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references. All terms in BTO are evaluated and classified according to the OBO-format, and are connected by specific relationships. Each term is a distinct entry within the ontology and is automatically assigned to a unique BTO-identifier (BTO-ID). The BTO-IDs serve as stable accession numbers in order to create cross-references to further external biochemical databases. Further tissue und cell-type specific terms from external databases (i.e.
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Most of the terms are clearly associated with specific organisms, organs, tissues, or cell types. There are several identical designations for tissues both in plants and animals, e.g. “epidermis”. To distinguish between those tissue terms and to classify them correctly into BTO for plant tissues the
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BTO draws upon the comprehensive enzyme specific data of the BRENDA enzyme information system. Presently (October 2019) 112,200 enzyme-organism-tissue specific data from more than 11,000 proteins are stored in BRENDA. These entries were manually annotated from more than 150,000 different literature
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Development of BTO started in 2003, aimed to connect the biochemical and molecular biological enzyme data of BRENDA with a hierarchical and standardized collection of tissue-specific terms. The functional enzyme data and information in BRENDA have been manually annotated and structured by experts
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the organism-specific tissue terms linked to enzyme functional data are an important resource for the understanding of the metabolism and regulation in life sciences. Ontologies represent classification systems that provide controlled and structured vocabularies. They are important tools to
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from biochemistry, biology, and chemistry. By
October 2022, the BTO contained over 6,527 terms, linked to 6,065 synonyms and 5,474 definitions. The terms are classified under generic categories, rules, and formats of the Gene Ontology Consortium (GO,), organized as a
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Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L.J., Eilbeck, K., Ireland, A., Mungall, C.J.; OBI Consortium, Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S.A., Scheuermann, R.H., Shah, N., Whetzel, P.L, Lewis, S. (2010):
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OBO-Edit. All terms from each level are directly connected the enzyme data in BRENDA. BTO is a suitable tool to distinguish between different enzymes which are expressed in a tissue-specific manner.
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More than 80% of the tissue terms have definitions that describe the meaning and context. These definitions are obtained from i.e. medical dictionaries and cell line databases (
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Further levels are defined below the main categories (=nodes), classifying the “parent”, “child”, and “grandchild” all connected via specific relationships (=edges)
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The entries in BTO are updated bi-annually as part of the major update of BRENDA. It is available via the BRENDA website in the category “
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in
Stanford, USA rely on BTO and implement the encyclopedia as an essential repository of information into their respective platform.
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The Gene
Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments
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Roncaglia, P., Martone, M.E., Hill, D.P., Berardini, T.Z., Foulger, R.E., Imam, F.T., Drabkin, H., Mungall, C.J., Lomax, J. (2013): „
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Chang, A., Jeske, L., Ulbrich, S., Hofmann, J., Koblitz, J., Schomburg, I., Neumann-Schaal, M., Jahn, D., Schomburg, D. (2021): „
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related_to (description of more general relationships between terms which are not covered by the other ones)
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Standardization in enzymology—Data integration in the world's enzyme information system BRENDA
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BTO and BRENDA are freely accessible for academic users. It can be freely downloaded via the “
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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
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detection of disease-related enzymes in tissues, which play an important role in
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BRENDA, the ELIXIR core data resource in 2021: new developments and updates
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develops/derives_from (e.g.myoma cell develops/derives_from muscle fibre)
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Bioportal des
National Center for Biomedical Ontology, Stanford, USA
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prefix “plant” is placed before the term, e.g. “plant epidermis”.
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The terms are classified in 4 main categories (subgraphs):
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http://www.brenda-enzymes.org/ontology.php?ontology_id=3
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is_a (e.g. skeletal muscle fibre is_a muscle fibre)
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372:J. Biomed. Semantics
288:Webster's Dictionary
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425:Obofoundry
357:, 1: 15–23
321:References
315:Obofoundry
148:ontologies
117:cell lines
113:cell types
205:diagnosis
182:Bioportal
133:protozoon
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480:Enzymes
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176:of the
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101:tissues
80:Website
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Text is available under the Creative Commons Attribution-ShareAlike License. Additional terms may apply.
