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115 Publications visible to you, out of a total of 115
Classification of chemical compounds to support complex queries in a pathway database.

Abstract (Expand)

Data quality in biological databases has become a topic of great discussion. To provide high quality data and to deal with the vast amount of biochemical data, annotators and curators need to be supported … by software that carries out part of their work in an (semi-) automatic manner. The detection of errors and inconsistencies is a part that requires the knowledge of domain experts, thus in most cases it is done manually, making it very expensive and time-consuming. This paper presents two tools to partially support the curation of data on biochemical pathways. The tool enables the automatic classification of chemical compounds based on their respective SMILES strings. Such classification allows the querying and visualization of biochemical reactions at different levels of abstraction, according to the level of detail at which the reaction participants are described. Chemical compounds can be classified in a flexible manner based on different criteria. The support of the process of data curation is provided by facilitating the detection of compounds that are identified as different but that are actually the same. This is also used to identify similar reactions and, in turn, pathways.

Authors: U. Wittig, A. Weidemann, R. Kania, C. Peiss, I. Rojas

Date Published: 17th Jul 2008

Publication Type: Journal

Developing a protein-interactions ontology.

Abstract

Not specified

Authors: E. Ratsch, J. Schultz, J. Saric, P. C. Lavin, U. Wittig, U. Reyle, I. Rojas

Date Published: 17th Jul 2008

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

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

SABIO-RK: A data warehouse for biochemical reactions and their kinetics

Abstract

Not specified

Authors: Olga Krebs, Martin Golebiewski, Renate Kania, Saqib Mir, Jasmin Saric, Andreas Weidemann, Ulrike Wittig, Isabel Rojas

Date Published: 1st Mar 2007

Publication Type: Journal

SABIO-RK: Integration and Curation of Reaction Kinetics Data

Abstract

Not specified

Authors: Ulrike Wittig, Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Andreas Weidemann, Stefanie Anstein, Jasmin Saric, Isabel Rojas

Date Published: 2006

Publication Type: Journal

Web-based visualisation of the transcriptional control network of Escherichia coli.

Abstract (Expand)

Transcription is one of the basic processes of gene expression, controlled by a complex network of biochemical reactions. Despite its importance, most work on the visualisation of biochemical networks … focuses on the representation of metabolic pathways. The visualisation of the complex networks controlling transcription requires the implementation of a hierarchical approach that allows the display of the structure of each regulatory region with its transcription factors and regulated operons. This paper presents a web-based application for the visualisation of transcriptional control networks. It takes as case study the organism Escherichia coli. The definition of the visual components implemented is mainly based on those proposed by Shen-Orr et al., 2002, slightly extended to visualise complex networks.

Authors: N. Sosa, A. Kremling, E. Ratsch, I. Rojas

Date Published: 28th Oct 2004

Publication Type: Journal

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