README.md

---
license: other
license_name: mixed-cc-by-4.0-and-cc0
license_link: https://reactome.org/license
language:
  - en
tags:
  - knowledge-graph
  - graph-database
  - cypher
  - biology
  - bioinformatics
  - pathways
  - proteomics
  - gene-ontology
pretty_name: "Pathways Knowledge Graph (PARTIAL BUILD — known gaps)"
size_categories:
  - 100K<n<1M
configs:
  - config_name: protein
    data_files: nodes/protein.csv
  - config_name: goterm
    data_files: nodes/goterm.csv
  - config_name: gene
    data_files: nodes/gene.csv
  - config_name: complex
    data_files: nodes/complex.csv
  - config_name: drug
    data_files: nodes/drug.csv
  - config_name: disease
    data_files: nodes/disease.csv
  - config_name: pathway
    data_files: nodes/pathway.csv
  - config_name: edge_annotated_with
    data_files: edges/annotated_with.csv
  - config_name: edge_interacts_with
    data_files: edges/interacts_with.csv
  - config_name: edge_is_a
    data_files: edges/is_a.csv
  - config_name: edge_targets
    data_files: edges/targets.csv
  - config_name: edge_encodes
    data_files: edges/encodes.csv
  - config_name: edge_regulates
    data_files: edges/regulates.csv
  - config_name: edge_associated_with
    data_files: edges/associated_with.csv
  - config_name: edge_part_of
    data_files: edges/part_of.csv
  - config_name: edge_participates_in
    data_files: edges/participates_in.csv
  - config_name: edge_child_of
    data_files: edges/child_of.csv
  - config_name: edge_component_of
    data_files: edges/component_of.csv
---

# 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](https://github.com/samyama-ai/samyama-graph).
Loader: [samyama-ai/pathways-kg](https://github.com/samyama-ai/pathways-kg).

## Known gaps

Measured against the engine directly, not inferred:

| # | Gap | Detail |
|---|-----|--------|
| **1** | **`PARTICIPATES_IN` is 2% of its reported size** | The Reactome loader reports `participates_in_edges=143723`. The graph holds **3,423**. **140,300 edges the loader says it created do not exist.** Confirmed by querying the engine, so this is not an export artefact. |
| **2** | **29,712 orphan nodes — 21.4% of the graph** | `Complex` **15,711 of 16,169 (97% isolated)** · `Protein` 13,015 of 46,122 (28%) · `Pathway` 986. Concentrated exactly where gap 1 removes edges. |
| **3** | **WikiPathways genes unmatched** | The WikiPathways phase loaded 986 pathways but reported **42,791 unmatched genes**. All 986 of those pathways are therefore isolated — they carry no member edges. |
| **4** | **`Reaction` and `Compound` are zero** | Both are defined in the repository schema. Neither was produced by this build. Reactome contributed pathways, proteins and complexes only. |

**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.

| Source | Version / file | Retrieved | Licence | Verified at |
|--------|----------------|-----------|---------|-------------|
| [Reactome](https://reactome.org/) | `current` — `ReactomePathways.txt`, `ReactomePathwaysRelation.txt`, `UniProt2Reactome_All_Levels.txt`, `reactome.homo_sapiens.interactions.tab-delimited.txt`, `ComplexParticipantsPubMedIdentifiers_human.txt` | 2026-08-29 | **CC BY 4.0** | [reactome.org/license](https://reactome.org/license) |
| [STRING](https://string-db.org/) | **v12.0**, organism 9606 — `9606.protein.links`, `.info`, `.aliases`; confidence threshold **700** | 2026-08-29 | **CC BY 4.0** | [string-db.org/cgi/access](https://string-db.org/cgi/access) |
| [Gene Ontology](https://geneontology.org/) | `current.geneontology.org/ontology/go.json` + `goa_human.gaf` | 2026-08-29 | **CC BY 4.0** | [GO citation policy](https://geneontology.org/docs/go-citation-policy/) |
| [WikiPathways](https://www.wikipathways.org/) | `wikipathways-20260810-gmt-Homo_sapiens.gmt` | 2026-08-29 | **CC0** | [wikipathways.org/terms.html](https://www.wikipathways.org/terms.html) |
| [UniProt](https://www.uniprot.org/) | reviewed human proteome (Swiss-Prot), TSV | 2026-08-29 | **CC BY 4.0** | [rest.uniprot.org/help/license](https://rest.uniprot.org/help/license) |

### 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](https://github.com/samyama-ai/pathways-kg) 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:

| Source | Repository pins | 404s? | Used here |
|--------|-----------------|-------|-----------|
| WikiPathways | `wikipathways-20240310-gmt-Homo_sapiens.gmt` | **yes** | `wikipathways-20260810-gmt-Homo_sapiens.gmt` |
| Gene Ontology | `release.geneontology.org/2024-06-17/ontology/go.json.gz` | **yes** | `current.geneontology.org/ontology/go.json` |

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

## Contents

### `nodes/`

| File | Rows |
|------|-----:|
| `protein.csv` | 46,122 |
| `goterm.csv` | 38,092 |
| `gene.csv` | 19,086 |
| `complex.csv` | 16,169 |
| `drug.csv` | 8,486 |
| `disease.csv` | 6,901 |
| `pathway.csv` | 3,869 |

`Pathway` = 2,883 Reactome + 986 WikiPathways.

### `edges/`

| File | Rows | Connects | Status |
|------|-----:|----------|--------|
| `annotated_with.csv` | 232,365 | Protein → GOTerm | ✅ matches loader report |
| `interacts_with.csv` | 227,971 | Protein → Protein | ✅ matches loader report |
| `is_a.csv` | 57,456 | GOTerm → GOTerm | ✅ |
| `targets.csv` | 32,793 | Drug → Protein | ✅ |
| `encodes.csv` | 19,152 | Gene → Protein | ✅ |
| `regulates.csv` | 8,190 | GOTerm → GOTerm | ✅ |
| `associated_with.csv` | 7,302 | Protein → Disease | ✅ |
| `part_of.csv` | 7,058 | GOTerm → GOTerm | ✅ |
| `participates_in.csv` | **3,423** | Protein → Pathway | ⚠️ **loader reported 143,723** |
| `child_of.csv` | 2,899 | Pathway → Pathway | ✅ |
| `component_of.csv` | 2,713 | Protein → Complex | ⚠️ leaves 97% of complexes isolated |

## Usage

```python
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:

```cypher
// 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.
```