Dataset Information

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

ABSTRACT: WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities.

SUBMITTER: Slenter DN

PROVIDER: S-EPMC5753270 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Publications

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

Slenter Denise N DN Kutmon Martina M Hanspers Kristina K Riutta Anders A Windsor Jacob J Nunes Nuno N Mélius Jonathan J Cirillo Elisa E Coort Susan L SL Digles Daniela D Ehrhart Friederike F Giesbertz Pieter P Kalafati Marianthi M Martens Marvin M Miller Ryan R Nishida Kozo K Rieswijk Linda L Waagmeester Andra A Eijssen Lars M T LMT Evelo Chris T CT Pico Alexander R AR Willighagen Egon L EL

Nucleic acids research 20180101 D1

WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway ...[more]

PMID: 29136241

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Project description:Calls for biodiversity conservation practice to be more evidence based are growing, and we agree evidence use in conservation practice needs improvement. However, evidence-based conservation will not be realized without improved access to evidence. In medicine, unlike in conservation, a well-established and well-funded layer of intermediary individuals and organizations engage with medical practitioners, synthesize primary research relevant to decision making, and make evidence easily accessible. These intermediaries prepare targeted evidence summaries and distribute them to practitioners faced with time-sensitive and value-laden decisions. To be effective, these intermediaries, who we refer to as evidence bridges, should identify research topics based on the priorities of practitioners; synthesize evidence; prepare and distribute easy-to-find and easy-to-use evidence summaries; and develop and maintain networks of connections with researchers and practitioners. Based on a review of the literature regarding evidence intermediaries in conservation and environmental management, as well as an anonymous questionnaire searching for such organizations, we found few intermediaries that met all these criteria. Few evidence bridges that do exist are unable to reach most conservation practitioners, which include resource managers in government and industry, conservation organizations, and farmers and other private landowners. We argue that the lack of evidence bridges from research to practitioners contributes to evidence complacency and limits the use of evidence in conservation action. Nevertheless, several existing organizations help reduce the gap between evidence and practice and could serve as a foundation for building additional components of evidence bridges in conservation. Although evidence bridges need expertise in research and evidence synthesis, they also require expertise in identifying and communicating with the community of practitioners most in need of clear and concise syntheses of evidence. Article Impact Statement: Evidence-based conservation will not be realized without improved access to evidence. We call for intermediary evidence bridges.

Dataset Information

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

Publications

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

Similar Datasets

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