Reference#

Bionty.

Import the package:

import bionty as bt

Entities:

Organism([organism, source, version])

Organism.

Gene([organism, source, version])

Gene.

Protein([organism, source, version])

Protein.

CellMarker([organism, source, version])

Cell markers.

CellType([organism, source, version])

Cell type ontologies.

CellLine([organism, source, version])

Cell line.

Tissue([organism, source, version])

Tissue.

Disease([organism, source, version])

Disease ontologies.

Phenotype([organism, source, version])

Phenotype.

Pathway([organism, source, version])

Pathway.

ExperimentalFactor([organism, source, version])

Experimental Factor.

DevelopmentalStage([organism, source, version])

Developmental Stage.

Drug([organism, source, version])

Drug ontologies.

Ethnicity([organism, source, version])

Ethnicity.

BFXPipeline([organism, source, version])

Bioinformatics pipelines.

BioSample([organism, source, version])

BioSample attributes.

Base model of entity classes:

Bionty([source, version, organism, ...])

Bionty base model.

BiontyField(parent, name)

Field of a Bionty model.

Bionty sources:

display_available_sources()

Displays all available sources.

display_currently_used_sources()

Displays all currently used sources.

LOCAL_SOURCES

Path subclass for non-Windows systems.

reset_sources()

Reset local bionty sources file.

External API:

Ontology([handle, import_depth, timeout, ...])

Interface with ontologies via pronto.