted among French speaking general practice residents. We designed a multi-lingual query builder to facilitate information retrieval, based on available MeSH translations and providing users with both an interface and a controlled vocabulary in their own language. Participating residents were randomly allocated either the French or the English version of the query builder. They were asked to translate 12 short medical questions into MeSH queries. The main outcome was the quality of the query. Two librarians blind to the arm independently evaluated each query, using a modified published classification that differentiated eight types of errors. RESULTS: Twenty residents used the French version of the query builder and 22 used the English version. 492 queries were analysed. There were significantly more perfect queries in the French group vs. the English group (respectively 37.9% vs. 17.9%; p < 0.01). It took significantly more time for the members of the English group than the members of the French group to build each query, respectively 194 sec vs. 128 sec; p < 0.01. CONCLUSIONS: This multi-lingual query builder is an effective tool to improve the quality of PubMed queries in particular for researchers whose first language is not English.


Assuntos
Armazenamento e Recuperação da Informação/normas , Multilinguismo , PubMed/normas , Humanos , Idioma , Bibliotecários , Tradução
6.
Am J Ind Med ; 59(3): 221-6, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26681491

RESUMO

BACKGROUND: Reliability and credibility of research conducted by industry have been questioned, including in the field of occupational health. METHODS: Cohort studies on occupational cancer published between 2000 and 2010 were compared according to their results, their conclusions, their funding, and the affiliation of their authors. RESULTS: Overall, 510 articles were included. Studies published by authors with public affiliation or funded by public grants concluded that their study showed an excess of cancer more frequently (P = 0.01) than studies published by authors with private affiliation or funded by private grants (88% [95%CI = 85-91] vs. 73% [95%CI = 56-88] and 92% [95%CI = 86-97] vs. 71% [95%CI = 57-84], respectively). Discrepancies between statistical results and conclusion occurred more frequently in articles written by authors from the private sector than from the public sector (42% [IC95% = 26-60] vs. 23% [IC95% = 18-26], P = 0.02). CONCLUSIONS: Industry affiliations of authors or industry support of studies are associated with the results of published studies on occupational cancer. The underlying mechanisms warrant further investigation.


Assuntos
Conflito de Interesses , Neoplasias , Doenças Profissionais , Pesquisadores , Apoio à Pesquisa como Assunto , Estudos de Coortes , Humanos , Indústrias , Reprodutibilidade dos Testes
7.
BMC Med Inform Decis Mak ; 14: 17, 2014 Mar 11.
Artigo em Inglês | MEDLINE | ID: mdl-24618037

RESUMO

BACKGROUND: Visualization of Concepts in Medicine (VCM) is a compositional iconic language that aims to ease information retrieval in Electronic Health Records (EHR), clinical guidelines or other medical documents. Using VCM language in medical applications requires alignment with medical reference terminologies. Alignment from Medical Subject Headings (MeSH) thesaurus and International Classification of Diseases - tenth revision (ICD10) to VCM are presented here. This study aim was to evaluate alignment quality between VCM and other terminologies using different measures of inter-alignment agreement before integration in EHR. METHODS: For medical literature retrieval purposes and EHR browsing, the MeSH thesaurus and the ICD10, both organized hierarchically, were aligned to VCM language. Some MeSH to VCM alignments were performed automatically but others were performed manually and validated. ICD10 to VCM alignment was entirely manually performed. Inter-alignment agreement was assessed on ICD10 codes and MeSH descriptors, sharing the same Concept Unique Identifiers in the Unified Medical Language System (UMLS). Three metrics were used to compare two VCM icons: binary comparison, crude Dice Similarity Coefficient (DSCcrude), and semantic Dice Similarity Coefficient (DSCsemantic), based on Lin similarity. An analysis of discrepancies was performed. RESULTS: MeSH to VCM alignment resulted in 10,783 relations: 1,830 of which were manually performed and 8,953 were automatically inherited. ICD10 to VCM alignment led to 19,852 relations. UMLS gathered 1,887 alignments between ICD10 and MeSH. Only 1,606 of them were used for this study. Inter-alignment agreement using only validated MeSH to VCM alignment was 74.2% [70.5-78.0]CI95%, DSCcrude was 0.93 [0.91-0.94]CI95%, and DSCsemantic was 0.96 [0.95-0.96]CI95%. Discrepancy analysis revealed that even if two thirds of errors came from the reviewers, UMLS was nevertheless responsible for one third. CONCLUSIONS: This study has shown strong overall inter-alignment agreement between MeSH to VCM and ICD10 to VCM manual alignments. VCM icons have now been integrated into a guideline search engine (http://www.cismef.org) and a health terminologies portal (http://www.hetop.eu).


