Evaluation for spoke
Evaluator: Not specified
Evaluated on: 2025-08-23
This is a manual evaluation intended to identify potential barriers to reuse.
Access Level and Types
| Question | Answer | Comment |
|---|---|---|
| Access to data outside of the knowledge graph | Y | Neighborhood explorer; limited to 10k nodes; API https://spoke.rbvi.ucsf.edu/swagger/ |
| API or online access to the knowledge graph | Y | Neighborhood explorer; limited to 10k nodes |
| Multiple access options available | Y | |
| Source code availability | N | |
| Downloadable knowledge graph | N |
Section Score: 3/5
Provenance of Nodes and Edges
| Question | Answer | Comment |
|---|---|---|
| Source list provided | Y | In supplemental and on website |
| Source versions information | Y | Pulled each week |
| Import dependencies | N | |
| Node and edge sources | Y | Https://spoke.rbvi.ucsf.edu/docs/index.html |
| Edges deduplication | Y | Sort of; genes and protiens are considered different |
| Triples source details | Y | Some for instance specifies PPI for humans comes from STRING; human disease ontology provides disease associated gene |
| Edge type schema | Y |
Section Score: 6/7
Documented standards, schema, construction
| Question | Answer | Comment |
|---|---|---|
| Biological usable data | Y | No custom data transforms that are KG specific |
| Resolvable IDs | Y | Uses Ensembl |
| Construction documentation | Y | Edge and node types specified with source |
| Transformation documentation | Y | Data is downloaded and integrated as is |
| Schema used | Y | Uses Biolink when practical |
Section Score: 5/5
Update frequency and versioning
| Question | Answer | Comment |
|---|---|---|
| Stable versions | N | |
| Public tracker information | N | |
| Knowledge graph contact information | Y | Email provided |
| Updated annually | Y | Updated weekly according to paper |
| Prior versions access | N |
Section Score: 2/5
Evaluation - Metrics and Fitness for Purpose
| Question | Answer | Comment |
|---|---|---|
| Use case provided | N | |
| Evaluation against other models | N | |
| Defined scope | Y | Biomedical applications such as drug reuposing, disease prediction, embedding EHR data |
| Multiple evaluation methods | N | |
| Accuracy metrics | N |
Section Score: 1/5
License Information
| Question | Answer | Comment |
|---|---|---|
| License | CC BY 4.0 |