pxseek 0.5.1

Query, filter, and retrieve proteomics dataset metadata from ProteomeXchange

Query, filter, and retrieve proteomics dataset metadata from ProteomeXchange.

pxseek replaces the original Selenium-based web scraper with a clean, API-driven approach using the ProteomeCentral bulk TSV and per-dataset XML endpoints. No browser or ChromeDriver required.

pxseek has three core commands.

• fetch downloads the clean summary table.
• filter narrows that table by metadata.
• lookup fetches richer XML-derived metadata for a shortlist.

Installation

Requires Python 3.12-3.14.

pip install pxseek

Or with uv:

uv tool install pxseek

For development setup and source checkout, see the Installation guide.

CLI Quickstart

The shortest useful workflow is:

uv run pxseek fetch -o px_datasets.tsv
uv run pxseek filter -i px_datasets.tsv -s "Homo sapiens" -k "cancer" -o shortlist.tsv
uv run pxseek lookup --input shortlist.tsv -o detailed.tsv

One rule matters most. filter expects the cleaned artifact written by pxseek fetch, not the raw ProteomeCentral export.

If you want machine-friendly outputs, use --format json or -o - and keep the rest of the workflow the same. The detailed format and pipeline behavior live in the docs.

Python API

pxseek is CLI-first, but it exposes a small stable workflow API for code that should not shell out to the CLI.

from pxseek import fetch_datasets, filter_datasets, lookup_datasets

summary = fetch_datasets().df
filtered, _ = filter_datasets(summary, species="Homo sapiens", keywords="cancer")
details = lookup_datasets(filtered["dataset_id"]).df

The supported root imports are fetch_datasets(), filter_datasets(), lookup_datasets(), read_artifact(), render_artifact(), and write_artifact().

Documentation

More detailed documentation and examples live in the GitHub wiki.

• Installation
• CLI Quickstart
• Python API
• Data Formats
• Search Recipes
• Troubleshooting and FAQ

Development

The local development workflow matches CI.

uv sync --extra dev
uv run --extra dev pytest
uv run --extra dev ruff check src/ tests/
uv run --extra dev ruff format --check src/ tests/
uv build

Legacy

The original single-file Selenium scraper is preserved in legacy/proteomeXchange_scraper.py for reference.

Citation

If you use pxseek in your work, please cite it:

@software{pxseek2026,
  title = {pxseek: Query, filter, and retrieve proteomics dataset metadata from ProteomeXchange},
  author = {Enes K. Ergin and Kimia Rostin and Philipp F. Lange},
  year = {2026},
  url = {https://github.com/LangeLab/pxseek},
  version = {0.5.1},
}

A CITATION.cff file is also available in the repository root.

License

MIT License. See LICENSE for details.