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The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

M. Gremse, A. Chang, I. Schomburg, A. Grote, M. Scheer, C. Ebeling, D. Schomburg
2010 Nucleic Acids Research  
The project started in 2003 to create a connection between the enzyme data collection of the BRENDA enzyme database and a structured network of source tissues and cell types.  ...  BTO, the BRENDA Tissue Ontology (http://www .BTO.brenda-enzymes.org) represents a comprehensive structured encyclopedia of tissue terms.  ...  The BTO has been developed according to the rules and formats of the GO Consortium and provides the first ontology for all organisms with respect to the diversity of enzyme sources.  ... 
doi:10.1093/nar/gkq968 pmid:21030441 pmcid:PMC3013802 fatcat:lm6n4ywgarfodmkun64pyze6yi

BRENDA in 2015: exciting developments in its 25th year of existence

Antje Chang, Ida Schomburg, Sandra Placzek, Lisa Jeske, Marcus Ulbrich, Mei Xiao, Christoph W. Sensen, Dietmar Schomburg
2014 Nucleic Acids Research  
The human anatomy atlas CAVEman is linked to the BRENDA Tissue Ontology terms providing a connection between anatomical and functional enzyme data.  ...  The BRENDA enzyme information system (http:// www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible  ...  In 2003, BRENDA started to develop the BRENDA Tissue Ontology (BTO), a structured comprehensive Encyclopedia of tissue terms from multicellular organisms (5) .  ... 
doi:10.1093/nar/gku1068 pmid:25378310 pmcid:PMC4383907 fatcat:sdwv66mdaffetnkky63xabh3jm

BRENDA, the ELIXIR core data resource in 2021: new developments and updates

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg
2020 Nucleic Acids Research  
In 2018, BRENDA was selected as an ELIXIR Core Data Resource. BRENDA provides reliable data, continuous curation and updates of classified enzymes, and the integration of newly discovered enzymes.  ...  The new EnzymeDetector combines BRENDA enzyme annotations with protein and genome databases for the detection of eukaryotic and prokaryotic enzymes.  ...  Last but not least, we thank all collaborating scientists who performed the literature annotation and created the molecular structures for the enzyme ligands.  ... 
doi:10.1093/nar/gkaa1025 pmid:33211880 fatcat:pxtkejg5cbeifipq7cjc5e6dim

BRENDA in 2019: a European ELIXIR core data resource

Lisa Jeske, Sandra Placzek, Ida Schomburg, Antje Chang, Dietmar Schomburg
2018 Nucleic Acids Research  
An organism summary page showing all relevant information, e.g. taxonomy and synonyms linked to enzyme data, was implemented.  ...  The BRENDA enzyme database (www.brendaenzymes.org), recently appointed ELIXIR Core Data Resource, is the main enzyme and enzyme-ligand information system.  ...  All described databases and features are accessible via the main BRENDA website: https://www.brenda-enzymes. org/.  ... 
doi:10.1093/nar/gky1048 pmid:30395242 fatcat:llyx55uua5aqbfjj5apwohr3xu

BRENDA, the enzyme database: updates and major new developments

I. Schomburg
2004 Nucleic Acids Research  
In the past year BRENDA has undergone major changes including a large increase in updating speed with >50% of all data updated in 2002 or in the ®rst half of 2003, the development of a new EC-tree browser  ...  , a taxonomy-tree browser, a chemical substructure search engine for ligand structure, the development of controlled vocabulary, an ontology for some information ®elds and a thesaurus for ligand names.  ...  SOURCE/TISSUE The BRENDA team has created a hierarchical ontology for enzyme sources or tissue.  ... 
doi:10.1093/nar/gkh081 pmid:14681450 pmcid:PMC308815 fatcat:l6aqm2qfurfrvb3as6oqcrkmt4

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  
Search criteria now include the search for organism taxonomy based on NCBI (7), compound classification based on ChEBI ontology (8) and tissue ontology based on BRENDA tissue ontology (BTO) (9) offering  ...  The tissue search in SABIO-RK includes the possibility to use BRENDA Tissue Ontology terms, e.g. search for 'liver (BTO)' offering more liver related entries compared to simple 'liver' search ( Figure  ... 
doi:10.1093/nar/gkr1046 pmid:22102587 pmcid:PMC3245076 fatcat:rybadguwrbhaxne67gcy5w5h2y

BRENDA in 2017: new perspectives and new tools in BRENDA

Sandra Placzek, Ida Schomburg, Antje Chang, Lisa Jeske, Marcus Ulbrich, Jana Tillack, Dietmar Schomburg
2016 Nucleic Acids Research  
New interactive and intuitive BRENDA pathway maps give an overview on biochemical processes and facilitate the visualization of enzyme, ligand and organism information in the biochemical context.  ...  The BRENDA enzyme database (www.brendaenzymes.org) has developed into the main enzyme and enzyme-ligand information system in its 30 years of existence.  ...  Organs, tissues and cell cultures, based on the terms of the BRENDA Tissue Ontology (BTO) are specified for eukaryotic enzymes (4). Table 1 shows the data content of a selection of data fields.  ... 
doi:10.1093/nar/gkw952 pmid:27924025 pmcid:PMC5210646 fatcat:kltw4gqvqvfc5ijvwuddbe4vhi

