Evaluation for molecular-data-kp
Evaluator: Automated Evaluation
Evaluated on: 2026-01-06
⚠️ Automated Evaluation: This evaluation was generated automatically using an AI-based system. It is distinct from manual evaluations curated by human experts. Please review findings carefully and report any inaccuracies.
Evaluation Criteria: This evaluation uses the KG-Registry evaluation rubric as described in Cortes et al. (2025) . The rubric assesses knowledge graphs across multiple dimensions including access, provenance, documentation, maintenance, and fitness for purpose.
Access Level and Types
| Question | Answer | Comment |
|---|---|---|
| Access to data outside of the knowledge graph | Y | Broad Institute web interface and KGX files available at molepro.s3.amazonaws.com |
| API or online access to the knowledge graph | N | Part of Translator network but direct KG API not documented for public use |
| Multiple access options available | Y | KGX nodes/edges TSV downloads and source code access available |
| Source code availability | Y | Complete source at github.com/broadinstitute/molecular-data-provider |
| Downloadable knowledge graph | N | KGX files available but no comprehensive RDF/graph database dumps |
Section Score: 3/5
Provenance of Nodes and Edges
| Question | Answer | Comment |
|---|---|---|
| Source list provided | Y | Integrates data from multiple molecular databases and biomedical sources |
| Source versions information | N | No version tracking for upstream molecular data sources |
| Import dependencies | Y | Source code shows integration pipeline and data dependencies |
| Node and edge sources | Y | Molecular entities and relationships sourced from documented databases |
| Edges deduplication | N | No documentation of deduplication strategy |
| Triples source details | N | Schema not formally documented |
| Edge type schema | N | Relationship types not formally mapped to ontologies |
Section Score: 3/7
Documented standards, schema, construction
| Question | Answer | Comment |
|---|---|---|
| Biological usable data | Y | Molecular data translates from chemical scale to systems biology applications |
| Resolvable IDs | Y | Uses standard chemical and gene identifiers resolvable through external databases |
| Construction documentation | N | ETL methodology not formally documented beyond source code |
| Transformation documentation | N | Data integration steps not transparent in published documentation |
| Schema used | N | Schema documentation not published; KGX format used but ontology mapping unclear |
Section Score: 2/5
Update frequency and versioning
| Question | Answer | Comment |
|---|---|---|
| Stable versions | Y | GitHub releases available with tagged versions |
| Public tracker information | Y | GitHub issues tracker active; Broad Institute maintains project |
| Knowledge graph contact information | Y | Sandrine Muller (ORCID 0000-0001-5998-3003) available for contact |
| Updated annually | Y | Part of Translator network with continuous updates |
| Prior versions access | Y | Full GitHub history and releases available |
Section Score: 5/5
Evaluation - Metrics and Fitness for Purpose
| Question | Answer | Comment |
|---|---|---|
| Use case provided | Y | Translator use case: molecular to systems-level knowledge integration |
| Evaluation against other models | N | No benchmarking against other molecular data providers documented |
| Defined scope | Y | Focused on molecular-scale biomedical data translation |
| Multiple evaluation methods | N | No systematic validation framework published |
| Accuracy metrics | N | No accuracy, precision, or recall metrics reported |
Section Score: 2/5
License Information
| Question | Answer | Comment |
|---|---|---|
| License |