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KOFFI and Anabel 2.0-a new binding kinetics database and its integration in an open-source binding analysis software

2019 Database: The Journal of Biological Databases and Curation  
The kinetics of featured interactions (KOFFI) database is a novel tool and resource for binding kinetics data from biomolecular interactions.  ...  To date, over 270 articles were manually curated and binding data on over 1705 interactions was collected and stored in the (KOFFI) database.  ...  Acknowledgements We thank Normann Kilb, Lisa-Marie Sehls, Philipp Andreas Meyer and Jürgen Burger of ZBSA Center for Biological Systems Analysis, University of Freiburg for their support during the annotation  ... 
doi:10.1093/database/baz101 pmid:31608948 pmcid:PMC6790968 fatcat:rwxvaia2pzfx3ccuvqqvli65ta

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA

Ida Schomburg, Antje Chang, Sandra Placzek, Carola Söhngen, Michael Rother, Maren Lang, Cornelia Munaretto, Susanne Ulas, Michael Stelzer, Andreas Grote, Maurice Scheer, Dietmar Schomburg
2012 Nucleic Acids Research  
BRENDA contains 2.7 million manually annotated data on enzyme occurrence, function, kinetics and molecular properties. Each entry is connected to a reference and the source organism.  ...  KENDA (Kinetic ENzyme DAta), a new amendment extracts and displays kinetic values from PubMed abstracts.  ...  ACKNOWLEDGEMENTS The authors wish to express their thanks to all collaborating scientists, who performed the literature annotation and created the ligand structures.  ... 
doi:10.1093/nar/gks1049 pmid:23203881 pmcid:PMC3531171 fatcat:xzcsbi44aff7vdhbcyxpn4ww5m

cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK [article]

Matthias König
2016 bioRxiv   pre-print
The app allows for easy comparison of kinetic data, visual inspection of the elements involved in the kinetic record and simple access to the annotation information of the kinetic record.  ...  The kinetic information is accessible via a combination of graph structure and annotations of nodes, with provided information consisting of: (I) reaction details, enzyme and organism; (II) kinetic law  ...  SABIORK is a manually curated database for kinetic data storing comprehensive information about biochemical reactions and their kinetic properties, with data manually extracted from the literature and  ... 
doi:10.1101/062091 fatcat:jkvmvi66wfhh7cpxapz73xbdi4

opm: an R package for analysing OmniLog(R) phenotype microarray data

L. A. I. Vaas, J. Sikorski, B. Hofner, A. Fiebig, N. Buddruhs, H.-P. Klenk, M. Goker
2013 Bioinformatics  
opm is an R package designed to analyse multidimensional OmniLog Õ phenotype microarray (PM) data. opm provides management, visualization and statistical analysis of PM data, including curveparameter estimation  ...  and discretization, dedicated and customizable plots, metadata management, automated generation of textual and tabular reports, mapping of substrates to databases, batch conversion of files and export  ...  Meier-Kolthoff and S. Ehrentraut (DSMZ) for helpful advice.  ... 
doi:10.1093/bioinformatics/btt291 pmid:23740744 fatcat:aq6jifpbdbcj7gqaxo3zsd6ili

Kinetic Modeling Using BioPAX Ontology

Oliver Ruebenacker, Ion I. Moraru, James C. Schaff, Michael L. Blinov
2007 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007)  
We describe a software system that enables a variety of operations facilitating the use of BioPAX data to create kinetic models that can be visualized, edited, and simulated using the Virtual Cell (VCell  ...  However, the BioPAX ontology does not encode the necessary information for kinetic modeling and simulation.  ...  Some of this data, such as data taken from the VCell repository of BioPAX files and BioPAX-annotated SBML files, might already be in a state that allows a straight-forward translation into kinetic simulation  ... 
doi:10.1109/bibm.2007.55 pmid:20862270 pmcid:PMC2941992 fatcat:m7zbzfdnfrbmvobxcbpjh6g3ey

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

Olga Krebs, Martin Golebiewski, Renate Kania, Saqib Mir, Jasmin Saric, Andreas Weidemann, Ulrike Wittig, Isabel Rojas
2007 Journal of Integrative Bioinformatics  
The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data.  ...  biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks.  ...  We would also like to thank the members of the Bioinformatics and Computational Biochemistry and the Molecular and Cellular Modelling Groups of EML Research for their helpful discussions and comments.  ... 
doi:10.1515/jib-2007-49 fatcat:esupiapcqjedlfvk2ame6nsrku

cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK

Matthias König
2016 F1000Research  
The app allows for easy comparison of kinetic data, visual inspection of the elements involved in the kinetic record and simple access to the annotation information of the kinetic record.  ...  The kinetic information is accessible via a combination of graph structure and annotations of nodes, with provided information consisting of: (I) reaction details, enzyme and organism; (II) kinetic law  ...  A special thanks to the curation team of SABIO-RK including additional kinetic data in the database based on provided publications. Supplementary material  ... 
doi:10.12688/f1000research.9211.1 fatcat:gt5l6qcb3rag7jdlyaasyeabd4

