Evaluation for sldb
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 | Available through KGHub web portal at kghub.io/sldb/ for browsing synthetic lethal interaction data |
| API or online access to the knowledge graph | N | No direct programmatic API interface; access primarily through KGHub web interface only |
| Multiple access options available | N | Web portal represents the single access method; no downloadable formats or alternative access mechanisms documented |
| Source code availability | Y | Complete source code available at github.com/monarch-initiative/SLDBGen under Monarch Initiative organization |
| Downloadable knowledge graph | N | No bulk download option available; users must query through web interface or reconstruct from source repositories |
Section Score: 2/5
Provenance of Nodes and Edges
| Question | Answer | Comment |
|---|---|---|
| Source list provided | N | Source data and dependency information not documented in publicly available README or documentation files |
| Source versions information | N | No version tracking for upstream synthetic lethal databases; unclear how frequently data sources are updated |
| Import dependencies | N | ETL pipeline and data dependencies not explicitly declared in source repository |
| Node and edge sources | N | No documentation mapping synthetic lethal pairs to their primary research sources or evidence base |
| Edges deduplication | N | No documentation of deduplication strategies for redundant interactions across sources |
| Triples source details | N | No RDF triples or semantic specifications documented for interaction relationships |
| Edge type schema | N | Schema and relationship types for synthetic lethal interactions not formally documented |
Section Score: 0/7
Documented standards, schema, construction
| Question | Answer | Comment |
|---|---|---|
| Biological usable data | Y | Synthetic lethal gene pairs provide direct biological utility for drug target discovery and cancer therapeutics research |
| Resolvable IDs | Y | Nodes appear to use standard gene identifiers resolvable through Monarch Initiative and external databases |
| Construction documentation | N | No formal documentation of KG construction methodology, data preprocessing steps, or quality control procedures |
| Transformation documentation | N | ETL and data transformation steps not documented; unclear how raw data was processed into graph format |
| Schema used | N | No explicit schema documentation (RDF, Property Graph, or other formats); ontologies used are not specified |
Section Score: 2/5
Update frequency and versioning
| Question | Answer | Comment |
|---|---|---|
| Stable versions | Y | GitHub releases available at github.com/monarch-initiative/SLDBGen providing tagged stable versions |
| Public tracker information | Y | GitHub issues tracker available for bug reports and feature requests; active Monarch Initiative project |
| Knowledge graph contact information | Y | Maintainer contact available through GitHub (pnrobinson); Monarch Initiative maintains stewardship |
| Updated annually | Y | GitHub repository shows recent commits and active maintenance; part of continuously updated KGHub ecosystem |
| Prior versions access | Y | Full version history available through GitHub releases and commit history for reproducibility |
Section Score: 5/5
Evaluation - Metrics and Fitness for Purpose
| Question | Answer | Comment |
|---|---|---|
| Use case provided | Y | Clear use cases: supports drug target discovery for cancer therapeutics by identifying essential gene pairs |
| Evaluation against other models | N | No comparative benchmarking against other synthetic lethal databases or interaction prediction models documented |
| Defined scope | Y | Focused scope on synthetic lethal gene-gene interactions relevant to cell survival and drug sensitivity |
| Multiple evaluation methods | N | No systematic evaluation methodology or validation protocol published; lacks experimental validation metrics |
| Accuracy metrics | N | No reported precision, recall, or F1 scores; no quantitative accuracy assessment available |
Section Score: 2/5
License Information
| Question | Answer | Comment |
|---|---|---|
| License |