Assuntos
Armazenamento e Recuperação da Informação/normas , Terminologia como Assunto , Vocabulário Controlado , Registros Eletrônicos de Saúde/normas , Humanos , Classificação Internacional de Doenças/estatística & dados numéricos , Medical Subject Headings/estatística & dados numéricos , Unified Medical Language System/normas
8.
Front Digit Health ; 5: 1217694, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37497185

RESUMO

Background: Drug-related problems (DRPs) can lead to serious health issues and have significant economic impacts on healthcare systems. One solution to address this issue is the use of computerized physician order entry systems (CPOE), which can help prevent DRPs by reducing the risk of medication errors. Objective: The purpose of this study is to provide an analysis on scientific production of the past 20 years in order to describe trends in academic publishing on CPOE and to identify the major topics as well as the predominant actors (journals, countries) involved in this field. Methods: A PubMed search was carried out to extract articles related to computerized provider order entry during the period January 1st 2003- December 31st 2022 using a specific query. Data were downloaded from PubMed in Extensible Markup Language (XML) and were processed through a dedicated parser. Results: A total of 2,946 articles were retrieved among 623 journals. One third of these articles were published in eight journals. Publications grew strongly from 2002 to 2006, with a dip in 2008 followed by an increase again in 2009. After 2009, there follows a decreasing until 2022.The most producing countries are the USA with 51.39% of the publication over the period by France (3.80%), and Canada (3.77%). About disciplines, the top 3 is: "medical informatics" (21.62% of articles), "pharmacy" (19.04%), and "pediatrics" (6.56%). Discussion: This study provides an overview of publication trends related to CPOE, which exhibited a significant increase in the first decade of the 21st century followed by a decline after 2009. Possible reasons for this decline include the emergence of digital health tools beyond CPOE, as well as healthcare professionals experiencing alert fatigue of the current system. Conclusion: Future research should focus on analyzing publication trends in the field of medical informatics and decision-making tools to identify other areas of interest that may have surpassed the development of CPOE.

9.
Yearb Med Inform ; 32(1): 27-35, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38147847

RESUMO

OBJECTIVE: Planning reliable long-term planning actions to handle disruptive events requires a timely development of technological infrastructures, as well as the set-up of focused strategies for emergency management. The paper aims to highlight the needs for standardization, integration, and interoperability between Accident & Emergency Informatics (A&EI) and One Digital Health (ODH), as fields capable of dealing with peculiar dynamics for a technology-boosted management of emergencies under an overarching One Health panorama. METHODS: An integrative analysis of the literature was conducted to draw attention to specific foci on the correlation between ODH and A&EI, in particular: (i) the management of disruptive events from private smart spaces to diseases spreading, and (ii) the concepts of (health-related) quality of life and well-being. RESULTS: A digitally-focused management of emergency events that tackles the inextricable interconnectedness between humans, animals, and surrounding environment, demands standardization, integration, and systems interoperability. A consistent and finalized process of adoption and implementation of methods and tools from the International Standard Accident Number (ISAN), via findability, accessibility, interoperability, and reusability (FAIR) data principles, to Medical Informatics and Digital Health Multilingual Ontology (MIMO) - capable of looking at different approaches to encourage the integration between the ODH framework and the A&EI vision, provides a first answer to these needs. CONCLUSIONS: ODH and A&EI look at different scales but with similar goals for converging health and environmental-related data management standards to enable multi-sources, interdisciplinary, and real-time data integration and interoperability. This allows holistic digital health both in routine and emergency events.


