standards > terminology artifact > DOI:10.25504/FAIRsharing.1414v8


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ready BRENDA tissue / enzyme source

Abbreviation: BTO


General Information
A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.

Homepage http://www.brenda-enzymes.info

Countries that developed this resource Germany

Created in 1991

Taxonomic range




How to cite this record FAIRsharing.org: BTO; BRENDA tissue / enzyme source; DOI: https://doi.org/10.25504/FAIRsharing.1414v8; Last edited: July 14, 2019, 1:55 p.m.; Last accessed: Jul 21 2019 8:39 p.m.


Record updated: July 14, 2019, 1:55 p.m. by The FAIRsharing Team.

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In Collections



Tools

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Schemas

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Access / Retrieve Data


Publications

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


Nucleic Acids Res. 2011

View Paper (PubMed)

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

Chang A,Schomburg I,Placzek S,Jeske L,Ulbrich M,Xiao M,Sensen CW,Schomburg D
Nucleic Acids Res 2014

View Paper (PubMed) View Publication

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

Schomburg I,Chang A,Placzek S,Sohngen C,Rother M,Lang M,Munaretto C,Ulas S,Stelzer M,Grote A,Scheer M,Schomburg D
Nucleic Acids Res 2012

View Paper (PubMed) View Publication

BRENDA in 2019: a European ELIXIR core data resource.

Jeske L,Placzek S,Schomburg I,Chang A,Schomburg D
Nucleic Acids Res 2018

View Paper (PubMed) View Publication

BRENDA, the enzyme database: updates and major new developments.

Schomburg I,Chang A,Ebeling C,Gremse M,Heldt C,Huhn G,Schomburg D
Nucleic Acids Res 2003

View Paper (PubMed) View Publication

BTO Ontology Display

View in BioPortal.


Disclaimer: This widget assumes the availability of the ontology resources in the NCBO BioPortal.

View in OBO Foundry.



Related Standards

Identifier Schemas

No identifier schema standards defined

Metrics

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Implementing Databases (15)
ChEMBL
ChEMBL is an open large-scale bioactivity database containing information largely manually extracted from the medicinal chemistry literature. Information regarding the compounds tested (including their structures), the biological or physicochemical assays performed on these and the targets of these assays are recorded in a structured form, allowing users to address a broad range of drug discovery questions.

neXtProt
neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.

Stem Cell Discovery Engine
Comparison system for cancer stem cell analysis

MetaboLights
MetaboLights is a database is a collection of metabolite structures. This resource provides information on the compound origins,the biological roles, locations and concentrations, as well as experimental data from metabolic experiments. The tools and capabilities of this database is firmly routed in collaborative working worldwie with the metabolomics community such as the Metabolomics Society and the associated Metabolomics Standards Initiative (MSI).

BRENDA
BRENDA is the main collection of enzyme functional data available to the scientific community.

SABIO-RK Biochemical Reaction Kinetics Database
SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.

The Global Proteome Machine Database
Rather than being a complete record of a proteomics experiment, this database holds the minimum amount of information necessary for certain bioinformatics-related tasks, such as sequence assignment validation. Most of the data is held in a set of XML files.

Biological General Repository for Interaction Datasets
BioGRID is an interaction repository with data compiled through comprehensive curation efforts. BioGRID currently holds over 980,000 interactions curated from both high-throughput datasets and individual focused studies, as derived from over 55,000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding year (S. cerevisiae), fission yeast (S. pome), and thale cress (A. thaliana), and efforts to expand curation across multiple metazoan species are underway. All data are freely provided via the search index and available for download in standardized formats.

ReMap
ReMap is an integrative analysis of transcription factor ChIP-seq experiments publicly available, merged with the Encode dataset. The resource is an extensive regulatory catalogue of transcription factor binding sites from transcription factors (TFs). The data is available to browse or download either for a given transcription factor or for the entire dataset.

SIGnaling Network Open Resource
SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The entire network can be freely downloaded and used to support logic modeling or to interpret high content datasets. The core of this project is a collection of more than 11000 manually-annotated causal relationships between proteins that participate in signal transduction. Each relationship is linked to the literature reporting the experimental evidence. In addition each node is annotated with the chemical inhibitors that modulate its activity. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.

Immune Epitope Database
The IEDB provides the scientific community with a central repository of freely accessible epitope data and epitope prediction and analysis resources. The IEDB is a publicly accessible, comprehensive immune epitope database containing peptidic linear and conformational epitopes and non peptidic epitopes such as lipids, metals, drugs, carbohydrates, etc, with published or submitted antibody, T cell, MHC binding or MHC ligand elution experimental assays. Epitope data related to infectious diseases, allergy, autoimmunity and transplant tested in humans, non human primates, and any other species can be found in the IEDB.

Target Central Resource Database
TCRD is the central resource behind the Illuminating the Druggable Genome Knowledge Management Center (IDG-KMC). TCRD contains information about human targets, with special emphasis on four families of targets that are central to the NIH IDG initiative: GPCRs, kinases, ion channels and nuclear receptors. Olfactory GPCRs (oGPCRs) are treated as a separate family. A key aim of the KMC is to classify the development/druggability level of targets. The official public portal for TCRD is Pharos (pharos.nih.gov). Based on modern web design principles the Pharos interface provides facile access to all data types collected by the KMC. Given the complexity of the data surrounding any target, efficient and intuitive visualization has been a high priority, to enable users to quickly navigate & summarize search results and rapidly identify patterns. A critical feature of the interface is the ability to perform flexible search and subsequent drill down of search results. Underlying the interface is a RESTful API that provides programmatic access to all KMC data, allowing for easy consumption in user applications.

OBO Foundry
The Open Biological and Biomedical Ontology (OBO) Foundry is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The mission of the OBO Foundry is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. To achieve this, OBO Foundry participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations, based on ontology models that work well, such as the Gene Ontology (GO). The OBO Foundry is overseen by an Operations Committee with Editorial, Technical and Outreach working groups.

Bovine Genome Database
The Bovine Genome Database project is developed to support the efforts of bovine genomics researchers by providing data mining, genome navigation and annotation tools for the bovine reference genome based on the hereford cow, L1 Dominette 01449.

BovineMine
BovineMine integrates the bovine reference genome assembly with many other biological data sets, including genomes of other species. The sheep and goat genomes allow comparison across ruminants. Model organism data (human, mouse, rat) allow well-curated data sets to be applied to ruminants using orthology.

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Grant Number(s)

  • 01KX1235 (The Federal Ministry of Education and Research (BMBF))

  • 021902 (RII3) (European Union, Free European Life-Science Information and Computational Services (FELICS))

  • 226073 (European Union, Serving Life-science Information for the Next Generation (SLING))

  • 74ZN1122 (Ministry of Science and Culture of Lower Saxony, Hannover, Germany)