Bionty: Data model generator for biology.
Project description
Bionty: Basic biological entities
Access public & custom ontologies with auto-complete. Map synonyms with ease.
To manage in-house bioregistries along with ontologies, see lnschema_bionty.
Out-of-the-box ontologies
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 OntologyReadout- 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
Look up ontology records with auto-complete
import bionty as bt
lookup = bt.Readout().lookup()
# dot access of Pythonic keys
lookup.single_cell_rna_sequencing
# bracket access of free text dictionary keys
lookup_dict = lookup.dict()
lookup_dict["single-cell RNA sequencing"]
Search ontology terms
import bionty as bt
celltype_bionty = bt.CellType()
# Free text search against a field
celltype_bionty.search("gamma delta T cell")
Inspect & standardize identifiers
import bionty as bt
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"])
Reference tables of ontologies
import bionty as bt
# 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-0.23.1.tar.gz
(52.6 kB
view details)
Built Distribution
File details
Details for the file bionty-0.23.1.tar.gz.
File metadata
- Download URL: bionty-0.23.1.tar.gz
- Upload date:
- Size: 52.6 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 7fb029ce5d2b9268e4a28f1a97652b95f0fe2dfaa90bd4491b6bf09fc3c13916 |
|
| MD5 | c5efbb86766db6fb20a458174053940f |
|
| BLAKE2b-256 | f3b8d41f58b805be4b797f2ac34db0df7ffadc44e385c6135c5197fb7e297211 |
Provenance
File details
Details for the file bionty-0.23.1-py2.py3-none-any.whl.
File metadata
- Download URL: bionty-0.23.1-py2.py3-none-any.whl
- Upload date:
- Size: 31.7 kB
- Tags: Python 2, Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 21190bfb0d2b4ea49cd67e0a95413da4ac9ea88aa3c8943f53bbe9e89ce3fa5c |
|
| MD5 | 5dca7315266e3f64779fe9f09b0d3c30 |
|
| BLAKE2b-256 | d727bc8a4d73173a9482a17ea6e10d9b97e9f70a50afeed8dfafd354d0dd1849 |
