1. The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining
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Stefanie De Bodt, Yves Van de Peer, Sara Jover-Gil, José Luis Micol, Jesper T. Gronlund, Richard G. H. Immink, Katja Baerenfaller, Sofie Van Landeghem, Gerco C. Angenent, Rubén Casanova-Sáez, Wilhelm Gruissem, Vicky Buchanan-Wollaston, Dóra Szakonyi, Pierre Hilson, Lieven Baeyens, Aalt D. J. van Dijk, Jonas Blomme, David Wilson-Sánchez, Fabio Fiorani, Asuka Kuwabara, Sean Walsh, David Esteve-Bruna, Nathalie Gonzalez, Tamara Muñoz-Nortes, Dirk Inzé, Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University [Belgium] (UGENT), Department of Biology, Swiss Federal Institute of Technology, Instituto de Bioingeniería, Universidad Miguel Hernández [Elche] (UMH), Warwick Systems Biology Centre, and School of Life Sciences, University of Warwick, Plant Research International, Bioscience, Wageningen University and Research Center (WUR), Genomics Research Institute (GRI), University of Pretoria (UPSpace), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Universiteit Gent = Ghent University [Belgium] (UGENT), and Wageningen University and Research [Wageningen] (WUR)
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EXPRESSION ,Leaf growth ,INFORMATION ,Relational database ,Computer science ,[SDV]Life Sciences [q-bio] ,Arabidopsis ,Context (language use) ,Plant Science ,Scientific literature ,computer.software_genre ,Biochemistry ,Wiskundige en Statistische Methoden - Biometris ,TEXT ,Open Biomedical Ontologies ,Consistency (database systems) ,BIOS Applied Bioinformatics ,lcsh:Botany ,Genetics ,Laboratorium voor Moleculaire Biologie ,TOOL ,BIOS Plant Development Systems ,Mathematical and Statistical Methods - Biometris ,Literature curation ,Data integration ,Data curation ,PLANT ONTOLOGY ,Biology and Life Sciences ,Cell Biology ,15. Life on land ,Data science ,GENE ,lcsh:QK1-989 ,PROTEIN INTERACTIONS ,Data sharing ,DIFFERENTIATION ,MAINTENANCE ,Data mining ,Laboratory of Molecular Biology ,computer ,Developmental Biology ,GENERATION - Abstract
The information that connects genotypes and phenotypes is essentially embedded in research articles written in natural language. To facilitate access to this knowledge, we constructed a framework for the curation of the scientific literature studying the molecular mechanisms that control leaf growth and development in Arabidopsis thaliana (Arabidopsis). Standard structured statements, called relations, were designed to capture diverse data types, including phenotypes and gene expression linked to genotype description, growth conditions, genetic and molecular interactions, and details about molecular entities. Relations were then annotated from the literature, defining the relevant terms according to standard biomedical ontologies. This curation process was supported by a dedicated graphical user interface, called Leaf Knowtator. A total of 283 primary research articles were curated by a community of annotators, yielding 9947 relations monitored for consistency and over 12,500 references to Arabidopsis genes. This information was converted into a relational database (KnownLeaf) and merged with other public Arabidopsis resources relative to transcriptional networks, protein–protein interaction, gene co-expression, and additional molecular annotations. Within KnownLeaf, leaf phenotype data can be searched together with molecular data originating either from this curation initiative or from external public resources. Finally, we built a network (LeafNet) with a portion of the KnownLeaf database content to graphically represent the leaf phenotype relations in a molecular context, offering an intuitive starting point for knowledge mining. Literature curation efforts such as ours provide high quality structured information accessible to computational analysis, and thereby to a wide range of applications., Current Plant Biology, 2, ISSN:2214-6628
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