Rabies Risk: Difficulties Encountered during Management of Grouped Cases of Bat Bites in 2 Isolated Villages in French Guiana.

In French Guiana, from 1984 to 2011, 14 animal rabies cases and 1 human rabies case (2008) were diagnosed. In January 2011, vampire-bat attacks occurred in 2 isolated villages. In mid-January, a medical team from the Cayenne Centre for Anti-Rabies Treatment visited the sites to manage individuals potentially exposed to rabies and, in April, an anti-rabies vaccination campaign for dogs was conducted. Twenty individuals were bitten by bats in 1 month, most frequently on the feet. The median time to start management was 15 days. The complete Zagreb vaccination protocol (2 doses on day 0 and 1 dose on days 7 and 21) was administered to 16 patients, 12 also received specific immunoglobulins. The antibody titration was obtained for 12 patients (different from those who received immunoglobulins). The antibody titers were ≥0.5 EU/mL for all of them. The serology has not been implemented for the 12 patients who received immunoglobulins. Accidental destruction of a vampire-bat colony could be responsible for the attacks. The isolation and absence of sensitization of the populations were the main explanations for the management difficulties encountered. Sensitization programs should be conducted regularly.

Deforestation, agriculture and farm jobs: a good recipe for Plasmodium vivax in French Guiana.

BACKGROUND: In a malaria-endemic area the distribution of patients is neither constant in time nor homogeneous in space. The WHO recommends the stratification of malaria risk on a fine geographical scale. In the village of Cacao in French Guiana, the study of the spatial and temporal distribution of malaria cases, during an epidemic, allowed a better understanding of the environmental factors promoting malaria transmission. METHODS: A dynamic cohort of 839 persons living in 176 households (only people residing permanently in the village) was constituted between January 1st, 2002 and December 31st, 2007.The information about the number of inhabitants per household, the number of confirmed cases of Plasmodium vivax and house GPS coordinates were collected to search for spatial or temporal clustering using Kurlldorff's statistical method. RESULTS: Of the 839 persons living permanently in the village of Cacao, 359 persons presented at least one vivax malaria episode between 2002 and 2007. Five temporal clusters and four spatial clusters were identified during the study period. In all temporal clusters, April was included. Two spatial clusters were localized at the north of the village near the Comté River and two others localized close to orchards. CONCLUSION: The spatial heterogeneity of malaria in the village may have been influenced by environmental disturbances due to local agricultural policies: deforestation, cultures of fresh produce, or drainage of water for agriculture. This study allowed generating behavioural, entomological, or environmental hypotheses that could be useful to improve prevention campaigns.

Design and validation of an automated method to detect known adverse drug reactions in MEDLINE: a contribution from the EU-ADR project.

OBJECTIVES: The aim of this research was to automate the search of publications concerning adverse drug reactions (ADR) by defining the queries used to search MEDLINE and by determining the required threshold for the number of extracted publications to confirm the drug/event association in the literature. METHODS: We defined an approach based on the medical subject headings (MeSH) 'descriptor records' and 'supplementary concept records' thesaurus, using the subheadings 'chemically induced' and 'adverse effects' with the 'pharmacological action' knowledge. An expert-built validation set of true positive and true negative drug/adverse event associations (n=61) was used to validate our method. RESULTS: Using a threshold of three of more extracted publications, the automated search method presented a sensitivity of 90% and a specificity of 100%. For nine different drug/event pairs selected, the recall of the automated search ranged from 24% to 64% and the precision from 93% to 48%. CONCLUSIONS: This work presents a method to find previously established relationships between drugs and adverse events in the literature. Using MEDLINE, following a MeSH approach to filter the signals, is a valid option. Our contribution is available as a web service that will be integrated in the final European EU-ADR project (Exploring and Understanding Adverse Drug Reactions by integrative mining of clinical records and biomedical knowledge) automated system.

Assisting the translation of the CORE subset of SNOMED CT into French.

