| --- |
| 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. |
| ``` |
|
|
