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Data extraction for the reaction kinetics database SABIO-RK

Citation

Wittig, U and Kania, R and Bittkowski, M and Wetsch, E and Shi, L and Jong, L and Golebiewski, M and Rey, M and Weidemann, A and Rojas, I and Muller, W, Data extraction for the reaction kinetics database SABIO-RK, Perspectives in Science, 1, (1-6) pp. 33-40. ISSN 2213-0209 (2014) [Refereed Article]


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

DOI: doi:10.1016/j.pisc.2014.02.004

Abstract

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.

Item Details

Item Type:Refereed Article
Keywords:database, biocuration, reaction kinetics, ontology
Research Division:Information and Computing Sciences
Research Group:Computer Software
Research Field:Computer Software not elsewhere classified
Objective Division:Expanding Knowledge
Objective Group:Expanding Knowledge
Objective Field:Expanding Knowledge in the Biological Sciences
Author:Jong, L (Dr Lenneke Jong)
ID Code:102789
Year Published:2014
Deposited By:IMAS Research and Education Centre
Deposited On:2015-09-04
Last Modified:2015-10-06
Downloads:113 View Download Statistics

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