BACKGROUND: the Core Subset of SNOMED CT is part of the UMLS-Core Project dedicated to study problem list vocabularies. SNOMED CT is not yet translated into French. OBJECTIVE: to propose an automated method to assist the translation of the CORE Subset of SNOMED CT into French. MATERIAL: the 2009 AA versions of the CORE Subset of SNOMED CT and UMLS; use of four French-language terminologies integrated into the UMLS Metathesaurus: SNOMED International, ICD10, MedDRA, and MeSH. METHOD: an exact mapping completed by a close mapping between preferred terms of the CORE Subset of SNOMED CT and those of the four terminologies. RESULTS: 89% of the preferred terms of the CORE Subset of SNOMED CT are mapped with at least one preferred term in one of the four terminologies. DISCUSSION: if needed, synonymous terms could be added by the means of synonyms in the terminologies; the proposed method is independent from French and could be applied to other natural languages.

Mapping the ATC classification to the UMLS metathesaurus: some pragmatic applications.

ATC classification is a WHO international classification used to classify drugs. The aim of this paper is to evaluate two lexical methods in English and in French to map ATC to UMLS. Several applications have been impemented to illustrate the use of the ATC mapping in English and French: (a) MeSH translation in Norwegian, (b) Drug Information Portal, and (c) ATC to PubMed tool. Two lexical methods were used to map ATC to UMLS. The first approach used a French natural language processing tool to map French terms of ATC to the French terminologies of UMLS. The second approach used the MetaMap tool to map English terms of ATC to UMLS. The English MetaMap provides slightly more mappings than the French NLP tool (3,170 vs. 2,992). On the other hand, the French NLP tool provides a slightly better precision than MetaMap (88% vs. 86%). Using a manual mapping between ATC and MeSH, the union of the validated mappings between ATC and MeSH provides 2,824 mappings (68.7% of ATC codes of the fifth level). Lexical methods are powerful methods to map health terminologies to the UMLS Metathesaurus. Manual mapping is still necessary to complete the mapping.

Influence of climate and river level on the incidence of malaria in Cacao, French Guiana.

BACKGROUND: The epidemiological profiles of vector-borne diseases, such as malaria, are strongly associated with environmental conditions. An understanding of the effect of the climate on the occurrence of malaria may provide indirect insight into the anopheles mosquito vectors endemic to a particular region. The association between meteorological and hydrographical factors and the occurrence of malaria was studied in a village in French Guiana during an epidemic caused essentially by Plasmodium vivax. METHODS: A cohort of confirmed cases of P. vivax malaria occurring between 2002 and 2007 was studied to search for an association between the number of new infection episodes occurring each month, mean, maximum and minimum monthly temperatures, cumulative rainfall for the month and the mean monthly height of the river bordering the village, with the aid of time series. Cross-correlation analysis revealed that these meteorological factors had large effects on the number of episodes, over a study period of 12 months. RESULTS: Climatic factors supporting the continuance of the epidemic were identified in the short-term (low minimum temperatures during the month), medium-term (low maximum temperatures two months before) and long-term (low maximum temperatures nine months before and high lowest level of the river 12 months before). Cross-correlation analysis showed that the effects of these factors were greatest at the beginning of the short rainy season. CONCLUSION: The association between the river level and the number of malaria attacks provides clues to better understand the environment of malaria transmission and the ecological characteristics of the vectors in the region.

An automated approach to map a French terminology to UMLS.

BACKGROUND: CCAM is a French terminology for coding clinical procedures. CCAM is a multi-hierarchical structured classification for procedures used in France for reimbursement in health care, which is external to UMLS. OBJECTIVE: The objective of this work is to describe a French lexical approach allowing mapping CCAM procedures to the UMLS Metathesaurus to achieve interoperability to multiple international terminologies. This approach used a preliminary step intended to take only the significant characters used to code CCAM corresponding to anatomical and actions axes. RESULTS: According to the 7,926 CCAM codes used in this study, 5,212 possible matches (exact matching, single to multiple matching, partial matching) are found using the French CCAM to UMLS based mapping, 65% of the corresponding anatomical terms in the CCAM code are mapped to at least one UMLS Concept and 37% of the corresponding action terms in the CCAM code are mapped to at least one UMLS Concept. For all the exact matches found (n=200), 91% were rated by a human expert as narrower than the mapped UMLS Concepts, while only 3% were irrelevant.

