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16 Publications visible to you, out of a total of 16
BioHackEU24 report: Creating user benefit from ARC-ISA RO-Crate machine-actionability & Increasing FAIRness of digital agrosystem resources by extending Bioschemas

Abstract (Expand)

As part of the BioHackathon Europe 2024, we here report on the progress that both project 19 and project 24 have made during the event. For the purpose of this report we will present the abstract of … abstract of both projects and then dive deeper on what work was done during the BioHackathon.

Authors: Sebastian Beier, Daniel Arend, Daniel Bauer, Marco Brandizi, Dominik Brilhaus, Eli Chadwick, Vera Clemens, Michael Robin Crusoe, Manuel Feser, Jonas Grieb, Xiaoming Hu, Abigail Miller, Timo Mühlhaus, Stuart Owen, Maja Rey, Gabriel Schneider, Julian Schneider, Kevin Schneider, Heinrich Lukas Weil, Florian Wetzels

Date Published: 2nd Feb 2025

Publication Type: Tech report

Improved insights into the SABIO-RK database via visualization.

Abstract (Expand)

SABIO-RK is a database for biochemical reactions and their kinetics. Data in SABIO-RK are inherently multidimensional and complex. The complex relationships between the data are often difficult to … follow or even not represented when using standard tabular views. With an increasing number of data points the mismatch between tables and insights becomes more obvious, and getting an overview of the data becomes harder. Such complex data benefit from being presented using specially adapted visual tools. Visualization is a natural and user-friendly way to quickly get an overview of the data and to detect clusters and outliers. Here, we describe the implementation of a variety of visualization concepts into a common interface within the SABIO-RK biochemical reaction kinetics database. For that purpose, we use a heat map, parallel coordinates and scatter plots to allow the interactive visual exploration of general entry-based information of biochemical reactions and specific kinetic parameter values. Database URL https://sabiork.h-its.org/.

Authors: D. Dudas, U. Wittig, M. Rey, A. Weidemann, W. Muller

Date Published: 31st Mar 2023

Publication Type: Journal

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

Abstract (Expand)

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.

Authors: Andreas Weidemann, Dorotea Dudas, Maja Rey, Ulrike Wittig, Wolfgang Müller

Date Published: 1st Aug 2022

Publication Type: InCollection

Towards Effortless Navigation of Scientific-Literature Screen Reading for Biocuration

Abstract

Not specified

Authors: Sucheta Ghosh, Wolfgang Müller, Ulrike Wittig, Maja Rey

Date Published: 5th May 2022

Publication Type: InProceedings

Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases.

Abstract (Expand)

This article describes some use case studies and self-assessments of FAIR status of de.NBI services to illustrate the challenges and requirements for the definition of the needs of adhering to the FAIR … (findable, accessible, interoperable and reusable) data principles in a large distributed bioinformatics infrastructure. We address the challenge of heterogeneity of wet lab technologies, data, metadata, software, computational workflows and the levels of implementation and monitoring of FAIR principles within the different bioinformatics sub-disciplines joint in de.NBI. On the one hand, this broad service landscape and the excellent network of experts are a strong basis for the development of useful research data management plans. On the other hand, the large number of tools and techniques maintained by distributed teams renders FAIR compliance challenging.

Authors: G. Mayer, W. Muller, K. Schork, J. Uszkoreit, A. Weidemann, U. Wittig, M. Rey, C. Quast, J. Felden, F. O. Glockner, M. Lange, D. Arend, S. Beier, A. Junker, U. Scholz, D. Schuler, H. A. Kestler, D. Wibberg, A. Puhler, S. Twardziok, J. Eils, R. Eils, S. Hoffmann, M. Eisenacher, M. Turewicz

Date Published: 2nd Sep 2021

Publication Type: Journal

Word-Level Alignment of Paper Documents with their Electronic Full-Text Counterparts

Abstract

Not specified

Authors: Mark-Christoph Müller, Sucheta Ghosh, Ulrike Wittig, Maja Rey

Date Published: 11th Jun 2021

Publication Type: InProceedings

FAST, ADAPTED, CURATED FAIR DATA FOR COVID-19 RESEARCH

Abstract (Expand)

Research projects such as the international COVID-19 Disease Map initiative and the German COVID-19 study hub of NFDI are supported by de.NBI-SysBio tools and services in organizing and sharing research … data ’FAIRly‘. This is done via the data management platform FAIRDOMHub/SEEK which is quickly adapted to the users' needs. COVID-19 related literature is manually curated and used for basic research about the curation process of SABIO-RK to provide the research community with high quality kinetics data.

Authors: Maja Rey, Andreas Weidemann, Ulrike Wittig, Dorotea Dudas, Sucheta Ghosh, Martin Golebiewski, Xiaoming Hu, Wolfgang Müller

Date Published: 2021

Publication Type: Booklet

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