Bionty.
Project description
Bionty
Public biological ontologies for data scientists: look up, search, inspect, validate, and standardize terms.
To make it easy to customize and extend ontologies in a simple database backend, Bionty plugs into LaminDB: see this guide.
Entities
Gene- Ensembl, NCBI GeneProtein- UniprotOrganism- Ensembl Species. NCBI TaxonomyCellLine- Cell Line OntologyCellType- Cell OntologyCellMarker- CellMarkerTissue- UberonDisease- Mondo, Human DiseasePhenotype- 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!
Installation
Bionty is a Python package available for
pip install bionty
Usage overview & quickstart
import bionty as bt
Look up terms with auto-complete
lookup = bt.ExperimentalFactor().lookup()
# access via Python-friendly keys
lookup.single_cell_rna_sequencing
# access via dictionary
lookup_dict = lookup.dict()
lookup_dict["single-cell RNA sequencing"]
Search ontology terms
celltype_bionty = bt.CellType()
# Free text search against a field
celltype_bionty.search("gamma delta T cell")
Validate, inspect & standardize terms
gene_bionty = bt.Gene()
# Validate against a field of reference
gene_bionty.validate(["A1BG", "FANCD1"], gene_bionty.symbol)
# Run full inspection on the gene symbols
gene_bionty.inspect(["A1BG", "FANCD1"], gene_bionty.symbol)
# Convert synonyms to standardized gene symbols
gene_bionty.standardize(["A1BG", "FANCD1"])
Access a reference DataFrame
# Reference table of the human genes
df = bt.Gene(organism="human").df()
Track ontology sources
# 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")
Documentation
Read the docs.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
bionty-0.35.1.tar.gz
(63.2 kB
view details)
Built Distribution
File details
Details for the file bionty-0.35.1.tar.gz.
File metadata
- Download URL: bionty-0.35.1.tar.gz
- Upload date:
- Size: 63.2 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | e95dcd243d113315aec577c0bddef1947493191516de674ade1dbf6bfd9b35d6 |
|
| MD5 | 67851719f11e3afb3687c61fc0cd8e07 |
|
| BLAKE2b-256 | 0d2237782d5905f5410d7f532946c63b8cde5f525c19d12dcf96c09b6621e364 |
Provenance
File details
Details for the file bionty-0.35.1-py2.py3-none-any.whl.
File metadata
- Download URL: bionty-0.35.1-py2.py3-none-any.whl
- Upload date:
- Size: 39.8 kB
- Tags: Python 2, Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 5a35616aa4c23a82605e9c9404ff59bb981c34888a247e3f23220e45c16c3ff6 |
|
| MD5 | e5fd0b93766b4e462374643e686ebbeb |
|
| BLAKE2b-256 | de281865c7de59d425e665aeba5bf8701b05d299e9efdd1f944313897303e5d9 |
