학술논문
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).
Document Type
Academic Journal
Author
Touré V; Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.; Vercruysse S; Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.; Acencio ML; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.; Lovering RC; Functional Gene Annotation, Preclinical and Fundamental Science, Institute of Cardiovascular Science, UCL, University College London, London WC1E 6JF, UK.; Orchard S; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.; Bradley G; Computational Biology, Functional Genomics, GSK, Stevenage SG1 2NY, UK.; Casals-Casas C; Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, 1211 Geneva 4, Switzerland.; Chaouiya C; Aix Marseille Univ, CNRS, Centrale Marseille, I2M Marseille 13331, France.; Del-Toro N; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.; Flobak Å; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.; The Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, Trondheim 7030, Norway.; Gaudet P; SIB Swiss Institute of Bioinformatics, Geneva 1211, Switzerland.; Hermjakob H; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.; Hoyt CT; Enveda Therapeutics, 53225 Bonn, Germany.; Licata L; Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.; Lægreid A; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.; Mungall CJ; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.; Niknejad A; Vital-IT Group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, Amphipole Building, 1015 Lausanne, Switzerland.; Panni S; Department of Biology, Ecology and Earth Sciences, University of Calabria, Ecology and Earth Science, Via Pietro Bucci Cubo 6/C, Rende 87036, CS, Italy.; Perfetto L; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.; Porras P; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.; Pratt D; Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.; Saez-Rodriguez J; Institute of Computational Biomedicine, Heidelberg University, Faculty of Medicine, 69120 Heidelberg, Germany.; Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, Aachen 52062, Germany.; Thieffry D; Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.; Thomas PD; Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90007, USA.; Türei D; Joint Research Centre for Computational Biomedicine (JRC-COMBINE), Faculty of Medicine, RWTH Aachen University, Aachen 52062, Germany.; Kuiper M; Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim 7491, Norway.
Source
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Subject
Language
English
Abstract
Motivation: A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a so-called 'causal interaction' takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g. gene regulation) need to be described with a careful appreciation of the underlying molecular reactions. A proper description of this information enables archiving, sharing and reuse by humans and for automated computational processing. Various representations of causal relationships between biological components are currently used in a variety of resources.
Results: Here, we propose a checklist that accommodates current representations, called the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while fostering uniformity and interoperability of the data across resources.
Availability and Implementation: The checklist together with examples is accessible at https://github.com/MI2CAST/MI2CAST.
Supplementary Information: Supplementary data are available at Bioinformatics online.
(© The Author(s) 2020. Published by Oxford University Press.)
Results: Here, we propose a checklist that accommodates current representations, called the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while fostering uniformity and interoperability of the data across resources.
Availability and Implementation: The checklist together with examples is accessible at https://github.com/MI2CAST/MI2CAST.
Supplementary Information: Supplementary data are available at Bioinformatics online.
(© The Author(s) 2020. Published by Oxford University Press.)