Design and evaluation of a semantic approach for the homogeneous identification of events in eight patient databases: a contribution to the European EU-ADR project.

The overall objective of the EU-ADR project is the design, development, and validation of a computerised system that exploits data from electronic health records and biomedical databases for the early detection of adverse drug reactions. Eight different databases, containing health records of more than 30 million European citizens, are involved in the project. Unique queries cannot be performed across different databases because of their heterogeneity: Medical record and Claims databases, four different terminologies for coding diagnoses, and two languages for the information described in free text. The aim of our study was to provide database owners with a common basis for the construction of their queries. Using the UMLS, we provided a list of medical concepts, with their corresponding terms and codes in the four terminologies, which should be considered to retrieve the relevant information for the events of interest from the databases.

A twofold strategy for translating a medical terminology into French.

OBJECTIVE: The goal of this study is to assist the translation of a medical terminology (MedlinePlus) into French. METHODS: We combined two types of approaches to acquire French translations of English MedlinePlus terms. The first is knowledge-based and relies on the conceptual information of the UMLS metathesaurus. The second method is a corpus-based NLP technique using a bilingual parallel corpus. RESULTS: The knowledge-based method brought translations for 611 terms, among which 67.6% were considered valid. The corpus-based approach provided translations for 143 terms of which 71.3% were considered valid. We thus acquired a total of 435 translated terms (51.3%). CONCLUSION: Combining two approaches allowed us to semi-automatically translate more than half of the terminology, while focusing on only one would have provided a more partial translation. From an applicative viewpoint, this French version is now integrated in the catalogue of online health resources CISMeF.

Automatic indexing in a drug information portal.

OBJECTIVE: The objective of this work is to create a bilingual (French/English) Drug Information Portal (DIP), in a multi-terminological context and to emphasize its exploitation by an ATC automatic indexing allowing having more pertinent information about substances, organs or systems on which drugs act and their therapeutic and chemical characteristics. METHODS: The development of the DIP was based on the CISMeF portal, which catalogues and indexes the most important and quality-controlled sources of institutional health information in French. DIP has created specific functionalities and uses specific drugs terminologies such as the ATC classification which used to automatic index the DIP resources. RESULTS: DIP is the result of collaboration between the CISMeF team and the VIDAL Company, specialized in drug information. DIP is conceived to facilitate the user information retrieval. The ATC automatic indexing provided relevant results in 76% of cases. CONCLUSION: Using multi-terminological context and in the framework of the drug field, indexing drugs with the appropriate codes or/and terms revealed to be very important to have the appropriate information storage and retrieval. The main challenge in the coming year is to increase the accuracy of the approach.

A semantic approach for the homogeneous identification of events in eight patient databases: a contribution to the European eu-ADR project.

The overall objective of the eu-ADR project is the design, development, and validation of a computerised system that exploits data from electronic health records and biomedical databases for the early detection of adverse drug reactions. Eight different databases, containing health records of more than 30 million European citizens, are involved in the project. Unique queries cannot be performed across different databases because of their heterogeneity: Medical record and Claims databases, four different terminologies for coding diagnoses, and two languages for the information described in free text. The aim of our study was to provide database owners with a common basis for the construction of their queries. Using the UMLS, we provided a list of medical concepts, with their corresponding terms and codes in the four terminologies, which should be considered to retrieve the relevant information for the events of interest from the databases.

Projection and inheritance of SNOMED CT relations between MeSH terms.

