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PubMatrixPython v0.1

Python port of the PubMatrixR R package.

For every pair of search terms (A, B), it counts how many PubMed or PMC publications mention both. Good for mapping relationships between genes, diseases, and pathways across the literature.

Based on: Becker et al. (2003) PubMatrix: a tool for multiplex literature mining. BMC Bioinformatics 4:61. https://doi.org/10.1186/1471-2105-4-61

Setup

Requires uv. Install it with:

curl -LsSf https://astral.sh/uv/install.sh | sh

Clone and install dependencies:

git clone <repo-url>
cd PubMatrixPython
uv sync --all-groups

Running the notebooks

All uv commands must be run from the project root (PubMatrixPython/), where pyproject.toml lives.

cd /path/to/PubMatrixPython
uv run jupyter lab

Then open any notebook from the notebooks/ folder in the browser.

Notebook What it covers
01_pubmatrix.ipynb Basic queries, date filtering, PMC database, file input, CSV export, heatmap visualisation
02_example_wnt.ipynb Full worked example: WNT genes × obesity genes

Quick start (script or REPL)

Interactive REPL

uv run python
from pubmatrix import pubmatrix, plot_pubmatrix_heatmap

A = ["WNT1", "WNT2", "CTNNB1"]
B = ["obesity", "diabetes", "cancer"]

result = pubmatrix(A=A, B=B)
print(result)

plot_pubmatrix_heatmap(result, title="WNT × Disease")

Running a script

Create a file my_analysis.py:

from pubmatrix import pubmatrix, plot_pubmatrix_heatmap

A = ["WNT1", "WNT2", "WNT3A", "WNT5A", "CTNNB1"]
B = ["obesity", "diabetes", "cancer", "inflammation"]

result = pubmatrix(
    A=A,
    B=B,
    database="pubmed",
    daterange=[2010, 2024],   # optional date filter
    outfile="results",
    export_format="csv",      # saves results.csv with PubMed hyperlinks
)

print(result)

plot_pubmatrix_heatmap(
    result,
    title="WNT Genes × Disease",
    filename="heatmap.png",   # saves to file instead of displaying
)

Run it with:

uv run python my_analysis.py

Loading terms from a file

Create terms.txt:

WNT1
WNT2
CTNNB1
#
obesity
diabetes
cancer

from pubmatrix import pubmatrix_from_file

result = pubmatrix_from_file("terms.txt")
print(result)
uv run python my_analysis.py

API reference

pubmatrix(A, B, ...)

Query PubMed and return a pandas.DataFrame (rows = B, cols = A).

pubmatrix(
    A,                        # list of str — column terms
    B,                        # list of str — row terms
    api_key=None,             # NCBI API key (10 req/s vs 3 req/s default)
    database="pubmed",        # "pubmed" or "pmc"
    daterange=None,           # e.g. [2015, 2024]
    outfile=None,             # base filename for export
    export_format=None,       # None | "csv" | "ods"
    n_tries=2,                # retries on network failure
)

pubmatrix_from_file(filepath, ...)

Load terms from a plain-text file and run pubmatrix().

File format:

WNT1
WNT2
#
obesity
diabetes

result = pubmatrix_from_file("terms.txt", database="pubmed")

plot_pubmatrix_heatmap(matrix, ...)

Heatmap of overlap percentages with optional hierarchical clustering.

plot_pubmatrix_heatmap(
    matrix,                                        # DataFrame from pubmatrix()
    title="PubMatrix Co-occurrence Heatmap",
    cluster_rows=True,
    cluster_cols=True,
    show_numbers=True,
    color_palette=None,                            # list of hex colours
    filename=None,                                 # save to PNG if set
    width=10, height=8,
    scale_font=True,
)

pubmatrix_heatmap(matrix, title=...)

Quick wrapper around plot_pubmatrix_heatmap() with all defaults.

NCBI API key

Without a key: 3 requests/second. With a key: 10 requests/second. Get one at https://account.ncbi.nlm.nih.gov/

result = pubmatrix(A=A, B=B, api_key="YOUR_KEY_HERE")