William Digan

William Digan
Hôpital Européen Georges-Pompidou (Hôpitaux Universitaires Paris-Ouest) · Informatique

MS

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17
Publications
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97
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Publications

Publications (17)
Chapter
Primary Immunodeficiencies (PIDs) are associated with more than 400 rare monogenic diseases affecting various biological functions (e.g., development, regulation of the immune response) with a heterogeneous clinical expression (from no symptom to severe manifestations). To better understand PIDs, the ATRACTion project aims to perform a multi-omics...
Chapter
Introduction: The implication of viruses in human cancers, as well as the emergence of next generation sequencing has permitted to investigate further their role and pathophysiology in the development of this disease. One such mechanism is the integration of portions of viral genomes in the human genome, as well as the specific action of viral onc...
Article
Full-text available
Introduction Une maladie émergente pose des problèmes spécifiques pour les outils informatiques. L’informatique biomédicale repose en grande partie sur les données structurées qui requièrent l’existence de données ou de modèles de connaissances. Cependant, une nouvelle maladie ne peut avoir de modèle de connaissances préexistant. Au cours d’une épi...
Article
The context of medical conditions is an important feature to consider when processing clinical narratives. NegEx and its extension ConText became the most well-known rule-based systems that allow determining whether a medical condition is negated, historical or experienced by someone other than the patient in English clinical text. In this paper, w...
Article
Full-text available
Background The increasing complexity of data streams and computational processes in modern clinical health information systems makes reproducibility challenging. Clinical natural language processing (NLP) pipelines are routinely leveraged for the secondary use of data. Workflow management systems (WMS) have been widely used in bioinformatics to han...
Article
Full-text available
Background A novel disease poses special challenges for informatics solutions. Biomedical informatics relies for the most part on structured data, which require a preexisting data or knowledge model; however, novel diseases do not have preexisting knowledge models. In an emergent epidemic, language processing can enable rapid conversion of unstruct...
Preprint
BACKGROUND A novel disease poses special challenges for informatics solutions: biomedical informatics relies for the most part on structured data; structured data require a pre-existing data/knowledge model; but novel diseases do not have pre-existing knowledge models. In an emergent epidemic, language processing could allow rapid conversion of uns...
Article
Full-text available
Pharmacogenomics (PGx) studies how individual gene variations impact drug response phenotypes, which makes PGx-related knowledge a key component towards precision medicine. A significant part of the state-of-the-art knowledge in PGx is accumulated in scientific publications, where it is hardly reusable by humans or software. Natural language proces...
Article
Full-text available
A significant part of medical knowledge is stored as unstructured free text. However, clinical narratives are known to contain duplicated sections due to clinicians' copy/paste parts of a former report into a new one. In this study, we aim at evaluating the duplications found within patient records in more than 650,000 French clinical narratives. W...
Preprint
Full-text available
Pharmacogenomics (PGx) studies how individual gene variations impact drug response phenotypes, which makes knowledge related to PGx a key component towards precision medicine. A significant part of the state-of-the-art knowledge in PGx is accumulated in scientific publications, where it is hardly usable to humans or software. Natural language proce...
Article
Full-text available
Theranostic assays are based on single gene testing but the ability of next-generation sequencing (NGS) to interrogate numerous genetic alterations will progressively replace single gene assays. Although NGS was evaluated to screen for theranostic mutations, its usefulness in clinical practice on large series of samples remains to be demonstrated....
Conference Paper
Full-text available
La détection du contexte des conditions cliniques présentes dans un dossier patient est un élément important dans le traitement automatique des textes médicaux. Ce papier décrit l’adaptation au français du système anglais ConText qui permet de détecter si une condition clinique identifiée dans un texte est affirmée ou niée, récente ou historique, e...
Article
Full-text available
Background Next Generation Sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Repr...
Preprint
Full-text available
Data analysis tools have become essential to the study of biology. Here, we applied language workbench technology (LWT) to create data analysis languages tailored for biologists with a diverse range of experience: from beginners with no programming experience to expert bioinformaticians and statisticians. A key novelty of our approach is its abilit...
Article
Full-text available
Data analysis tools have become essential to the study of biology. Tools available today were constructed with layers of technology developed over decades. Here, we explain how some of the principles used to develop this technology are sub-optimal for the construction of data analysis tools for biologists. In contrast, we applied language workbench...
Article
Full-text available
Data analysis tools have become essential to the study of biology. Tools available today were constructed with layers of technology developed over decades. Here, we explain how some of the principles used to develop this technology are sub-optimal for the construction of data analysis tools for biologists. In contrast, we applied language workbench...
Article
Full-text available
Data analysis tools have become essential to the study of biology. Tools available today were constructed with layers of technology developed over decades. Here, we explain how some of the principles used to develop this technology are sub-optimal for the construction of data analysis tools for biologists. In contrast, we applied language workbench...

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Projects

Projects (4)
Project
The Cancer Research and Personalized Medicine (CARPEM) program is a translational research program research program funded by the French National Cancer Center. The CARPEM Translational Research Platform aims at providing researchers and clinicians with tools to integrate retrospective, prospective studies as well as day-to-day care data.