Assuntos
Informática Médica , Saúde Única , Humanos , Qualidade de Vida , Gerenciamento de Dados , Padrões de Referência
10.
Int J Med Inform ; 170: 104976, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36599261

RESUMO

INTRODUCTION: The cytochrome P450 (CYP450) enzyme system is involved in the metabolism of certain drugs and is responsible for most drug interactions. These interactions result in either an enzymatic inhibition or an enzymatic induction mechanism that has an impact on the therapeutic management of patients. Detecting these drug interactions will allow for better predictability in therapeutic response. Therefore, computerized solutions can represent a valuable help for clinicians in their tasks of detection. OBJECTIVE: The objective of this study is to provide a structured data-source of interactions involving the CYP450 enzyme system. These interactions are aimed to be integrated in the cross-lingual multi-terminology server HeTOP (Health Terminologies and Ontologies Portal), to support the query processing of the clinical data warehouse (CDW) EDSaN (Entrepôt de Données de Santé Normand). MATERIAL AND METHODS: A selection and curation of drug components (DCs) that share a relationship with the CYP450 system was performed from several international data sources. The DCs were linked according to the type of relationship which can be substrate, inhibitor, or inducer. These relationships were then integrated into the HeTOP server. To validate the CYP450 relationships, a semantic query was performed on the CDW, whose search engine is founded on HeTOP data (concepts, terms, and relations). RESULTS: A total of 776 DCs are associated by a new interaction relationship, integrated in HeTOP, by 14 enzymes. These are CYP450 1A2, 2A6, 2B6, 2C8, 2C9, 2C18, 2C19, 2D6, 2E1, 3A4, 3A7, 11B1,11B2 mitochondrial and P-glycoprotein, constituting a total of 2,088 relationships. A general modelling of cytochromic interactions was performed. From this model, 233,006 queries were processed in less than two hours, demonstrating the usefulness and performance of our CDW implementation. Moreover, they showed that in our university hospital, the concurrent prescription that could cause a cytochromic interaction is Bisoprolol with Amiodarone by enzymatic inhibition for 2,493 patients. DISCUSSION: The queries submitted to the CDW EDSaN allowed to highlight the most prescribed molecules simultaneously and potentially responsible for cytochromic interactions. In a second step, it would be interesting to evaluate the real clinical impact by looking for possible adverse effects of these interactions in the patients' files. Other computational solutions for cytochromic interactions exist. The impact of CYP450 is particularly important for drugs with narrow therapeutic window (NTW) as they can lead to increased toxicity or therapeutic failure. It is also important to define which drug component is a pro-drug and to considerate the many genetic polymorphisms of patients. CONCLUSION: The HeTOP server contains a non-negligible number of relationships between drug components and CYP450 from multiple reference sources. These data allow us to query our Clinical Data Warehouse to highlight these cytochromic interactions. It would be interesting in the future to assess the actual clinical impact in hospital reports.


Assuntos
Sistema Enzimático do Citocromo P-450 , Data Warehousing , Humanos , Sistema Enzimático do Citocromo P-450/genética , Sistema Enzimático do Citocromo P-450/metabolismo
11.
BMC Bioinformatics ; 13 Suppl 14: S11, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23095521

RESUMO

BACKGROUND: The Internet is a major source of health information but most seekers are not familiar with medical vocabularies. Hence, their searches fail due to bad query formulation. Several methods have been proposed to improve information retrieval: query expansion, syntactic and semantic techniques or knowledge-based methods. However, it would be useful to clean those queries which are misspelled. In this paper, we propose a simple yet efficient method in order to correct misspellings of queries submitted by health information seekers to a medical online search tool. METHODS: In addition to query normalizations and exact phonetic term matching, we tested two approximate string comparators: the similarity score function of Stoilos and the normalized Levenshtein edit distance. We propose here to combine them to increase the number of matched medical terms in French. We first took a sample of query logs to determine the thresholds and processing times. In the second run, at a greater scale we tested different combinations of query normalizations before or after misspelling correction with the retained thresholds in the first run. RESULTS: According to the total number of suggestions (around 163, the number of the first sample of queries), at a threshold comparator score of 0.3, the normalized Levenshtein edit distance gave the highest F-Measure (88.15%) and at a threshold comparator score of 0.7, the Stoilos function gave the highest F-Measure (84.31%). By combining Levenshtein and Stoilos, the highest F-Measure (80.28%) is obtained with 0.2 and 0.7 thresholds respectively. However, queries are composed by several terms that may be combination of medical terms. The process of query normalization and segmentation is thus required. The highest F-Measure (64.18%) is obtained when this process is realized before spelling-correction. CONCLUSIONS: Despite the widely known high performance of the normalized edit distance of Levenshtein, we show in this paper that its combination with the Stoilos algorithm improved the results for misspelling correction of user queries. Accuracy is improved by combining spelling, phoneme-based information and string normalizations and segmentations into medical terms. These encouraging results have enabled the integration of this method into two projects funded by the French National Research Agency-Technologies for Health Care. The first aims to facilitate the coding process of clinical free texts contained in Electronic Health Records and discharge summaries, whereas the second aims at improving information retrieval through Electronic Health Records.


