VaidhyaMegha/pathways-kg

Pathways Knowledge Graph — partial build

138,725 nodes. 601,322 edges. Human biological pathways, protein interactions, Gene Ontology annotations, genes, drugs and diseases in one graph.

Built with Samyama Graph. Loader: samyama-ai/pathways-kg.

Known gaps

Measured against the engine directly, not inferred:

Consequence for the totals: the repository documents ~835K edges; this build has 601,322. Gap 1 accounts for the majority of that 234K difference. The newer source releases used here (see below) add nodes and cannot explain missing edges.

What is sound in this build

• —Node and edge totals reconcile exactly against the snapshot header: 138,725 / 601,322.
• —0 dangling edges — every src and tgt resolves to a node present in this dataset.
• —0 duplicate ids within any node file, and 0 ids reused across files.
• —INTERACTS_WITH (227,971) and ANNOTATED_WITH (232,365) match their loader-reported counts exactly, as do the GO hierarchy edges. The STRING and Gene Ontology layers appear complete.

So the protein-interaction and GO-annotation halves of the graph are usable; the Reactome pathway-membership and complex-composition halves are not.

Sources and licences

Every licence below was read at the upstream source, not taken from repository documentation.

Required attribution

CC BY 4.0 makes attribution a condition of use for four of the five sources, and it travels to anything you redistribute or build on:

Contains data from Reactome (CC BY 4.0), STRING v12.0 (CC BY 4.0), the Gene Ontology (CC BY 4.0) and UniProt (CC BY 4.0). WikiPathways content is released under CC0. None of these projects endorses this dataset or any analysis derived from it.

STRING additionally asks that you "inform users of any changes or additions that you might have made to the data" — this build applies a confidence threshold of 700 and maps ENSP identifiers to UniProt accessions.

The Gene Ontology asks that a release be cited; this build used the current release as of 2026-08-29 rather than a pinned dated release (see Source substitutions).

⚠️ UniProt rights caveat

UniProt's licence page carries a limitation that must travel with the data:

"We cannot provide unrestricted permission regarding the use of the data, as some data may be covered by patents or other rights."

CC BY 4.0 covers UniProt's own copyrightable content; it does not clear third-party patent or other rights that may attach to particular records. Satisfy yourself of this before commercial use of the UniProt-derived layer (Protein, Gene, Disease, Drug nodes).

Repository licence is separate

The pathways-kg repository code is Apache-2.0. That covers the loader and schema only. It does not govern the data in this dataset, which is bound by the five upstream licences above. license: other is used here because no single SPDX tag expresses "four CC BY 4.0 sources plus one CC0 source".

KEGG is deliberately absent. The repository's design notes record that "KEGG has restrictive licensing (no bulk download, no redistribution). We use open alternatives that collectively exceed KEGG's coverage." That was a licence decision made at design time.

Source substitutions

Two of the five pinned source URLs in the repository are dead, so newer releases were substituted. This is part of why counts differ from the documented figures:

Both substitutions increase node counts relative to the pinned versions. Neither can account for missing edges.

Contents

nodes/

Pathway = 2,883 Reactome + 986 WikiPathways.

edges/

Usage

from datasets import load_dataset
proteins = load_dataset("VaidhyaMegha/pathways-kg", "protein")

Given the gaps above, the layers worth using in this build are protein–protein interaction (STRING) and protein–GO annotation:

// Sound: STRING interaction neighbourhood
MATCH (p:Protein {name: $gene})-[:INTERACTS_WITH]-(q:Protein)
RETURN q.name LIMIT 25

// Sound: GO annotation with ontology closure
MATCH (p:Protein)-[:ANNOTATED_WITH]->(t:GOTerm)-[:IS_A*1..3]->(a:GOTerm)
WHERE a.name = $term
RETURN DISTINCT p.name

// NOT SOUND in this build — pathway membership is 2% populated
// MATCH (p:Protein)-[:PARTICIPATES_IN]->(pw:Pathway) ...

Other limitations

• —GO annotation coverage. 906,445 annotations were parsed; 232,365 loaded, with 105,433 skipped for having no matching protein. Absence of an annotation here does not mean absence upstream.
• —STRING is thresholded at confidence 700 — medium-to-high confidence only. Lower-scored interactions are excluded by design.
• —Human only (NCBI taxon 9606).
• —Point-in-time build of live sources; see the retrieval dates above.

Not clinical or diagnostic advice.

Citation

Pathways Knowledge Graph — PARTIAL BUILD (138,725 nodes, 601,322 edges).
Built with Samyama Graph. https://huggingface.co/datasets/VaidhyaMegha/pathways-kg
Loader: https://github.com/samyama-ai/pathways-kg
Sources: Reactome (CC BY 4.0); STRING v12.0 (CC BY 4.0); Gene Ontology (CC BY 4.0);
         WikiPathways (CC0); UniProt (CC BY 4.0). All retrieved 2026-08-29.
NOTE: partial build with known gaps — see the dataset card. Not a v1.0 release.