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Data extraction for the reaction kinetics database SABIO-RK

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posted on 2023-05-18, 12:46 authored by Wittig, U, Kania, R, Bittkowski, M, Wetsch, E, Shi, L, Lenneke JongLenneke Jong, Golebiewski, M, Rey, M, Weidemann, A, Rojas, I, Muller, W

SABIO-RK (http://sabio.h-its.org/) is a web-accessible, manually curated database that has been established as a resource for biochemical reactions and their kinetic properties with a focus on supporting the computational modeling to create models of biochemical reaction networks. SABIO-RK data are mainly extracted from literature but also directly submitted from lab experiments. In most cases the information in the literature is distributed across the whole publication, insufficiently structured and often described without standard terminology. Therefore the manual extraction of knowledge from the literature requires biological experts to understand the paper and interpret the data. The database offers the literature data in a structured format including annotations to controlled vocabularies, ontologies and external databases which supports modellers, as well as experimentalists, in the very time consuming process of collecting information from different publications.

Here we describe the data extraction and curation efforts needed for SABIO-RK and give recommendations for publishing kinetic data in a complete and structured manner.

History

Publication title

Perspectives in Science

Issue

1-6

Pagination

33-40

ISSN

2213-0209

Department/School

Institute for Marine and Antarctic Studies

Publisher

Elsevier

Place of publication

Netherlands

Rights statement

Copyright 2014 The Authors Licenced under the CC BY license http://creativecommons.org/licenses/by/3.0/

Repository Status

  • Open

Socio-economic Objectives

Expanding knowledge in the biological sciences

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