BRENDA Tissue Ontology

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The BTO ( B RENDA T issue O ntology) is a comprehensive, structured encyclopedia . It refers to terms and designations for tissues , organs , anatomical structures, plant parts, cell cultures , cell types and cell lines in organisms from all taxonomic groups (animals, plants, fungi and protozoa) from which the enzymes were isolated or in which they were detected .

The BTO is one of the first tissue-specific ontologies in the field of life sciences that does not focus on one organism or a group of organisms and thus enables easy access to the comprehensive information. It is used as a data source by other databases or integrated into their search functions, for example by the Ontology Lookup Service and MIRIAM Registry of the EBI-EMBL or by the TissueDistributionDB with a tissue synonym library at the German Cancer Research Center Heidelberg or on the websites of the Bioportal (National Center for Biomedical Ontology, Stanford, USA). The users of the BTO come from the fields of medicine and pharmacy, which deal with the occurrence and histological detection of disease-relevant enzymes in tissues, which play an important role in diagnosis and treatment as well as in drug development. In biochemical and biotechnological research, tissue-specific detection of enzymes is used to better understand metabolic processes, regulations and functions. With the help of structured and controlled vocabulary, ontologies are an important tool for depicting evolutionary relationships and linking them with one another.

The development of the BTO began in 2003 with the aim of combining the biochemical and molecular biological enzyme data from BRENDA ("BRaunschweig ENzyme DAtabase") with a hierarchical and standardized collection of tissue-specific terms. The enzyme-specific data and information in BRENDA are manually annotated from scientific literature by biochemists, biologists and chemists. Currently (as of October 2019) the BTO contains 6042 terms, to which 5173 synonyms and 5074 definitions are assigned; each term is assigned to at least one literature reference and one enzyme. The so-called terms (= terms) are classified according to the general categories, rules and formats of the Gene Ontology Consortium (GO,). The terms are not represented as a classic hierarchy, but in the form of a directed acyclic graph (DAG) and created with the help of the editor (processing program) OBO-Edit. Direct access to the functional enzyme data in BRENDA is possible from every level of the hierarchy. Many enzymes are expressed in a tissue-specific manner, so that the BTO is suitable for distinguishing them from one another.

Content and functionality

The BTO accesses the extensive enzyme-specific data of the BRENDA enzyme information system. BRENDA currently (October 2019) contains 112,200 enzyme-organism-tissue-specific data for over 11,000 proteins. These were manually annotated from over 150,000 literature references. All BTO terms are evaluated and classified in the ontology, in the so-called OBO format, with each term having a defined relationship to another term. Each term only occurs once in the ontology and is automatically assigned a unique BTO identification number (BTO ID). These BTO IDs are used to be able to link the information with other databases. In addition, terms from external sources were integrated into the BTO, e.g. B. UniProt .

The terms are classified into four main categories, called subgraphs:

  • animal
  • plans
  • fungus
  • other sources

Below these categories (= nodes) are the other levels in which the "children", "siblings" and "grandchildren" etc. are defined. These categories are linked to one another via defined relationships (= edges):

  • "Is" ("is_a", e.g. skeletal muscle fiber is_a muscle fiber)
  • "Part of" ("part_of", e.g. muscle fiber part_of muscle)
  • "Develops from" ("develops / derives_from", e.g. myoma cell develops / derives_from muscle fiber)
  • "Similar" ("related_to", describes general relationships that are not recorded via "is_a", "part_of" or "develops / derives_from").

Many terms in the BTO can be assigned to specific organisms, organs, tissues or cell types. These are named in the hierarchy in the corresponding definition. In the case of ambiguous expressions such as B. epidermis, which can belong to both animals and plants, a prefix is ​​introduced to distinguish them, e.g. B. "Plant epidermis".

Many of the definitions come from specific specialist dictionaries from the field of medicine, cell line databases, etc. (e.g. Webster's Dictionary , DSMZ ).

Availability

The entries in the BTO are updated every six months in parallel to BRENDA and are freely accessible on the BRENDA website in the "Ontology Explorer". The user can search the BTO using a simple search mask and access the enzyme data in BRENDA directly via the results output. Another way to search the BTO is via the quick search mode "Source Tissue" on the BRENDA website ("Classic View"). The entries in the result list are directly linked to the search in the BTO.

The use of the BTO and thus also of BRENDA is free for academic users. The BTO can be downloaded from “Obofoundry”. Commercial users can purchase licenses from biobase GmbH .

Literature references

  1. ↑ Gremse, M., Chang, A., Schomburg, I., Grote, A., Scheer, M., Ebeling, C., Schomburg, D. (2011): “ The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources ", Nucleic Acids Res. , 39 (Database issue): D507-D513
  2. ↑ Schomburg, I., Chang, A., Schomburg, D. (2014): “ Standardization in enzymology — Data integration in the world's enzyme information system BRENDA ”, Perspectives in Science , 1: 15-23
  3. ↑ Schomburg, I., Chang, A., Placzek, S., Söhngen, C., Rother. M., Lang, M., Munaretto, C., Ulas, S., Stelzer, M., Grote, A., Scheer, M., Schomburg, D. (2013): “ BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA ", Nucleic Acids Res. , 41 (Database issue): D764-D772
  4. ↑ Roncaglia, P., Martone, ME, Hill, DP, Berardini, TZ, Foulger, RE, Imam, FT, Drabkin, H., Mungall, CJ, Lomax, J. (2013): " The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments ”, J. Biomed. Semantics , 4:20
  5. ↑ Smith, B., Ashburner, M. , Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, LJ, Eilbeck, K., Ireland, A., Mungall, CJ; OBI Consortium, Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, SA, Scheuermann, RH, Shah, N., Whetzel, PL, Lewis, S. (2010): " The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration ”, Nat. Biotechnol. , 25: 1251-1255

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