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  
(iii) Additional interlinkages with other databases in our field have been established; this enables users to gain directly comprehensive knowledge about the properties of enzymes and kinetics beyond SABIO-RK  ...  The data are made available to the public by a web-based search interface and by web services for programmatic access.  ...  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

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  
The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes.  ...  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.  ...  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

iCTNet2: integrating heterogeneous biological interactions to understand complex traits

Lili Wang, Daniel S. Himmelstein, Adam Santaniello, Mousavi Parvin, Sergio E. Baranzini
2015 F1000Research  
Reference Source 15. Gremse M, Chang A, Schomburg I, et al.: The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources.  ...  .: Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res. 2012; 40(Database issue): D940-6. PubMed Abstract | Publisher Full Text | Free Full Text 10.  ...  Tissues. Tissue types were taken from BRENDA tissue ontology 15 . We rooted the ontology at 'whole body' (BTO:0001489) to exclude the non-animal tissue portions of the ontology. Drugs.  ... 
doi:10.12688/f1000research.6836.2 pmid:26834985 pmcid:PMC4706053 fatcat:kkoi3hzrf5a45pj6rupak5lngu

Comparison, alignment, and synchronization of cell line information between CLO and EFO

Edison Ong, Sirarat Sarntivijai, Simon Jupp, Helen Parkinson, Yongqun He
2017 BMC Bioinformatics  
We examined Cellosaurus resources for EFO-CLO cross-references. Text labels of cell lines from both ontologies were verified by biological information axiomatized in each source.  ...  All of these cell lines were updated to CLO and the cell line related information was merged. A design pattern that integrates EFO and CLO was also developed.  ...  Acknowledgements The authors would like to thank the organizers of the International Conference on Biomedical Ontology for providing comments and scientific reviews of the work at the Cell in Experimental  ... 
doi:10.1186/s12859-017-1979-z pmid:29322915 pmcid:PMC5763470 fatcat:y7mrf7dqbncdvjrm7z52xemvda

Standardization in enzymology—Data integration in the world׳s enzyme information system BRENDA

Ida Schomburg, Antje Chang, Dietmar Schomburg
2014 Perspectives in Science  
The definition of the biological enzyme sources are based on ontologies and controlled vocabularies.  ...  In addition to the enzyme names unambiguousness is needed for the ligand names, the enzyme's origin as given by the organism name, a tissue name and the description of the subcellular localisation.  ...  Acknowledgements We wish to thank all scientists who maintain the BRENDA website, performed the literature annotation and created the molecular structures for the enzyme ligands.  ... 
doi:10.1016/j.pisc.2014.02.002 fatcat:yjc32fxmqfd3dm4sf6tzwu6v5y

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  
The BRENDA (BRaunschweig ENzyme Database, http://www.brenda-enzymes.org) enzyme information system is the main collection of enzyme functional and property data for the scientific community.  ...  A new SBML output format of BRENDA kinetic data allows the construction of organism-specific metabolic models.  ...  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

Data extraction for the reaction kinetics database SABIO-RK

Ulrike Wittig, Renate Kania, Meik Bittkowski, Elina Wetsch, Lei Shi, Lenneke Jong, Martin Golebiewski, Maja Rey, Andreas Weidemann, Isabel Rojas, Wolfgang Müller
2014 Perspectives in Science  
the computational modeling to create models of biochemical reaction networks.  ...  Therefore the manual extraction of knowledge from the literature requires biological experts to understand the paper and interpret the data.  ...  Virtual Liver and SysMO-LAB (Systems Biology of Microorganisms), and the DFG LIS (http://www.dfg.de/) as part of the project Integrierte Immunoblot Umgebung.  ... 
doi:10.1016/j.pisc.2014.02.004 fatcat:fn2cw4lzivcztcux7whqb4vpbq

The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons

Shannan J. Ho Sui, Kimberly Begley, Dorothy Reilly, Brad Chapman, Ray McGovern, Philippe Rocca-Sera, Eamonn Maguire, Gabriel M. Altschuler, Terah A. A. Hansen, Ramakrishna Sompallae, Andrei Krivtsov, Ramesh A. Shivdasani (+6 others)
2011 Nucleic Acids Research  
We thank Dr Miguel Andrade-Navarro for access to the StemBase data. Thank you also to Emily Merrill and Dr Sudeshna Das for their input on ontology usage.  ...  ACKNOWLEDGEMENTS We acknowledge assistance from the Harvard Stem Cell Institute for contributing CSC data and are grateful for discussions and assistance from Dr Amit Sinha.  ...  stage EFO Disease state ICD-9, NCI Thesaurus, Disease Ontology Organism part (tissue type) Foundational Model of Anatomy, Mouse Gross Anatomy, BRENDA tissue/enzyme source (BTO), EFO Cell type Cell  ... 
doi:10.1093/nar/gkr1051 pmid:22121217 pmcid:PMC3245064 fatcat:jf6rmgi74jfjxburc22niclt4y
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