This paper proposes a methodology to achieve the automatic inheritance of SNOMED CT relations applied to MeSH preferred terms using UMLS as knowledge source server. We propose an interoperability wildcard to achieve this objective. A quantitative and a qualitative analysis were performed on top four SNOMED CT relations inherited between MeSH preferred terms. A total of 12,030 couples of MeSH preferred terms are in relation via at least one SNOMED CT relationship. For the top-four relations inherited between MeSH preferred terms, overall 79.25% of them are relevant, 16.25% as intermediate and 4.5% as irrelevant, as judged by a medical librarian. This work should lead to an optimization of multi-terminology indexing tools, multi-terminology information retrieval and navigation among a multi-terminology server.

Relevance of Google-customized search engine vs. CISMeF quality-controlled health gateway.

CISMeF (acronym for Catalog and Index of French Language Health Resources on the Internet) is a quality-controlled health gateway conceived to catalog and index the most important and quality-controlled sources of institutional health information in French. The goal of this study is to compare the relevance of results provided by this gateway from a small set of documents selected and described by human experts to those provided by a search engine from a large set of automatically indexed and ranked resources. The Google-Customized search engine (CSE) was used. The evaluation was made using the 10th first results of 15 queries and two blinded physician evaluators. There was no significant difference between the relevance of information retrieval in CISMeF and Google CSE. In conclusion, automatic indexing does not lead to lower relevance than a manual MeSH indexing and may help to cope with the increasing number of references to be indexed in a controlled health quality gateway.

Drug information portal in Europe: information retrieval with multiple health terminologies.

The objective of this work is the creation of a bilingual (French/English) drug information portal (DIP), in a multi-terminological context. The development of the DIP was based on the CISMeF portal, which catalogues and indexes the most important and quality-controlled sources of institutional health information in French. DIP has created specific functionalities related to drug and used specific drugs terminologies and classifications: the ATC classification, the CAS numbers, the French codes CIS, and CIP, as well as trade names and the International Nonproprietary Names of the drugs. DIP is the result of collaboration between the CISMeF team and the VIDAL private Company, specialized in drug information. DIP is conceived to facilitate the user information retrieval using several health terminologies. In the framework of the drug field, using multi-terminological context, indexing drugs with the appropriate codes or/and terms revealed to be very important to have the appropriate information storage and retrieval.

Automatic construction of dictionaries, application to product characteristics indexing.

Summary of Product Characteristics (SPC) indexing enables to extract all the information needed to analyze a prescription and find some inappropriate medications. We evaluate a French Multi-Terminology Indexer tool (F-MTI) for SPC automatic indexing. This tool uses a dictionary containing the textual forms that are likely to appear in natural language text for the drug clinical particular terms contained in the Vidal thesaurus (TUV). We developed a method to automatically generate this dictionary. The evaluation showed a precision of 52.9% and a recall of 46.2%. F-MTI will be integrated in a semi-automatic indexing tool.

Suicide attempt by ingestion of rotenone-containing plant extracts: one case report in French Guiana.

INTRODUCTION: Several species of plants in the Fabaceae family are traditionally used for poison fishing because they contain ichthyotoxic rotenoids. In French Guiana two species of Fabaceae belonging to Lonchocarpus genus with a toxic rotenone effect are used for such ancestral practices. Rotenone is of low toxicity for humans when it is diluted, but its neurotoxicity at higher concentrations is well known to users. CASE REPORT: The purpose of this article is to describe a case of self-poisoning by an 86-year-old woman who ingested a bowl of mashed ichthyotoxic plants. Despite early onset of severe symptoms, the patient regained consciousness and resumed normal breathing within a few hours with only symptomatic treatment. CONCLUSION: The clinical pattern observed in this patient (onset of digestive manifestations followed quickly by loss of conscience and respiratory insufficiency) is in agreement with the few poisonings reported in the literature involving other Fabaceae species containing rotenoids in Asia or involving concentrated rotenone used in insecticides. In patients, who survive the initial phase, symptoms usually regress quickly.

