Evaluation for gnbr
Evaluator: Not specified
Evaluated on: 2025-08-14
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 | Can access themes which relate to the path types and their score |
| API or online access to the knowledge graph | N | |
| Multiple access options available | N | |
| Source code availability | N | But can get code to process data |
| Downloadable knowledge graph | Y | But its very weirdly done; separated into files by edge types |
Section Score: 2/5
Provenance of Nodes and Edges
| Question | Answer | Comment |
|---|---|---|
| Source list provided | Y | But NLP so not many databases used |
| Source versions information | Y | Pubtator annotations from april 30, 2016 |
| Import dependencies | Y | Detailed dependancy path extraction; |
| Node and edge sources | Y | Each edge has a lot of information; NLP was used and the sentance that constructed something is listed |
| Edges deduplication | Y | Counted as a co occurance; feature not a bug used to inform network |
| Triples source details | Y | Very limited |
| Edge type schema | Y | NLP; had four interaction types and three node types |
Section Score: 7/7
Documented standards, schema, construction
| Question | Answer | Comment |
|---|---|---|
| Biological usable data | Y | All information coming from publications outside of KG |
| Resolvable IDs | Y | Uses UMLS IDs for rare diseases |
| Construction documentation | Y | Specifies where disease and drug nodes come from |
| Transformation documentation | Y | Eliminated paths containing dependencies of type conj |
| Schema used | Y | Self documented and reported with downloads |
Section Score: 5/5
Update frequency and versioning
| Question | Answer | Comment |
|---|---|---|
| Stable versions | Y | 7 versions available |
| Public tracker information | N | |
| Knowledge graph contact information | N | |
| Updated annually | Y | But not updated since 2019 |
| Prior versions access | Y | And indicated which version was used in the paper |
Section Score: 3/5
Evaluation - Metrics and Fitness for Purpose
| Question | Answer | Comment |
|---|---|---|
| Use case provided | Y | Drug disease indications ; 2 case studies |
| Evaluation against other models | Y | Compared to gold standard drug indications; relationships from other databases for those gotten using NLP methods |
| Defined scope | Y | Drug repurposing |
| Multiple evaluation methods | Y | Case studies; drug-disease path analysis; validation using DGIdb; used lit review to verify novel drug |
| Accuracy metrics | Y | Performance on gold standard drug indications calculate AUROC; dendrograms of the themes |
Section Score: 5/5
License Information
| Question | Answer | Comment |
|---|---|---|
| License | CC BY 4.0 |