Data extraction for the reaction kinetics database SABIO-RK

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

作者机构：Scientific Databases and Visualization Group Heidelberg Institute for Theoretical Studies (HITS) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg Germany 

出 版 物：《Perspectives in Science》 

年 卷 期：2014年第1卷第1期

页      面：33-40页

主　　题：Database Reaction kinetics Biocuration Ontology 

摘      要：SABIO-RK ( http://***/ ) 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.