Articles producció científica> Química Física i Inorgànica

Chemical reaction network knowledge graphs: the OntoRXN ontology

  • Identification data

    Identifier: imarina:9264773
  • Authors:

    Garay-Ruiz D
    Bo C
  • Others:

    Author, as appears in the article.: Garay-Ruiz D; Bo C
    Department: Química Física i Inorgànica
    URV's Author/s: Bo Jané, Carles / Garay Ruiz, Diego
    Keywords: entities markup reaction networks reactivity semantics span model xml Ontologies Reaction networks Reactivity Semantics World-wide-web
    Abstract: The organization and management of large amounts of data has become a major point in almost all areas of human knowledge. In this context, semantic approaches propose a structure for the target data, defining ontologies that state the types of entities on a certain field and how these entities are interrelated. In this work, we introduce OntoRXN, a novel ontology describing the reaction networks constructed from computational chemistry calculations. Under our paradigm, these networks are handled as undirected graphs, without assuming any traversal direction. From there, we propose a core class structure including reaction steps, network stages, chemical species, and the lower-level entities for the individual computational calculations. These individual calculations are founded on the OntoCompChem ontology and on the ioChem-BD database, where information is parsed and stored in CML format. OntoRXN is introduced through several examples in which knowledge graphs based on the ontology are generated for different chemical systems available on ioChem-BD. Finally, the resulting knowledge graphs are explored through SPARQL queries, illustrating the power of the semantic approach to standardize the analysis of intricate datasets and to simplify the development of complex workflows.© 2022. The Author(s).
    Thematic Areas: Biotecnología Chemistry, multidisciplinary Ciencias sociales Computer graphics and computer-aided design Computer science applications Computer science, information systems Computer science, interdisciplinary applications Library and information sciences Physical and theoretical chemistry Química
    licence for use: https://creativecommons.org/licenses/by/3.0/es/
    Author's mail: diego.garay@estudiants.urv.cat carles.bo@urv.cat
    Author identifier: 0000-0001-9581-2922
    Record's date: 2024-01-13
    Papper version: info:eu-repo/semantics/publishedVersion
    Link to the original source: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-022-00610-x
    Papper original source: Journal Of Cheminformatics. 14 (1): 29-29
    APA: Garay-Ruiz D; Bo C (2022). Chemical reaction network knowledge graphs: the OntoRXN ontology. Journal Of Cheminformatics, 14(1), 29-29. DOI: 10.1186/s13321-022-00610-x
    Licence document URL: http://repositori.urv.cat/ca/proteccio-de-dades/
    Article's DOI: 10.1186/s13321-022-00610-x
    Entity: Universitat Rovira i Virgili
    Journal publication year: 2022
    Publication Type: Journal Publications
  • Keywords:

    Chemistry, Multidisciplinary,Computer Graphics and Computer-Aided Design,Computer Science Applications,Computer Science, Information Systems,Computer Science, Interdisciplinary Applications,Library and Information Sciences,Physical and Theoretical Chemistry
    entities
    markup
    reaction networks
    reactivity
    semantics
    span model
    xml
    Ontologies
    Reaction networks
    Reactivity
    Semantics
    World-wide-web
    Biotecnología
    Chemistry, multidisciplinary
    Ciencias sociales
    Computer graphics and computer-aided design
    Computer science applications
    Computer science, information systems
    Computer science, interdisciplinary applications
    Library and information sciences
    Physical and theoretical chemistry
    Química
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