Maja Rey

Research Groups: Scientific Databases and Visualisation

Institutions: Heidelberg Institute for Theoretical Studies

Ulrike Wittig

Research Groups: Scientific Databases and Visualisation

Institutions: Heidelberg Institute for Theoretical Studies

https://orcid.org/0000-0002-9077-5664
Storing and annotating of kinetic data.

Abstract (Expand)

This paper briefly describes the SABIO-RK database model for the storage of reaction kinetics information and the guidelines followed within the SABIO-RK project to annotate the kinetic data. Such … annotations support the definition of cross links to other related databases and augment the semantics of the data stored in the database.

Authors: I. Rojas, M. Golebiewski, R. Kania, O. Krebs, S. Mir, A. Weidemann, U. Wittig

Date Published: 14th Sep 2007

Publication Type: Journal

Enzyme kinetics informatics: from instrument to browser.

Abstract (Expand)

A limited number of publicly available resources provide access to enzyme kinetic parameters. These have been compiled through manual data mining of published papers, not from the original, raw … experimental data from which the parameters were calculated. This is largely due to the lack of software or standards to support the capture, analysis, storage and dissemination of such experimental data. Introduced here is an integrative system to manage experimental enzyme kinetics data from instrument to browser. The approach is based on two interrelated databases: the existing SABIO-RK database, containing kinetic data and corresponding metadata, and the newly introduced experimental raw data repository, MeMo-RK. Both systems are publicly available by web browser and web service interfaces and are configurable to ensure privacy of unpublished data. Users of this system are provided with the ability to view both kinetic parameters and the experimental raw data from which they are calculated, providing increased confidence in the data. A data analysis and submission tool, the kineticswizard, has been developed to allow the experimentalist to perform data collection, analysis and submission to both data resources. The system is designed to be extensible, allowing integration with other manufacturer instruments covering a range of analytical techniques.

Authors: N. Swainston, M. Golebiewski, H. L. Messiha, N. Malys, R. Kania, S. Kengne, O. Krebs, S. Mir, H. Sauer-Danzwith, K. Smallbone, A. Weidemann, U. Wittig, D. B. Kell, P. Mendes, W. Muller, N. W. Paton, I. Rojas

Date Published: 27th Aug 2010

Publication Type: Journal

SABIO-RK--database for biochemical reaction kinetics.

Abstract (Expand)

SABIO-RK (http://sabio.h-its.org/) is a web-accessible database storing comprehensive information about biochemical reactions and their kinetic properties. SABIO-RK offers standardized data manually … extracted from the literature and data directly submitted from lab experiments. The database content includes kinetic parameters in relation to biochemical reactions and their biological sources with no restriction on any particular set of organisms. Additionally, kinetic rate laws and corresponding equations as well as experimental conditions are represented. All the data are manually curated and annotated by biological experts, supported by automated consistency checks. SABIO-RK can be accessed via web-based user interfaces or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language), e.g. for import in modelling tools.

Authors: U. Wittig, R. Kania, M. Golebiewski, M. Rey, L. Shi, L. Jong, E. Algaa, A. Weidemann, H. Sauer-Danzwith, S. Mir, O. Krebs, M. Bittkowski, E. Wetsch, I. Rojas, W. Muller

Date Published: 22nd Nov 2011

Publication Type: Journal

Challenges for an enzymatic reaction kinetics database.

Abstract (Expand)

The scientific literature contains a tremendous amount of kinetic data describing the dynamic behaviour of biochemical reactions over time. These data are needed for computational modelling to create … models of biochemical reaction networks and to obtain a better understanding of the processes in living cells. To extract the knowledge from the literature, biocurators are required to understand a paper and interpret the data. For modellers, as well as experimentalists, this process is very time consuming because the information is distributed across the publication and, in most cases, is insufficiently structured and often described without standard terminology. In recent years, biological databases for different data types have been developed. The advantages of these databases lie in their unified structure, searchability and the potential for augmented analysis by software, which supports the modelling process. We have developed the SABIO-RK database for biochemical reaction kinetics. In the present review, we describe the challenges for database developers and curators, beginning with an analysis of relevant publications up to the export of database information in a standardized format. The aim of the present review is to draw the experimentalist's attention to the problem (from a data integration point of view) of incompletely and imprecisely written publications. We describe how to lower the barrier to curators and improve this situation. At the same time, we are aware that curating experimental data takes time. There is a community concerned with making the task of publishing data with the proper structure and annotation to ontologies much easier. In this respect, we highlight some useful initiatives and tools.

Authors: U. Wittig, M. Rey, R. Kania, M. Bittkowski, L. Shi, M. Golebiewski, A. Weidemann, W. Muller, I. Rojas

Date Published: 30th Oct 2013

Publication Type: Journal

SYCAMORE--a systems biology computational analysis and modeling research environment

Abstract (Expand)

SYCAMORE is a browser-based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Thus, it allows e.g. database supported modelling, basic model … checking and the estimation of unknown kinetic parameters based on protein structures. In addition, it offers some guidance in order to allow non-expert users to perform basic computational modelling tasks.

Authors: A. Weidemann, S. Richter, M. Stein, S. Sahle, R. Gauges, R. Gabdoulline, I. Surovtsova, N. Semmelrock, B. Besson, I. Rojas, R. Wade, U. Kummer

Date Published: 13th Jun 2008

Publication Type: Journal

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