Assisting the translation of SNOMED CT into French using UMLS and four representative French-language terminologies.

OBJECTIVE: To provide a semantics-based method to assist the translation of SNOMED CT into French. To do so, we selected four French-language terminologies: ICD-10, SNOMED International, MedDRA, MeSH, as they are dedicated to different uses - epidemiology, clinical medicine, adverse reactions, medical literature, respectively - in order to map them to SNOMED Clinical Terms (CT), and thus associate French terms with SNOMED CT concepts. In this way, we measured the number of SNOMED CT concepts to be found in French-language terminologies. MATERIAL AND METHOD: We used the UMLS Metathesaurus. The mapping method was based on the coincidence of identifiers and on the explicit mappings present in the Metathesaurus. RESULTS: The study dealt exclusively with preferred terms (PTs) in the terminologies. The terminologies are mapped with varying success as regards PTs mapped to SNOMED terms (from 52% to 96%). Conversely, 45% of SNOMED CT terms are mapped by uniting the four terminologies. DISCUSSION: A more effective mapping technique than the current method is under consideration. CONCLUSION: The method presented will be refined. It could certainly provide useful assistance in the translation of SNOMED CT into French. Due to its general nature, it could be used to translate SNOMED CT into other languages than French.

Multi-terminology indexing for the assignment of MeSH descriptors to medical abstracts in French.

BACKGROUND: To facilitate information retrieval in the biomedical domain, a system for the automatic assignment of Medical Subject Headings to documents curated by an online quality-controlled health gateway was implemented. The French Multi-Terminology Indexer (F-MTI) implements a multiterminology approach using nine main medical terminologies in French and the mappings between them. OBJECTIVE: This paper presents recent efforts to assess the added value of (a) integrating four new terminologies (Orphanet, ATC, drug names, MeSH supplementary concepts) into F-MTI's knowledge sources and (b) performing the automatic indexing on the titles and abstracts (vs. title only) of the online health resources. METHODS: F-MTI was evaluated on a CISMeF corpus comprising 18,161 manually indexed resources. RESULTS: The performance of F-MTI including nine health terminologies on CISMeF resources with Title only was 27.9% precision and 19.7% recall, while the performance on CISMeF resources with Title and Abstract is 14.9 % precision (-13.0%) and 25.9% recall (+6.2%). CONCLUSION: In a few weeks, CISMeF will launch the indexing of resources based on title and abstract, using nine terminologies.

Using multi-terminology indexing for the assignment of MeSH descriptors to health resources in a French online catalogue.

BACKGROUND: To assist with the development of a French online quality-controlled health gateway(CISMeF), an automatic indexing tool assigning MeSH descriptors to medical text in French was created. The French Multi-Terminology Indexer (FMTI) relies on a multi-terminology approach involving four prominent medical terminologies and the mappings between them. OBJECTIVE: In this paper,we compare lemmatization and stemming as methods to process French medical text for indexing. We also evaluate the multi-terminology approach implemented in F-MTI. METHODS: The indexing strategies were assessed on a corpus of 18,814 resources indexed manually. RESULTS: There is little difference in the indexing performance when lemmatization or stemming is used. However, the multi-terminology approach outperforms indexing relying on a single terminology in terms of recall. CONCLUSION: F-MTI will soon be used in the CISMeF production environment and in a Health MultiTerminology Server in French.

Improving the quality of the coding of primary diagnosis in standardized discharge summaries.

We propose to design and test an information-processing model to participate in appraising the quality and the consistency of the coding, for billing, of Standardized Discharge Summaries (SDSs). We designed a model using both symbolic knowledge extracted from the NLM's UMLS and statistical knowledge. The aim is to retrieve from the ICD-10 terms recorded in a SDS the Principal Diagnosis (PD) at the time of coding. In 90% of cases the PD was retrieved 1st or 2nd in SDS including three ICD-10 codes or more. This model could contribute as part of an automated quality control process in a hospital information system by checking consistency in coded SDSs and improve the income of the hospital.