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 PhenotypePathway- Gene Ontology, Pathway OntologyReadout- Experimental Factor OntologyBFXPipeline- largely based on nf-core
Check out sources.yaml for details.
Installation
Bionty is a Python package available for
pip install bionty
Look up ontology records with auto-complete
import bionty as bt
gene = bt.Gene()
gene.lookup().LNMA
Track ontology sources
# Display all managed versions
bt.display_available_sources()
# Access to the Mondo ontology
disease = bt.Disease(database="mondo")
# Access to the Human Disease ontology
disease = bt.Disease(database="doid", version="2023-01-30")
Didn't see your favorite source or version? Bionty is extendable!
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-0.19.1.tar.gz
(110.0 kB
view details)
Built Distribution
File details
Details for the file bionty-0.19.1.tar.gz.
File metadata
- Download URL: bionty-0.19.1.tar.gz
- Upload date:
- Size: 110.0 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 944556987bd7aca7c1d80a78d88573c41ed508c36a2184fc880eb5c8d504cdc1 |
|
| MD5 | 8ae8b259b36bb2cfe236358997efb736 |
|
| BLAKE2b-256 | e93eb91d48070322e47e976b37802597b2bab4c25590725be961c74249266e60 |
Provenance
File details
Details for the file bionty-0.19.1-py2.py3-none-any.whl.
File metadata
- Download URL: bionty-0.19.1-py2.py3-none-any.whl
- Upload date:
- Size: 52.7 kB
- Tags: Python 2, Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: python-requests/2.31.0
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 77f5a26fffc0138d7c82d28c0b0be3932ed0119ddf4c4860d423596f744ca444 |
|
| MD5 | 31bb73f6833e64cb7e2a20432a3fb7da |
|
| BLAKE2b-256 | eeeb2607cb2b2cca6321597af3ba2c9476580feec9b31318461ef1817a78aa79 |
