2025

1. SparqLLM : Retrieval-Augmented SPARQL Query Processing

   Pascal Molli, Hala Skaf-Molli, Sebastien Ferré, and 2 more authors

   In The Semantic Web. 22nd European Semantic Web Conference, ESWC 2025, Jun 2025

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2. Predicting Clinical Outcomes from Patient Care Pathways Represented with Temporal Knowledge Graphs

   Jong Ho Jhee, Alberto Megina, Pacôme Constant Dit Beaufils, and 4 more authors

   In Lecture Notes in Computer Science, Jun 2025

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3. Assessing bioinformatics software annotations: bio.tools case-study

   Ulysse Le Clanche, Sarah Cohen-Boulakia, Yann Le Cunff, and 2 more authors

   In Proceedings JOBIM, Jul 2025

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4. A multi-modal and temporal antibiotic resistance knowledge graph

   Brieuc Quemeneur, Audrey Bihouée, Samuel Chaffron, and 3 more authors

   In SWAT4HCLS 2025 - 16th International SWAT4HCLS conference : Semantic Web Applications and Tools for Health Care and Life Sciences, Feb 2025

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5. Semantic Beacons: a framework to support federated querying over genomic variants and public Knowledge Graphs

   Alexandrina Bodrug-Schepers, Hugo Chabane, Gabriela Montoya, and 3 more authors

   In SWAT4HCLS 2025, Feb 2025

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2024

1. A generic framework to better understand and compare FAIRness measures

   Philippe Lamarre, Jennie Andersen, Alban Gaignard, and 1 more author

   In Knowledge Engineering and Knowledge Management - 24rd International Conference, EKAW 2024, Nov 2024

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2023

1. Schema.org : How is it used?

   Minh-Hoang Dang, Alban Gaignard, Hala Skaf-Molli, and 1 more author

   In International Semantic Web Conference (ISWC) 2023, Nov 2023

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2. FAIR-Checker: supporting digital resource findability and reuse with Knowledge Graphs and Semantic Web standards

   Alban Gaignard, Thomas Rosnet, Frédéric Lamotte, and 2 more authors

   Journal of Biomedical Semantics, Dec 2023

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3. Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems

   Marine Djaffardjy, George Marchment, Clémence Sebe, and 5 more authors

   Computational and Structural Biotechnology Journal, Dec 2023

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   Data analysis pipelines are now established as an effective means for specifying and executing bioinformatics data analysis and experiments. While scripting languages, particularly Python, R and notebooks, are popular and sufficient for developing small-scale pipelines that are often intended for a single user, it is now widely recognized that they are by no means enough to support the development of large-scale, shareable, maintainable and reusable pipelines capable of handling large volumes of data and running on high performance computing clusters. This review outlines the key requirements for building large-scale data pipelines and provides a mapping of existing solutions that fulfill them. We then highlight the benefits of using scientific workflow systems to get modular, reproducible and reusable bioinformatics data analysis pipelines. We finally discuss current workflow reuse practices based on an empirical study we performed on a large collection of workflows.

4. Extraction d’informations sur les workflows scientifiques à partir de la littérature

   Clémence Sebe, Aurélie Névéol, Sarah Cohen-Boulakia, and 1 more author

   In 23ème conférence francophone sur l’Extraction et la Gestion des Connaissances (EGC), Jan 2023

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2022

1. A taxonomy of tools and approaches for distributed genomic analyses

   Wilmer Garzón, Luis Benavides, Alban Gaignard, and 2 more authors

   Informatics in Medicine Unlocked, Jan 2022

2021

1. Large-scale regulatory and signaling network assembly through linked open data

   Marie Lefebvre, Alban Gaignard, Maxime Folschette, and 2 more authors

   Database: The Journal of Biological Databases and Curation, Jan 2021
2. Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development

   Rafael Ferreira Silva, Henri Casanova, Kyle Chard, and 55 more authors

   ArXiv, Jan 2021
3. Découvrabilité et réutilisation de données produites par des workflows : un cas d’usage en génomique

   Alban Gaignard, Hala Skaf-Molli, and Khalid Belhajjame

   In Journées Francophones d’Ingénierie des Connaissances, Jan 2021