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 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. UniProt) are integrated into BTO.
The terms are classified in 4 main categories (subgraphs):
* animal
* plant
* fungus
* other sources
Further levels are defined below the main categories (=nodes), classifying the “parent”, “child”, and “grandchild” all connected via specific relationships (=edges)
* is_a (e.g. skeletal muscle fibre is_a muscle fibre)
* part_of (e.g. muscle fibre part_of muscle)
* develops/derives_from (e.g.myoma cell develops/derives_from muscle fibre)
* related_to (description of more general relationships between terms which are not covered by the other ones)
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 prefix “plant” is placed before the term, e.g. “plant epidermis”.
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 (Webster's Dictionary, DSMZ).