Python API Usage

NetMedEx supports Python 3.11 and above. This page demonstrates how to use the library programmatically. The PubTatorAPI class retrieves articles from PubTator3, and PubTatorGraphBuilder constructs the co-occurrence network.

Retrieve Articles

from netmedex.pubtator import PubTatorAPI

collection = PubTatorAPI(
    query='"covid-19" AND "PON1"',
    sort="score",
    max_articles=100,
).run()

Save and Load Collections

import json

# Save to JSON
with open("collection.json", "w") as f:
    json.dump(collection.to_json(), f)

# Load from JSON
from netmedex.pubtator_data import PubTatorCollection
with open("collection.json") as f:
    loaded = PubTatorCollection.from_json(json.load(f))

# Or load from a PubTator file
from netmedex.pubtator_parser import PubTatorIO
loaded = PubTatorIO.parse("collection.pubtator")

Build and Export a Network

from netmedex.graph import PubTatorGraphBuilder, save_graph

builder = PubTatorGraphBuilder(node_type="all")
builder.add_collection(loaded)
graph = builder.build(weighting_method="freq", edge_weight_cutoff=1)

save_graph(graph, "network.html", output_filetype="html")

The notebook notebooks/netmedex_usage.ipynb contains a complete demonstration of these steps.