RDF Data integration using Shape Expressions

Abstract

The paper contains a report of the activities that have been done during the Biohackathon 2023 in Shodoshima, Japan in a project about RDF data integration using Shape Expressions. The paper describes several approaches that have been discussed to create RDF data subsets and some preliminary results applying some of those technologies. It also describes the work that has been done comparing RDF data modeling approaches like ShEx, LinkML and YAML files from rdfconfig.

Authors 18

1. José Emilio Labra Gayo

   Universidad de Oviedo

   Affiliation as printed

   WESO Lab, University of Oviedo, Spain

2. Andra Waagmeester
   Affiliation as printed

   Micelio, Belgium

3. Ángel Iglesias-Préstamo

   Database Center for Life Science

   Affiliation as printed

   Database Center for Life Science, Japan

4. Yasunori Yamamoto

   Universidad de Oviedo

   Affiliation as printed

   WESO Lab, University of Oviedo, Spain

5. Toshiaki Katayama

   Database Center for Life Science

   Affiliation as printed

   Database Center for Life Science, Japan

6. Thomas Liener
   Affiliation as printed

   Unaffiliated

7. Deepak Raveendran Unni

   SIB Swiss Institute of Bioinformatics

   Affiliation as printed

   SIB Swiss Institute of Bioinformatics, Switzerland

8. Jerven Tjalling Bolleman

   SIB Swiss Institute of Bioinformatics

   Affiliation as printed

   SIB Swiss Institute of Bioinformatics, Switzerland

9. Kiyoko Flora Aoki-Kinoshita

   Soka University

   Affiliation as printed

   Soka University, Hachioji, Tokyo, Japan

10. Masashi Yokochi

    The University of Osaka

    Affiliation as printed

    Osaka University, Suita, Osaka, Japan

11. Núria Queralt-Rosiñach Aachen

    Leiden University Medical Center

    Affiliation as printed

    Leiden University Medical Center, Netherlands

12. Hiroshi Mori

    National Institute of Genetics

    Affiliation as printed

    National Institute of Genetics, Mishima, Japan

13. Daniel Fernández-Álvarez

    Universidad de Oviedo

    Affiliation as printed

    WESO Lab, University of Oviedo, Spain

14. Alberto Labarga

    Barcelona Supercomputing Center

    Affiliation as printed

    Barcelona Supercomputing Center

15. Robert Hoehndorf
    Affiliation as printed

    MedOntology, LLC, USA

16. Eric Prud’hommeaux
    Affiliation as printed

    OKBP inc. Japan

17. Claude J Nanjo

    RIKEN Center for Integrative Medical Sciences

    Affiliation as printed

    RIKEN Center for Integrative Medical Sciences, Yokohama, JP

18. Nishad Thalhath