Peter D’Eustachio

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States

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Publications (2)0 Total impact

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    ABSTRACT: The behaviour of pervasive molecular processes in human biology can be studied through the large-scale modeling of the molecular events that define them. Constructing detailed models of such extent and scope is a considerable undertaking well beyond the reach and capability of individual efforts, due to the range of expertise required. Reactome (http://www.reactome.org) is an open-access project that collaborates with field experts to integrate their pathway knowledge into a single quality-checked human model. This resource dataset is systematically cross-referenced to major molecular and literature databases, and is accessible to the community in a number of well-established formats. Various tools have been developed to facilitate querying and interaction with this content. The salient features of the annotation strategy are discussed here, and examples of pathway and genomic data integration using flexible interfacing methods from the associated toolkit are also presented.
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    ABSTRACT: Reactome (www.reactome.org) is a curated database describing very diverse biological processes in a computationally accessible format. The data is provided by experts in the field and subject to a peer review process. The core unit of the Reactome data model is the reaction. The entities participating in reactions form a network of biological interactions. Reactions are grouped into pathways. Reactome data are cross-referenced to a wide selection of publically available databases (such as UniProt, Ensembl, GO, PubMed), facilitating overall integration of biological data. In addition to the manually curated, mainly human reactions, electronically inferred reactions to a wide range of other species, are presented on the website. All Reactome reactions are displayed as arrows on a Reactionmap. The Skypainter tool allows visualisation of user-supplied data by colouring the Reactionmap. Reactome data are freely available and can be downloaded in a number of formats. Keywordsknowledgebase-pathways-biological processes
    01/1970: pages 710-719;