More findability, more interoperability for SABIO-RK, the curated database for biochemical reaction kinetics

Abstract:

SABIO-RK represents a repository for structured, curated, and annotated data on reactions and their kinetics. The data are manually extracted from the scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions, and the data are made available to the public via a web-based search interface as well as easy-to-use JSON web services for programmatic access. Data are highly interlinked to external databases, ontologies, and controlled vocabularies. This includes cross-references with eg Uniprot, ChEBI, KEGG, BRENDA, Biomodels, and MetaNetX. In the past year we have worked on improving findability of SABIO-RK data as well as interoperability: SABIO-RK was extended to read the additional annotations in the EnzymeML data exchange format to allow the direct import of enzymology data from EnzymeML documents. SABIO-RK is part of the EnzymeML workflow to support the data transfer between experimental platforms, modelling tools and databases (Range et al. FEBS J 2021). In the BMBF-funded project SABIO-VIS we focused on visualizing SABIORK data for the purpose of interactive search and search refinement.

SEEK ID: https://publications.h-its.org/publications/1637

DOI: 10.7490/f1000research.1119079.1

Research Groups: Scientific Databases and Visualisation

Publication type: InCollection

Journal: F1000Research

Citation:

Date Published: 1st Aug 2022

URL: https://f1000research.com/posters/11-876

Registered Mode: manually

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Citation
Weidemann, A., Dudas, D., Rey, M., Wittig, U., & Müller, W. (2022). More findability, more interoperability for SABIO-RK, the curated database for biochemical reaction kinetics. F1000 Research Limited. https://doi.org/10.7490/F1000RESEARCH.1119079.1
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Created: 9th Mar 2023 at 15:33

Last updated: 5th Mar 2024 at 21:25

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