Assuntos
Algoritmos , Armazenamento e Recuperação da Informação , Informática Médica/métodos , Humanos , Internet , Idioma , Informática Médica/instrumentação , Vocabulário Controlado
12.
Occup Environ Med ; 69(8): 603-5, 2012 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-22693268

RESUMO

OBJECTIVES: Most physicians have received only limited training in occupational medicine (OM) during their studies. Since they rely mainly on one 'general medical' journal to keep their medical knowledge up to date, it is worthwhile questioning the importance of OM in these journals. The aim of this study was to measure the relative weight of OM in the major journals of general medicine and to compare the journals. METHODS: The 14,091 articles published in the Lancet, the NEJM, the JAMA and the BMJ in 1997, 2002 and 2007 were analysed. The relative weight of OM and the other medical specialties was determined by categorisation of all the articles, using a categorisation algorithm, which inferred the medical specialties relevant to each MEDLINE article file from the major medical subject headings (MeSH) terms used by the indexers of the US National Library of Medicine to describe each article. RESULTS: The 14,091 articles included in this study were indexed by 22,155 major MeSH terms, which were categorised into 73 different medical specialties. Only 0.48% of the articles had OM as a main topic. OM ranked 44th among the 73 specialties, with limited differences between the four journals studied. There was no clear trend over the 10-year period. CONCLUSIONS: The importance of OM is very low in the four major journals of general and internal medicine, and we can consider that physicians get a very limited view of the evolution of knowledge in OM.


Assuntos
Bibliometria , Pesquisa Biomédica/estatística & dados numéricos , Medicina do Trabalho , Publicações Periódicas como Assunto/estatística & dados numéricos , Editoração/estatística & dados numéricos , Humanos , MEDLINE , Medical Subject Headings , National Library of Medicine (U.S.) , Editoração/tendências , Estados Unidos
13.
J Med Libr Assoc ; 100(3): 176-83, 2012 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-22879806

RESUMO

BACKGROUND: As more scientific work is published, it is important to improve access to the biomedical literature. Since 2000, when Medical Subject Headings (MeSH) Concepts were introduced, the MeSH Thesaurus has been concept based. Nevertheless, information retrieval is still performed at the MeSH Descriptor or Supplementary Concept level. OBJECTIVE: The study assesses the benefit of using MeSH Concepts for indexing and information retrieval. METHODS: Three sets of queries were built for thirty-two rare diseases and twenty-two chronic diseases: (1) using PubMed Automatic Term Mapping (ATM), (2) using Catalog and Index of French-language Health Internet (CISMeF) ATM, and (3) extrapolating the MEDLINE citations that should be indexed with a MeSH Concept. RESULTS: Type 3 queries retrieve significantly fewer results than type 1 or type 2 queries (about 18,000 citations versus 200,000 for rare diseases; about 300,000 citations versus 2,000,000 for chronic diseases). CISMeF ATM also provides better precision than PubMed ATM for both disease categories. DISCUSSION: Using MeSH Concept indexing instead of ATM is theoretically possible to improve retrieval performance with the current indexing policy. However, using MeSH Concept information retrieval and indexing rules would be a fundamentally better approach. These modifications have already been implemented in the CISMeF search engine.


