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- UniprotSpecies- NCBI Taxonomy, Ensembl SpeciesCellLine- 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(species="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-0.32.0.tar.gz
(62.5 kB
view details)
Built Distribution
File details
Details for the file bionty-0.32.0.tar.gz.
File metadata
- Download URL: bionty-0.32.0.tar.gz
- Upload date:
- Size: 62.5 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | ae48125dd41ce7cf305c3ecdf0bcbdb28b11dfe9ca4f218b42fd812fd0748f3e |
|
| MD5 | bfdb1cf4dc47df0065523382646fc1da |
|
| BLAKE2b-256 | 75dcb68d0b3c9a59796797ecaf49d796f858b05f8d2e0e5a5753a490a872b6a6 |
Provenance
File details
Details for the file bionty-0.32.0-py2.py3-none-any.whl.
File metadata
- Download URL: bionty-0.32.0-py2.py3-none-any.whl
- Upload date:
- Size: 39.0 kB
- Tags: Python 2, Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | c7db581d99633688718b8d00b53b3c988a1a488d33484a2523dc10d5b3dd296e |
|
| MD5 | ba5c33b17e1eb9210ddf2b62d7fcaff6 |
|
| BLAKE2b-256 | 09f1a1de41c1a8c16c614702a3346d843afbe0f79b4f4717c0d58ed1d22908fe |
