Evaluation for clinicalkg
Evaluator: Not specified
Evaluated on: 2025-08-26
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 | N | |
| API or online access to the knowledge graph | Y | Both |
| Multiple access options available | Y | Neo4j, docker, csv, python library |
| Source code availability | Y | Well documented github https://github.com/MannLabs/CKG?tab=readme-ov-file |
| Downloadable knowledge graph | Y | Many different ways |
Section Score: 4/5
Provenance of Nodes and Edges
| Question | Answer | Comment |
|---|---|---|
| Source list provided | Y | In github with links as well as supplemental table S1 |
| Source versions information | N | |
| Import dependencies | Y | In github and documents on how to download and use |
| Node and edge sources | Y | Edges have pubmed identifiers |
| Edges deduplication | Y | Built in redundancy to assess overlap and disagreememnt of sources |
| Triples source details | N | |
| Edge type schema | N |
Section Score: 4/7
Documented standards, schema, construction
| Question | Answer | Comment |
|---|---|---|
| Biological usable data | Y | Use all external identifiers; ontolgies |
| Resolvable IDs | Y | Used standardized identifiers for nodes not described with exsiting terminoloies or ontologies |
| Construction documentation | Y | Well documented in the paper and a github is well done |
| Transformation documentation | N | |
| Schema used | Y | Custom; defined in paper figure 3A |
Section Score: 4/5
Update frequency and versioning
| Question | Answer | Comment |
|---|---|---|
| Stable versions | Y | Three versions |
| Public tracker information | Y | Encouraged through github |
| Knowledge graph contact information | Y | Mann labs |
| Updated annually | Y | Newest is from 2022 |
| Prior versions access | Y |
Section Score: 5/5
Evaluation - Metrics and Fitness for Purpose
| Question | Answer | Comment |
|---|---|---|
| Use case provided | Y | Non-alcoholic fatty liver disease; cancer biomarkers; identify theraputic options for chemorefractory cases |
| Evaluation against other models | Y | Compared their ability to identify cancer biomarkers with paper from 2018 |
| Defined scope | Y | Harmonization of proteomics with other omics data |
| Multiple evaluation methods | N | |
| Accuracy metrics | N |
Section Score: 3/5
License Information
| Question | Answer | Comment |
|---|---|---|
| License | C BY-NC 4.0 |