Public biological ontologies .md

Bionty gives you a single API for public ontologies, served from S3 with high availability and low latency.[1]

Modeling public ontologies

A biological entity type (e.g., Organism) is a variable that takes values from a vocabulary of terms with biological meaning:

  1. There are different roughly equivalent vocabularies for the same entity type. For example, one can describe organism with the vocabulary of the scientific names, the vocabulary of the common names, or the vocabulary of ontology IDs for the same organism.

  2. There are different versions & sources of these vocabularies.

  3. Terms in the vocabularies have different granularity, and are often hierarchical.

Often, vocabularies are based on a given version of a public reference ontology, but contain additional “custom” terms corresponding to “new knowledge” absent from reference ontologies. For example, new cell types or states, or new synthetic genes. If you face this situation, read how to extend public ontologies with in-house terms: Manage biological ontologies.

The central PublicOntology class models 3 of the 4 above-mentioned properties of biological entity types:

  1. Every PublicOntology object comes with a table of terms in which each column corresponds to an alternative vocabulary for the entity.

  2. Every table is versioned & has a tracked reference source (typically, a public ontology).

  3. Most tables have a children column that allows mapping hierarchies.

Public ontology guides

The guides cover the following entity types:

You can see all supported ontology versions here.