Data extraction for the reaction kinetics database SABIO-RK


SABIO-RK ( 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.


DOI: 10.1016/j.pisc.2014.02.004

Research Groups: Scientific Databases and Visualisation

Publication type: Journal

Journal: Perspectives in Science

Citation: Perspectives in Science 1(1-6):33-40

Date Published: 1st May 2014

Registered Mode: Not specified

Authors: Ulrike Wittig, Renate Kania, Meik Bittkowski, Elina Wetsch, Lei Shi, Lenneke Jong, Martin Golebiewski, Maja Rey, Andreas Weidemann, Isabel Rojas, Wolfgang Müller

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Wittig, U., Kania, R., Bittkowski, M., Wetsch, E., Shi, L., Jong, L., Golebiewski, M., Rey, M., Weidemann, A., Rojas, I., & Müller, W. (2014). Data extraction for the reaction kinetics database SABIO-RK. In Perspectives in Science (Vol. 1, Issues 1-6, pp. 33–40). Elsevier BV.

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Created: 6th Oct 2017 at 14:09

Last updated: 5th Mar 2024 at 21:23

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