Alban Gaignard
Publications
Publications
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A Standards-Based Knowledge Graph that Bridges Scientific Workflows, Run-Time Provenance, and Tool RegistriesSWAT4HCLS 2026, Mar 2026, Amsterdam, Netherlands |
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SparqLLM : Retrieval-Augmented SPARQL Query ProcessingESWC 2025 - 22nd European Semantic Web Conference, Jun 2025, Portoroz, Slovenia. pp.1-5 |
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Prédiction d'événements cliniques à partir des parcours de soins de patients représentés par des graphes de connaissances temporelsIC 2025 - 36e Journées Francophones d'Ingénierie des Connaissances, AFIA, Jul 2025, Dijon, France |
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Predicting clinical outcomes from patient care pathways represented with temporal knowledge graphsESWC 2025 - 22nd European Semantic Web Conference, Jun 2025, Portorož, Slovenia. pp.282-300, ⟨10.1007/978-3-031-94575-5_16⟩ |
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A Generic Framework to Better Understand and Compare FAIRness MeasuresEKAW 2024, Nov 2024, Amsterdam, Netherlands. pp.291-308, ⟨10.1007/978-3-031-77792-9_18⟩ |
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Semantic Beacons: a framework to support federated querying over genomic variants and public Knowledge GraphsSWAT4HCLS 2025, Feb 2025, Barcelona, Catalonia, Spain |
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Assessing bioinformatics software annotations: bio.tools case-studyJOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux & Online, France. pp.1-7 |
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A multi-modal and temporal antibiotic resistance knowledge graphSWAT4HCLS 2025 - 16th International SWAT4HCLS conference : Semantic Web Applications and Tools for Health Care and Life Sciences, Scientifika, Feb 2025, Barcelone, Spain |
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A generic framework to better understand and compare FAIRness measuresKnowledge Engineering and Knowledge Management - 24rd International Conference, EKAW 2024, Nov 2024, Amsterdam, Netherlands |
(more) Findable bioinformatics softwares with BioschemasElixir Tools platform, F2F meeting, Elixir, Mar 2023, Leyden, Netherlands |
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Schema.org : How is it used?International Semantic Web Conference (ISWC) 2023, Nov 2023, Athens, France |
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Extraction d'informations sur les workflows scientifiques à partir de la littérature23ème conférence francophone sur l'Extraction et la Gestion des Connaissances (EGC), Jan 2023, Lyon, France. pp.313-320 |
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Découvrabilité et réutilisation de données produites par des workflows : un cas d’usage en génomiqueJournées Francophones d'Ingénierie des Connaissances (IC) Plate-Forme Intelligence Artificielle (PFIA'21), Jun 2021, Bordeaux, France. pp 73-80 |
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On distributed collaboration for biomedical analysesCCGrid-Life 2019 Workshop on Clusters, Clouds and Grids for Life Sciences, May 2019, Larnaca, Cyprus. pp.1-10, ⟨10.1109/CCGRID.2019.00079⟩ |
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3D bifurcations characterization for intra-cranial aneurysms predictionSPIE Medical Imaging, Feb 2019, San Diego, CA, United States. ⟨10.1117/12.2504626⟩ |
INEX-MED: a Knowledge Graph to explore and link heterogeneous bio-medical dataJOBIM 2019, Jul 2019, Nantes, France |
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SHARP: Harmonizing cross-workflow provenanceSeWeBMeDA 2017 : Semantic Web solutions for large-scale BioMedical Data Analtics - 14th ESWC 2017, May 2017, Portoroz, Slovenia |
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SHARP: Harmonizing and Bridging Cross-Workflow ProvenanceThe Semantic Web: ESWC 2017 Satellite Events - ESWC 2017 Satellite Events, Jun 2017, Portoro, Slovenia. pp.219-234, ⟨10.1007/978-3-319-70407-4_35⟩ |
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SHARP: Harmonizing Galaxy and Taverna workflow provenanceSeWeBMeDA 2017 : Semantic Web solutions for large-scale BioMedical Data Analtics, May 2017, Portoroz, Slovenia |
