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PELinker

PELinker is a bio / science property–entity linker: encoder-based mention vectors, fused property clusters, and a small HTTP API for linking text to KB entities. This site hosts user-oriented notes and the Python API reference.

The current package version is defined in pyproject.toml (see the [project] version field). Release artifacts are the pelinker wheel/sdist and the documented CLIs below.

Documentation map

  • Run scripts & CLIs — pelinker-fit, pelinker-serves, pelinker-link-files, and how they connect to scripts under run/ (including OOV / anomaly analysis).
  • Vector representations — how texts_to_vrep turns text and transformer layers into pooled embeddings for sliding token windows.
  • API Reference — auto-generated from package docstrings (pelinker).
  • Repository run guide — long-form tables and preprocessing live in run/README.md on GitHub.

Development

Build the docs locally (from the repository root, with optional dependencies installed):

uv sync --extra docs
uv run mkdocs serve

Run the test suite with the same environment:

uv run pytest test