https://github.com/incatools/pandasaurus
Supporting simple queries over ontology annotations in dataframes, using UberGraph queries
https://github.com/incatools/pandasaurus
Last synced: 15 days ago
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Supporting simple queries over ontology annotations in dataframes, using UberGraph queries
- Host: GitHub
- URL: https://github.com/incatools/pandasaurus
- Owner: INCATools
- License: apache-2.0
- Created: 2023-03-23T13:28:54.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-11-28T12:36:51.000Z (7 months ago)
- Last Synced: 2025-11-30T18:46:42.724Z (7 months ago)
- Language: Python
- Size: 3.39 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Pandasaurus
Pandasaurus supports simple queries over ontology annotations in dataframes, powered by Ubergraph SPARQL queries. It keeps dependencies light while still offering CURIE validation, enrichment utilities, and graph exports for downstream tooling.
## Features
- Validate and update seed CURIEs, catching obsoleted terms with replacement suggestions.
- Enrich seed lists via simple, minimal, full, contextual, and ancestor-based strategies.
- Build tabular outputs (`pandas.DataFrame`) and transitive-reduced graphs (`rdflib.Graph`) for visualization.
- Batched SPARQL queries and deterministic tests with built-in mocking examples.
## Installation
```bash
pip install pandasaurus
```
or with Poetry:
```bash
poetry add pandasaurus
```
Requires Python 3.9–3.11.
## Quick Example
```python
from pandasaurus.curie_validator import CurieValidator
from pandasaurus.query import Query
seeds = ["CL:0000084", "CL:0000787", "CL:0000636"]
terms = CurieValidator.construct_term_list(seeds)
CurieValidator.get_validation_report(terms) # raises if invalid or obsoleted
query = Query(seeds, force_fail=True)
df = query.simple_enrichment()
print(df.head())
```
See the [Quick Start guide](docs/quickstart.rst) for a step-by-step workflow.
## Documentation
Full documentation (quick start, recipes, developer guide, and API reference) lives under `docs/` and is published from the `gh-pages` branch:
- [Hosted documentation](https://incatools.github.io/PandaSaurus/)
- [Quick Start (source)](docs/quickstart.rst)
- [Guides (source)](docs/guides/index.rst)
- [API reference (source)](docs/pandasaurus/index.rst)
To build docs locally:
```bash
poetry install -E docs
poetry run sphinx-build -b html docs docs/_build/html
```
## Contributing
Pull requests are welcome! See `docs/guides/contributing.rst` for details on environment setup, testing, linting, and the release workflow. Pandasaurus aims to remain a small, focused library; please open an issue before introducing large new features.
## Background
The first planned use case is to provide enrichment/query tooling for AnnData Cell x Gene matrices following the [CZ single cell curation standard](https://github.com/chanzuckerberg/single-cell-curation/blob/main/schema/3.0.0/schema.md).