Developing and sharing reproducible bioinformatics pipelines: best practicesJOBIM 2017, Jul 2017, Lille, France |
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Regulation and signalization graph assembly through Linked Open DataJOBIM 2017, Jul 2017, Lille, France |
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From scientific workflow patterns to 5-star linked open dataTaPP 2016: 8th USENIX Workshop on the Theory and Practice of Provenance, Jun 2016, Washington D.C., United States |
Global Initiative for Sentinel e-Health Network on Grid (GINSENG), Medical data integration and semantic developments for epidemiologyCCGRID, May 2014, Chicago, United States |
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Publication, partage et réutilisation de règles sur le Web de données25èmes Journées francophones d'Ingénierie des Connaissances, May 2014, Clermont-Ferrand, France. pp.237-248 |
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Fédération multi-sources en neurosciences : intégration de données relationnelles et sémantiquesIC pour l'Interopérabilité Sémantique dans les applications en e-Santé, Jun 2012, France. 6 p |
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Semantic Federation of Distributed NeurodataMICCAI Workshop on Data- and Compute-Intensive Clinical and Translational Imaging Applications, Oct 2012, Nice, France. pp.41-50 |
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KGRAM Versatile Inference and Query Engine for the Web of Linked DataIEEE/WIC/ACM International Conference on Web Intelligence, Dec 2012, Macao, China. pp.1-8 |
NeuroLOG: A framework for the sharing and reuse of distributed tools and data in neuroimagingOrganization for Human Brain Mapping (HBM'11), Jun 2011, Quebec, Canada |
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NeuroLOG: sharing neuroimaging data using an ontology-based federated approach.American Medical Informatics Association, Oct 2011, Washington DC, United States. pp.472-80 |
A federated system for sharing and reuse of images and image processing tools in neuroimagingComputer Assisted Radiology and Surgery (CARS'11), Jun 2011, Berlin, Germany |
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Characterizing semantic service parameters with Role concepts to infer domain-specific knowledge at runtimeInternational Conference on Knowledge Engineering and Ontology Development (KEOD'11), Oct 2011, Paris, France. pp.12 |
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Grid-wide neuroimaging data federation in the context of the NeuroLOG project.HealthGrid'10, Jun 2010, Paris, France. pp.112-123, ⟨10.3233/978-1-60750-583-9-112⟩ |
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Intégration des connaissances en neurosciences dans un environnement multi-centriqueJournées francophones d'Ingénierie des Connaissances (IC 2010), Jun 2010, Nîmes, France. pp.21-30 |
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A distributed security policy for neuroradiological data sharingHealthGrid 2009, Jun 2009, Berlin, Germany. pp.257-262, ⟨10.3233/978-1-60750-027-8-257⟩ |
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Managing Variability Complexity in Aspect-Oriented ModelingIn Proceedings of ACM/IEEE 11th International Conference on Model Driven Engineering Languages and Systems (MoDELS 08), 2008, Toulouse, France, France |
Managing Variability Complexity in Aspect Oriented Modelling12th International Conference on Model Driven Engineering Languages and Systems (MODELS'2009), ACM/IEEE, Sep 2008, Toulouse, France. pp.797-812 |
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NeuroLOG: a community-driven middleware designHealthGrid, Jun 2008, Chicago, United States. pp.49--58 |
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Introducing variability into Aspect-Oriented Modeling approachesIn Proceedings of ACM/IEEE 10th International Conference on Model Driven Engineering Languages and Systems (MoDELS 07), 2007, Nashville, TN, USA, United States |
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Sharing data and image processing tools in neuroimaging.CARS 2006 - Computer Assisted Radiology and Surgery, Jun 2006, Osaka, Japan. pp.41-42 |
