Evidence you can carry into Python

Read the same public snapshots as the browser, preserve every input decision, and open the resulting graph in BioWeaver. No account or API key is needed.

Install the free client

Download Python client source · Python 3.10 or newer · MIT-licensed code · no runtime dependencies.

uv pip install https://bioweaver.org/graph/bioweaver-client.tar.gz

The package is distributed here as source; it is not published to PyPI. Keep a copy of the package and your saved evidence for reproducible work. Source datasets retain their own terms and attribution.

Build a graph

from bioweaver import Client, write_document

client = Client(
    "https://bioweaver.org/trail/data/",
    "https://bioweaver.org/orthology/data/",
)
graph = client.graph(["TP53", "BRCA1", "TP53"], taxon="9606")
graph = client.expand(graph, "HGNC:11998", "9606", "10090")
write_document(graph, "evidence.json")

Open evidence.json using “Open a saved graph” in Graph Explorer. The browser reads the saved records without fetching current evidence. You can also open a browser-saved graph with Python’s read_document().

Local directories work too: pass paths to your Trail and Orthology snapshot directories instead of URLs. Each directory needs its manifest and the artifacts used by your inputs and expansions. Existing hosted snapshots may change; retain local copies when a workflow must be rerun.

What the document preserves

All original inputs, including duplicate, ambiguous and unresolved identifiers.
Complete loaded disease records, their original relation and polarity, references and named donors.
Directed orthology candidates, method support and the original best-match fields.
Full source manifests and snapshot dependencies, plus graph filters and selection.

The graph shows 25 matching annotation records per page and up to 12 references and 12 donors per displayed annotation. The complete graph file preserves all loaded records; figures show a bounded view. Limits are 20 inputs, 40 loaded genes, 2,000 orthology edges, 20,000 annotations and a 25 MiB document.

Download the version 1 format specification. Node and edge identities describe records, not causal pathways. Checksums verify downloaded artifacts against their manifests; editable saved graphs are not signed proofs of source authenticity.

Client and command line

bioweaver validate evidence.json
bioweaver graph --trail ./trail-data --orthology ./orthology-data \
  --taxon 9606 --output evidence.json TP53 BRCA1

The free client reads static snapshot artifacts. Version 0.2.0 also supports an optional authenticated batch-service pilot for operator-managed installations. No public paid endpoint, billing system or monitoring service is available in this release.

Network rendering uses Cytoscape.js under its MIT license.