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-0.25.1.tar.gz
(53.0 kB
view details)
Built Distribution
File details
Details for the file bionty-0.25.1.tar.gz.
File metadata
- Download URL: bionty-0.25.1.tar.gz
- Upload date:
- Size: 53.0 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 365a8ad6d11e65af944a977d85284fe32a6397e30e68a1951d9f1206c0aed795 |
|
| MD5 | 9e0dcb0bd7fc71e8b89a300223fb2ede |
|
| BLAKE2b-256 | 265d3a43da76e960a2ae4c8ea3c5f6d0e2ed13969388a0f95ed7b8533247243b |
Provenance
File details
Details for the file bionty-0.25.1-py2.py3-none-any.whl.
File metadata
- Download URL: bionty-0.25.1-py2.py3-none-any.whl
- Upload date:
- Size: 32.1 kB
- Tags: Python 2, Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | be76b1807f7080c73674ced437f493e3e2fd17be6168d16800dd39c8e0dc4c88 |
|
| MD5 | 406c341f329ac0c9444048ad7ef0f2c9 |
|
| BLAKE2b-256 | 6d33784dc7ed1cc736db1d38aea9d569f3b12d65c10eda8fd1f52a78132a4485 |
