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

   PDF
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

   PDF
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

   Abs

   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

   PDF

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

2020

1. Findable and reusable workflow data products: A genomic workflow case study

   Alban Gaignard, Hala Skaf-Molli, and Khalid Belhajjame

   Semantic Web, Jan 2020
2. Location of intracranial aneurysms is the main factor associated with rupture in the ICAN population

   Olivia Rousseau, Matilde Karakachoff, Alban Gaignard, and 15 more authors

   Journal of Neurology, Neurosurgery, and Psychiatry, Jan 2020
3. Prediction of Unruptured Intracranial Aneurysm Evolution: The UCAN Project.

   Vincent L’Allinec, Stéphanie Chatel, Matilde Karakachoff, and 12 more authors

   Neurosurgery, Jan 2020
4. EDAM: the ontology of bioinformatics operations, topics, data, and formats (update 2020)

   Matú\vs Kala\vs, Hervé Ménager, Alban Gaignard, and 3 more authors

   F1000Research, Jan 2020
5. Characterization of 3D bifurcations in micro-scan and MRA-TOF images of cerebral vasculature for prediction of intra-cranial aneurysms

   Anass Nouri, Florent Autrusseau, Romain Bourcier, and 7 more authors

   Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society, Jan 2020

2019

1. INEX-MED: INtegration and EXploration of heterogeneous bio-MEDical data

   Alban Gaignard, Julie Dawn Thompson, Kirsley Chennen, and 5 more authors

   In , Jan 2019
2. EDAM-bioimaging: the ontology of bioimage informatics operations, topics, data, and formats (2019 update)

   Matú\vs Kala\vs, Laure Plantard, Natasa Sladoje, and 23 more authors

   F1000Research, Jan 2019
3. On Distributed Collaboration for Biomedical Analyses

   Fatima-Zahra Boujdad, Alban Gaignard, Mario Südholt, and 3 more authors

   2019 19th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID), Jan 2019
4. 3D bifurcations characterization for intra-cranial aneurysms prediction

   Anass Nouri, Florent Autrusseau, Romain Bourcier, and 7 more authors

   In Medical Imaging: Image Processing, Jan 2019
5. INEX-MED: a Knowledge Graph to explore and link heterogeneous bio-medical data

   Maxime Folschette, Kirsley Chennen, Alban Gaignard, and 5 more authors

   In , Jan 2019