Assuntos
Indexação e Redação de Resumos/estatística & dados numéricos , Bases de Dados como Assunto/estatística & dados numéricos , Medical Subject Headings/estatística & dados numéricos , Terminologia como Assunto , Algoritmos , Doença Crônica , Processamento Eletrônico de Dados , França , Humanos , Armazenamento e Recuperação da Informação , Idioma , MEDLINE/estatística & dados numéricos , Controle de Qualidade , Doenças Raras
14.
Stud Health Technol Inform ; 180: 949-53, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22874333

RESUMO

UNLABELLED: The Health Terminology/Ontology Portal (HeTOP) was developed to provide easy access to health terminologies and ontologie. The repository is not only dedicated to professionals but is also a valuable teaching tool. Currently, it provides access to thirty two health terminologies and ontologies available mainly in French or in English, but also in German, Italian, Chinese, etc. HeTOP can be used by both humans and computers via Web services. To integrate new resources into HeTOP, three steps are necessary: (1) designing a meta-model into which each terminology (or ontology) can be integrated, (2) developing a process to include terminologies into HeTOP, (3) building and integrating existing and new inter & intra-terminology semantic harmonization into HeTOP. Currently, 600 unique machines use the MeSH version of HeTOP every day and restricted terminologies/ontologies are used for teaching purposes in several medical schools in France. The multilingual version of HeTOP is available (URL: http://hetop.eu/) and provides free access to ICD10 and FMA in ten languages. CONCLUSION: HeTOP is a rich tool, useful for a wide range of applications and users, especially in education and resource indexing but also in information retrieval or performing audits in terminology management.


Assuntos
Instrução por Computador/métodos , Educação Médica/métodos , Internet , Terminologia como Assunto , Vocabulário Controlado , Europa (Continente)
15.
PLoS One ; 17(8): e0264661, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35947594

RESUMO

INTRODUCTION: Preprints have been widely cited during the COVID-19 pandemics, even in the major medical journals. However, since subsequent publication of preprint is not always mentioned in preprint repositories, some may be inappropriately cited or quoted. Our objectives were to assess the reliability of preprint citations in articles on COVID-19, to the rate of publication of preprints cited in these articles and to compare, if relevant, the content of the preprints to their published version. METHODS: Articles published on COVID in 2020 in the BMJ, The Lancet, the JAMA and the NEJM were manually screened to identify all articles citing at least one preprint from medRxiv. We searched PubMed, Google and Google Scholar to assess if the preprint had been published in a peer-reviewed journal, and when. Published articles were screened to assess if the title, data or conclusions were identical to the preprint version. RESULTS: Among the 205 research articles on COVID published by the four major medical journals in 2020, 60 (29.3%) cited at least one medRxiv preprint. Among the 182 preprints cited, 124 were published in a peer-reviewed journal, with 51 (41.1%) before the citing article was published online and 73 (58.9%) later. There were differences in the title, the data or the conclusion between the preprint cited and the published version for nearly half of them. MedRxiv did not mentioned the publication for 53 (42.7%) of preprints. CONCLUSIONS: More than a quarter of preprints citations were inappropriate since preprints were in fact already published at the time of publication of the citing article, often with a different content. Authors and editors should check the accuracy of the citations and of the quotations of preprints before publishing manuscripts that cite them.


Assuntos
COVID-19 , Publicações Periódicas como Assunto , COVID-19/epidemiologia , Humanos , Revisão por Pares , PubMed , Reprodutibilidade dos Testes
16.
Stud Health Technol Inform ; 294: 302-306, 2022 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-35612081

RESUMO

Suitable causal inference in biostatistics can be best achieved by knowledge representation thanks to causal diagrams or directed acyclic graphs. However, necessary and sufficient causes are not easily represented. Since existing ontologies do not fill this gap, we designed OntoBioStat in order to enable covariate selection support based on causal relation representations. OntoBioStat automatic ontological causal diagram construction and inferences are detailed in this study. OntoBioStat inferences are allowed by Semantic Web Rule Language rules and axioms. First, statements made by the users include outcome, exposure, covariate, and causal relation specification. Then, reasoning enable automatic construction using generic instances of Meta_Variable and Necessary_Variable classes. Finally, inferred classes highlighted potential bias such as confounder-like. Ontological causal diagram built with OntoBioStat was compared to a standard causal diagram (without OntoBioStat) in a theoretical study. It was found that confounding and bias were not completely identified by the standard causal diagram, and erroneous covariate sets were provided. Further research is needed in order to make OntoBioStat more usable.


