Bionty.
Project description
Bionty
Biological ontologies for data scientists: look up, search, inspect, and map terms.
To manage custom bio-registries along with public ontologies, see this LaminDB guide: {doc}docs:biology/registries.
Entities
Gene- Ensembl, NCBI Gene, HGNC, MGIProtein- UniprotSpecies- NCBI Taxonomy, Ensembl SpeciesCellLine- Cell Line OntologyCellType- Cell OntologyCellMarker- CellMarkerTissue- UberonDisease- Mondo, Human DiseasePhenotype- Human Phenotype, Mammalian Phenotype, Zebrafish PhenotypePathway- Gene Ontology, Pathway OntologyExperimentalFactor- Experimental Factor OntologyDrug- Drug OntologyBFXPipeline- largely based on nf-core
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")
Inspect & map terms
gene_bionty = bt.Gene()
# Inspect if the gene symbols are mappable onto the reference
gene_bionty.inspect(["A1BG", "FANCD1"], gene_bionty.symbol)
# Map synonyms of gene symbols
gene_bionty.map_synonyms(["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-0.26.0.tar.gz
(54.2 kB
view details)
Built Distribution
File details
Details for the file bionty-0.26.0.tar.gz.
File metadata
- Download URL: bionty-0.26.0.tar.gz
- Upload date:
- Size: 54.2 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | acb3ea047d63e4e5057c0835bf139f5ccc11151d1336bd73a46e9e1375b275bb |
|
| MD5 | d97d0045819c24d1d4e11db58657f32b |
|
| BLAKE2b-256 | 8e34e4db34dbc09c7ac5c6ea264de3b0173421d0e4979de1566396f74c0041e0 |
Provenance
File details
Details for the file bionty-0.26.0-py2.py3-none-any.whl.
File metadata
- Download URL: bionty-0.26.0-py2.py3-none-any.whl
- Upload date:
- Size: 32.8 kB
- Tags: Python 2, Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | fea18371ee4493928c9444ebc132afbb422f11a362ebed59f0c255e00f2cd785 |
|
| MD5 | 66aae3b07da78524737a270f073ca225 |
|
| BLAKE2b-256 | 7122a61365a90ab4102d1cac0a8ad5c98a22babedb00b45b3bd00f6ebedf63ee |
