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A Meta-Graph for the Construction of an RNA-Centered Knowledge Graph

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Bioinformatics and Biomedical Engineering (IWBBIO 2023)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 13919))

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Abstract

The COVID-19 pandemic highlighted the importance of RNA-based technologies for the development of new vaccines. Besides vaccines, a world of RNA-based drugs, including small non-coding RNA, could open new avenues for the development of novel therapies covering the full spectrum of the main human diseases. In the context of the “National Center for Gene Therapy and Drugs based on RNA Technology” funded by the Italian PNRR and the NextGenerationEU program, our lab will contribute to the construction of a Knowledge Graph (KG) for RNA-drug analysis and the development of innovative algorithms to support RNA-drug discovery. In this paper, we describe the initial steps for the identification of public data sources from which information about different kinds of non-coding RNA sequences (and their relationships with other molecules) can be collected and used for feeding the KG. An in-depth analysis of the characteristics of these sources is provided, along with a meta-graph we developed to guide the RNA-KG construction by exploiting and integrating biomedical ontologies and relevant data from public databases.

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Notes

  1. 1.

    Initial results available at https://github.com/AnacletoLAB/RNA-KG.

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Acknowledgments

This research was supported by the “National Center for Gene Therapy and Drugs based on RNA Technology”, PNRR-NextGenerationEU program [G43C22001320007]. The authors wish to thank Tiffany J. Callahan, Justin T. Reese, and Peter N. Robinson for useful discussions on the topics of this paper.

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Authors and Affiliations

  1. AnacletoLab - Dipartimento di Informatica, Università degli Studi di Milano, Via Celoria 18, Milano, Italy

    Emanuele Cavalleri, Sara Bonfitto, Alberto Cabri, Jessica Gliozzo, Paolo Perlasca, Mauricio Soto-Gomez, Gabriella Trucco, Elena Casiraghi, Giorgio Valentini & Marco Mesiti

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  1. Emanuele Cavalleri
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  2. Sara Bonfitto
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  3. Alberto Cabri
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  4. Jessica Gliozzo
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Correspondence to Giorgio Valentini .

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Editors and Affiliations

  1. University of Granada, Granada, Spain

    Ignacio Rojas

  2. University of Granada, Granada, Spain

    Olga Valenzuela

  3. University of Granada, Granada, Spain

    Fernando Rojas Ruiz

  4. University of Granada, Granada, Spain

    Luis Javier Herrera

  5. University of Granada, Granada, Spain

    Francisco Ortuño

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Cavalleri, E. et al. (2023). A Meta-Graph for the Construction of an RNA-Centered Knowledge Graph. In: Rojas, I., Valenzuela, O., Rojas Ruiz, F., Herrera, L.J., Ortuño, F. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2023. Lecture Notes in Computer Science(), vol 13919. Springer, Cham. https://doi.org/10.1007/978-3-031-34953-9_13

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