Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Jan;39(Database issue):D507-13.
doi: 10.1093/nar/gkq968. Epub 2010 Oct 28.

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

Marion Gremse  1 , Antje Chang, Ida Schomburg, Andreas Grote, Maurice Scheer, Christian Ebeling, Dietmar Schomburg
Affiliations

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

Marion Gremse et al. Nucleic Acids Res. 2011 Jan.

Abstract

BTO, the BRENDA Tissue Ontology (http://www.BTO.brenda-enzymes.org) represents a comprehensive structured encyclopedia of tissue terms. 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. Currently, BTO contains more than 4600 different anatomical structures, tissues, cell types and cell lines, classified under generic categories corresponding to the rules and formats of the Gene Ontology Consortium and organized as a directed acyclic graph (DAG). Most of the terms are endowed with comments on their derivation or definitions. The content of the ontology is constantly curated with ∼1000 new terms each year. Four different types of relationships between the terms are implemented. A versatile web interface with several search and navigation functionalities allows convenient online access to the BTO and to the enzymes isolated from the tissues. Important areas of applications of the BTO terms are the detection of enzymes in tissues and the provision of a solid basis for text-mining approaches in this field. It is widely used by lab scientists, curators of genomic and biochemical databases and bioinformaticians. The BTO is freely available at http://www.obofoundry.org.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Web Interface with search and display capabilities of the BTO. As an example, the term ‘muscular system’ was chosen. The ‘condensed tree view’ provides an overview of the position of the term of interest in the hierarchical structure of the BTO.
Figure 2.
Figure 2.
Ontology relationships for ‘muscle fibre’ and its descendants, whereas the term ‘muscle fibre’ is a ‘part_of’ a ‘muscle’ (Symbol: P) and a ‘myoma cell’ ‘develops_from’ a ‘muscle fibre’ (Symbol: d). In contrast, the parent–child relationship between ‘muscle fibre’ and ‘electroplax’ is very general represented by the relationship type ‘related_to’ (Symbol: R).
Figure 3.
Figure 3.
Number of BTO terms since 2003.
Figure 4.
Figure 4.
BTO subgraph for ‘Animal’ with its direct child terms.
Figure 5.
Figure 5.
The assignment of ‘myoma cell’ in the BTO.
Figure 6.
Figure 6.
The ‘Source Tissue’ search form of the BRENDA web interface. As an example, parts of the search results for the tissue term ‘brain’ are shown (enzyme hits).
Figure 7.
Figure 7.
Search for the term ‘forebrain’ in the BRENDA enzyme database.
See this image and copyright information in PMC

References

    1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight S, Eppig JT, et al. Gene ontology: tool for the unification of biology. Nat. Genet. 2000;25:25–29. - PMC - PubMed
    1. Chang A, Scheer M, Grote A, Schomburg I, Schomburg D. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res. 2009;37:D588–D592. - PMC - PubMed
    1. Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D. BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res. 2004;32:D431–D433. - PMC - PubMed
    1. The Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010;38:D331–D335. - PMC - PubMed
    1. Smith B, Ashburner M, Rosse C, Bard C, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 2007;25:1251–1255. - PMC - PubMed

Publication types