BRENDA, the enzyme information system in 2011

M. Scheer, A. Grote, A. Chang, I. Schomburg, C. Munaretto, M. Rother, C. Sohngen, M. Stelzer, J. Thiele, D. Schomburg
2010 Nucleic Acids Research  
A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models.  ...  The number of manually annotated references increased by 30% to more than 100 000, the number of ligand structures by 45% to almost 100 000.  ...  ACKNOWLEDGEMENTS We wish to thank all collaborating scientists who performed the literature annotation and created the molecular structures for the enzyme ligands.  ... 
doi:10.1093/nar/gkq1089 pmid:21062828 pmcid:PMC3013686 fatcat:sf363c4w7fbidmu7fpgzuqrpye

BioModels Database: curation and annotation

Michael Schubert, Nicolas Le Novère, Michael Schubert, Ishan Ajmera, Vijayalakshmi Chelliah, Lukas Endler, Nicolas Rodriguez, Camille Laibe
2011 Nature Precedings  
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology 4:92 [2] Hucka M et al. (2003).  ...  Adding semantics in kinetic models of biochemical pathways. Proc. of the 2nd Int. ESCEC Symp. 137-53  ...  The MIRIAM guidelines [3] regarding the curation and annotation of quantitative kinetic models ascertain that proper metadata is added to a model.  ... 
doi:10.1038/npre.2011.6361 fatcat:zjpfif4gezdvhpla54fla3fkzu

BioModels Database: curation and annotation

Michael Schubert, Nicolas Le Novère, Michael Schubert, Ishan Ajmera, Vijayalakshmi Chelliah, Lukas Endler, Nicolas Rodriguez, Camille Laibe
2011 Nature Precedings  
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology 4:92 [2] Hucka M et al. (2003).  ...  Adding semantics in kinetic models of biochemical pathways. Proc. of the 2nd Int. ESCEC Symp. 137-53  ...  The MIRIAM guidelines [3] regarding the curation and annotation of quantitative kinetic models ascertain that proper metadata is added to a model.  ... 
doi:10.1038/npre.2011.6361.1 fatcat:hsaiicf5xzchrm3556ijb6zv24

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics

Ulrike Wittig, Maja Rey, Andreas Weidemann, Renate Kania, Wolfgang Müller
2017 Nucleic Acids Research  
The data are primarily extracted from scientific literature and stored in a relational database.  ...  (i) The website has been completely revised and (ii) allows now also free text search for kinetics data.  ...  The authors also would like to thank the database users and collaboration partners for permanent feedback and discussions about requirements and database improvements.  ... 
doi:10.1093/nar/gkx1065 pmid:29092055 pmcid:PMC5753344 fatcat:c6gwi35b3bdy3huhuo3hlabcg4

Social pathway annotation: extensions of the systems biology metabolic modelling assistant

I. Navas-Delgado, A. Real-Chicharro, M. A. Medina, F. Sanchez-Jimenez, J. F. Aldana-Montes
2010 Briefings in Bioinformatics  
These data are usually represented in different formats (and sometimes in technical documents) on the Web.  ...  These data may contain errors, but the curation of the vast amount of data generated in the 'omic' era cannot be done by individual researchers.  ...  Acknowledgements We would like to thank Daniel Pastor for his constant testing of the tool and advice, Amine Kerzazi for his continuous maintenance of the data wrappers and Ian Morilla for his invaluable  ... 
doi:10.1093/bib/bbq061 pmid:20965999 fatcat:3ls3d7nvj5edbaqrjaw3tc3pqa

SABIO-RK--database for biochemical reaction kinetics

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 (+3 others)
2011 Nucleic Acids Research  
As of October 2011, data from over 3400 publications have been curated and are stored in the database.  ...  SABIO-RK (1,2) was developed as a database to store and structure kinetic data of biochemical reactions and their related information to support modellers and wet-lab scientists in understanding complex  ... 
doi:10.1093/nar/gkr1046 pmid:22102587 pmcid:PMC3245076 fatcat:rybadguwrbhaxne67gcy5w5h2y

ModelBricks—modules for reproducible modeling improving model annotation and provenance

Ann E. Cowan, Pedro Mendes, Michael L. Blinov
2019 npj Systems Biology and Applications  
Most computational models in biology are built and intended for "single-use"; the lack of appropriate annotation creates models where the assumptions are unknown, and model elements are not uniquely identified  ...  Ultimately, a modeler would be able to construct large models by using multiple ModelBricks, preserving annotations and provenance of model elements, resulting in a highly annotated model.  ...  AUTHOR CONTRIBUTIONS A.E.C. and M.L.B. conceived the concept; A.E.C., P.M., and M.L.B. refined the concept and wrote the manuscript.  ... 
doi:10.1038/s41540-019-0114-3 pmid:31602314 pmcid:PMC6783478 fatcat:onyzqmes4vaufp3izqzpb74dxq

Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling

M. L. Blinov, J. C. Schaff, O. Ruebenacker, X. Wei, D. Vasilescu, F. Gao, F. Morgan, L. Ye, A. Lakshminarayana, I. I. Moraru, L. M. Loew
2013 Bioinformatics  
However, there is no standard mechanism for using these data (stored in BioPAX format) to annotate and build quantitative mathematical models.  ...  It provides pathway data retrieval and visualization and enables automatic creation of executable network models directly from qualitative connections between pathway nodes.  ...  Funding: National Institutes of Health (P41-GM103313, U54-RR022232, R01-GM095485).  ... 
doi:10.1093/bioinformatics/btt660 pmid:24273241 pmcid:PMC3892693 fatcat:4pqgu6tbvfeu7hnv4kt3btrivm
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