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Big data: The future of biocuration

Abstract

Not specified

Authors: Doug Howe, Maria Costanzo, Petra Fey, Takashi Gojobori, Linda Hannick, Winston Hide, David P. Hill, Renate Kania, Mary Schaeffer, Susan St Pierre, Simon Twigger, Owen White, Seung Yon Rhee

Date Published: 4th Sep 2008

Publication Type: Journal

LUCIFER status report: summer 2008

Abstract

Not specified

Authors: Holger Mandel, Walter Seifert, Reiner Hofmann, Marcus Jütte, Rainer Lenzen, Nancy Ageorges, Dominik Bomans, Peter Buschkamp, Ralf-Jürgen Dettmar, Carmen Feiz, Hans Gemperlein, André Germeroth, Lutz Geuer, Jochen Heidt, Volker Knierim, Werner Laun, Michael Lehmitz, Ulrich Mall, Peter Müller, Vianac Naranjo, Kai Polsterer, Andreas Quirrenbach, Ludwig Schäffner, Florian Schwind, Peter Weiser, Harald Weisz

Date Published: 15th Aug 2008

Publication Type: Journal

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

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

Abstract

Not specified

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

Protein-protein docking by simulating the process of association subject to biochemical constraints

Abstract

Not specified

Authors: Domantas Motiejunas, Razif Gabdoulline, Ting Wang, Anna Feldman-Salit, Tim Johann, Peter J. Winn, Rebecca C. Wade

Date Published: 1st Jun 2008

Publication Type: Journal

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