Bionty.
Project description
bionty-base
Access public biological ontologies.
Installation
Bionty-base is a Python package available for
pip install bionty-base
Entities
Gene
- Ensembl, NCBI GeneProtein
- UniprotOrganism
- Ensembl Species. NCBI TaxonomyCellLine
- Cell Line OntologyCellType
- Cell OntologyCellMarker
- CellMarkerTissue
- UberonDisease
- Mondo, Human Disease, ICDPhenotype
- Human Phenotype, Phecodes, PATO, Mammalian Phenotype, Zebrafish PhenotypePathway
- Gene Ontology, Pathway OntologyExperimentalFactor
- Experimental Factor OntologyDevelopmentalStage
- Human Developmental Stages, Mouse Developmental StagesDrug
- Drug OntologyEthnicity
- Human Ancestry OntologyBFXPipeline
- largely based on nf-coreBioSample
- NCBI BioSample attributes
Check out sources.yaml for details.
Didn't see your favorite source or version? Bionty is extendable!
Entity versions
import bionty_base as bt
# display currently used sources
bt.display_currently_used_sources()
# display all managed sources
bt.display_available_sources()
# local yaml file specifying all managed sources
bt.LOCAL_SOURCES
# access to the Mondo ontology
disease = bt.Disease(source="mondo")
# access to the Human Disease ontology
disease = bt.Disease(source="doid", version="2023-01-30")
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
bionty_base-0.38.0.tar.gz
(62.3 kB
view details)
Built Distribution
File details
Details for the file bionty_base-0.38.0.tar.gz
.
File metadata
- Download URL: bionty_base-0.38.0.tar.gz
- Upload date:
- Size: 62.3 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | 0ee9e7489ba62e93daed304884b9a12f380db07881b29448a2de8e5bbb2d9634 |
|
MD5 | dd51491890b2186db58000fff229abe5 |
|
BLAKE2b-256 | e3b13bd057fd754d8f08593af5d474c2dee61eeaeee22bc3633ab303eca29518 |
Provenance
File details
Details for the file bionty_base-0.38.0-py3-none-any.whl
.
File metadata
- Download URL: bionty_base-0.38.0-py3-none-any.whl
- Upload date:
- Size: 40.6 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | f3c52dfa537b41223eb188695a435ffd06c7db1fcddb9e5f97e2b077a70f73fc |
|
MD5 | 0360629e6a6816f579c52669f6d21ada |
|
BLAKE2b-256 | d7d3385ef635b7b1c3166c00a5f683902529659a2fb3851e13282313b1025d0b |