Assuntos
Biometria , Bioestatística , Viés , Causalidade
17.
Stud Health Technol Inform ; 290: 150-153, 2022 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-35672989

RESUMO

Clinical Data Warehouses (CDW) are gold mines and may be useful to manage the COVID-19 outbreak. This article details the use of CDW in order to retrieve patients for vaccination purposes. A list of 34 diseases (or conditions) was published by French Health Authorities to target individuals at a high risk of developing a severe form of COVID. Using a multilevel search engine, 23 queries were built based on structured or unstructured data using natural language processing features. The Diagnosis Related Group coding system was used alone in three queries (13.0%), coupled with unstructured data in four queries (17.4%), and unstructured data were used alone in 16 queries (69.6%). Eleven diseases (conditions) were too broad to be translated into queries. Finally, 6,006 unique re-identified patients were retrieved. This use case demonstrates the usefulness of the Rouen University Hospital CDW in retrieving patients for other purposes than translational research.


Assuntos
COVID-19 , Data Warehousing , COVID-19/prevenção & controle , Registros Eletrônicos de Saúde , Humanos , Processamento de Linguagem Natural , Vacinação
18.
Stud Health Technol Inform ; 289: 260-263, 2022 Jan 14.
Artigo em Inglês | MEDLINE | ID: mdl-35062142

RESUMO

The Normandy health data warehouse EDSaN integrates the medication orders from the University Hospital of Rouen (France). This study aims at describing the design and the evaluation of an information retrieval system founded on a complex and semantically augmented knowledge graph dedicated to EDSaN drugs' prescriptions. The system is intended to help the selection of drugs in the search process by health professionals. The manual evaluation of the relevance of the returned drugs showed encouraging results as expected. A deeper analysis in order to improve the ranking method is needed and will be performed in a future work.


Assuntos
Reconhecimento Automatizado de Padrão , Preparações Farmacêuticas , França , Humanos , Armazenamento e Recuperação da Informação , Conhecimento
19.
Stud Health Technol Inform ; 290: 1002-1003, 2022 Jun 06.
Artigo em Inglês | MEDLINE | ID: mdl-35673176

RESUMO

BACKGROUND: Although the drug is finished, identifiable, there is no universally accepted standard for naming them. The objective of this work is to evaluate qualitatively the HeTOP drug terminology server by two categories of students: (a) pharmacy students and (b) a control group. METHODS: A formal evaluation was built to measure the perception of users about the HeTOP drug server, using the three mains questions about "teaching interest", "skill interest" (or competence) and "ergonomics". RESULTS: The three pharmacy student subgroups gave the best and the worst score to the same categories. CONCLUSION: All three criteria are rated above 6.5 out of 10. The HeTOP drug terminology server is freely available to "non drug" specialists (URL: www.hetop.eu/hetop/drugs/).


Assuntos
Estudantes de Farmácia , Humanos , Farmacêuticos
20.
Int J Med Inform ; 167: 104860, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-36084537

RESUMO

BACKGROUND: Even if English is the leading language for international communication, it is essential to keep in mind that research runs at the local level by local teams generally communicating in their local/national language, especially in Europe among European projects. OBJECTIVE: Therefore, the European Federation for Medical Informatics - Working Group on Health Informatics for Inter-regional Cooperation" has one objective: To develop a multilingual ontology focusing on Health Informatics and Digital Health as a collaboration tool that improves international and, in particular, European collaborations. RESULTS: We have developed the Medical Informatics and Digital Health Multilingual Ontology (MIMO). Hosted on the Health Terminology/Ontology Portal (HeTOP), MIMO contains around 1,000 concepts, 460 MeSH Descriptors, 220 MeSH Concepts, and more than 300 newly created concepts. MIMO is continuously updated to comprise as recent as possible concepts and their translations in more than 30 languages. Moreover, the MIMO's development team constantly improves MIMO content and supporting information. Thus, during workshop discussions and one-on-one exchanges, the MIMO team has collected domain experts' opinions about the community's interests and suggestions for future enhancements. Moreover, MIMO will be integrated to support the annotation and categorization of research products into the HosmartAI European project involving more than 20 countries around Europe and worldwide. CONCLUSION: MIMO is hosted by HeTOP (Health Terminology/Ontology Portal), which integrates 100 terminologies and ontologies in 55 languages. MIMO is freely available online. MIMO is portable to other knowledge platforms as part of MIMO's main aims to facilitate communication between medical librarians, translators, and researchers as well as to support students' self-learning.


Assuntos
Informática Médica , Multilinguismo , Europa (Continente) , Humanos , Idioma
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