Reactome Pengine: a web-logic API to the Homo sapiens reactome

Abstract Summary Existing ways of accessing data from the Reactome database are limited. Either a researcher is restricted to particular queries defined by a web application programming interface (API) or they have to download the whole database. Reactome Pengine is a web service providing a logic p...

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Bibliographic Details
Published in:Bioinformatics Vol. 34; no. 16; pp. 2856 - 2858
Main Authors: Neaves, Samuel R, Tsoka, Sophia, Millard, Louise A C
Format: Journal Article
Language:English
Published: England Oxford University Press 15.08.2018
Subjects:
Applications Notes
Databases, Factual
Humans
Logic
Software
ISSN:1367-4803, 1367-4811, 1460-2059, 1367-4811
Online Access:Get full text
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Summary:Abstract Summary Existing ways of accessing data from the Reactome database are limited. Either a researcher is restricted to particular queries defined by a web application programming interface (API) or they have to download the whole database. Reactome Pengine is a web service providing a logic programming-based API to the human reactome. This gives researchers greater flexibility in data access than existing APIs, as users can send their own small programs (alongside queries) to Reactome Pengine. Availability and implementation The server and an example notebook can be found at https://apps.nms.kcl.ac.uk/reactome-pengine. Source code is available at https://github.com/samwalrus/reactome-pengine and a Docker image is available at https://hub.docker.com/r/samneaves/rp4/. Supplementary information Supplementary data are available at Bioinformatics online.
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ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bty181