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A multi-modal and temporal antibiotic resistance knowledge graphJOBIM 2025, Jul 2025, Bordeaux, France. , 2025 |
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Annotating Bioconductor packages using the EDAM ontologyJournées Ouvertes en Biologie Informatique et Mathématiques JOBIM 2025, Jul 2025, Bordeaux, France |
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Interoperability of Bioconductor packages within the ELIXIR Research Software Ecosystem using the EDAM ontologyEuropean Bioconductor Conference 2025, Sep 2025, Barcelone, Spain. Zenodo, 2025, ⟨10.5281/zenodo.17086358⟩ |
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Integrating Bioconductor packages with the ELIXIR research software ecosystem using EDAMELIXIR All Hands Meeting, 2025, Jun 2025, Thessalokini, Greece. F1000 Research Limited, F1000Research 2025, 14(ELIXIR):524 (poster), 2025, ⟨10.7490/f1000research.1120184.1⟩ |
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Monitoring inclusions and quality criteria on MRI imaging data in a multi-center contextPEPR-SanteNum 2025 - Journées Annuelles du PEPR Santé Numérique, Oct 2025, Lille, France. pp.1-1, 2025 |
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Orchestrating data flows throughout their whole life cycleJOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. , 2024 |
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The EDAM Framework and Control RoomJournées Ouvertes en Biologie Informatique et Mathématiques JOBIM 2024, Jun 2024, Toulouse, France |
Towards improving workflows reproducibility : Extracting information on workflows from text and code repositories31st Annual Intelligent Systems For Molecular Biology and 22nd Annual European Conference on Computational Biology (ISMB/ECCB 2023), Jul 2023, Lyon, France. |
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The ELIXIR research software ecosystem24th annual Bioinformatics Open Source Conference (BOSC 2023), Jul 2023, Lyon, France. , ⟨10.7490/f1000research.1119595.1⟩ |
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EDAM, the life-science ontology for data analysis and managementJOBIM, Jul 2022, Rennes, France. ⟨10.5281/zenodo.6769072⟩ |
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FAIR-Checker : Checking and Inspecting metadata for FAIR bioinformatics resourcesElixir AllHands 2022, Jun 2022, Amsterdam, Netherlands |
EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats (update 2019)3rd NEUBIAS Bioimage Analysis Community Conference 2019, Jun 2020, Luxembourg, Luxembourg |
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EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formats (update 2020)ELIXIR All Hands 2020, Jun 2020, Virtual, United Kingdom |
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EDAM-bioimaging : The ontology of bioimage informatics operations, topics, data, and formatsNEUBIAS, Feb 2019, Luxembourg, Luxembourg. ⟨10.7490/f1000research.1115257.1⟩ |
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INEX-MED: INtegration and EXploration of heterogeneous bio-MEDical dataJOBIM 2019, Jul 2019, Nantes, France |
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SHARP: Harmonizing and Bridging Cross-Workflow ProvenanceThe Semantic Web: ESWC 2017 Satellite Events Portorož, Slovenia, May 28 – June 1, 2017, Revised Selected Papers, 2017 |
Bio-Image Informatics Index BIII: A unique database of image analysis tools and workflows for and by the bioimaging community2024 |
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An evaluation of EDAM coverage in the Tools Ecosystem and prototype integration of Galaxy and WorkflowHub systemsELIXIR. 2023 |
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Atelier MoDaL (Multi-Scale Data Links)[Rapport de recherche] IRISA, Inria Rennes. 2020 |
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État des lieux MoDaL (Multi-Scale Data Links)[Rapport de recherche] IRISA, Inria Rennes. 2020 |
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Distributed knowledge sharing and production through collaborative e-Science platformsOther [cs.OH]. Université Nice Sophia Antipolis, 2013. English. ⟨NNT : 2013NICE4010⟩ |
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Sharing massive data analysis: from provenance to linked experiment reportsDoctoral. France. 2018 |