##### Public biological ontologies

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:

* Gene - Ensembl, NCBI Gene

* Protein - Uniprot

* Organism - Ensembl Species. NCBI Taxonomy

* CellLine - Cell Line Ontology

* CellType - Cell Ontology

* CellMarker - CellMarker

* Tissue - Uberon

* Disease - Mondo, Human Disease, ICD

* Phenotype - Human Phenotype, Phecodes, PATO, Mammalian Phenotype,
  Zebrafish Phenotype

* Pathway - Gene Ontology, Pathway Ontology

* ExperimentalFactor - Experimental Factor Ontology

* DevelopmentalStage - Human Developmental Stages, Mouse Developmental
  Stages

* Ethnicity - Human Ancestry Ontology

You can see all supported ontology versions here.

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[1] Given some of the original ontology services are slow or sometimes
 down.