Evaluation for chea-kg
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 | ChEA-KG Explorer web interface at maayanlab.cloud/chea-kg/ enables interactive exploration of TF-gene regulatory relationships with visualization |
| API or online access to the knowledge graph | Y | RESTful API available at maayanlab.cloud/chea-kg/api/ for programmatic access to transcription factor binding data |
| Multiple access options available | Y | Provides web portal, REST API, and Neo4j database access; accommodates both exploratory and computational workflows |
| Source code availability | Y | Complete source code available at github.com/MaayanLab/chea-kg under Ma'ayan Lab organization for transparency and reproducibility |
| Downloadable knowledge graph | Y | Neo4j database and processed ChIP-seq datasets available for download enabling local deployment and analysis |
Section Score: 5/5
Provenance of Nodes and Edges
| Question | Answer | Comment |
|---|---|---|
| Source list provided | N | ChEA-KG builds on ChEA3 ChIP-seq database but upstream sources and versions not explicitly listed in documentation |
| Source versions information | N | No version tracking for underlying ChIP-seq datasets or source database snapshots documented |
| Import dependencies | N | Data import pipeline and ontology dependencies not formally documented in available resources |
| Node and edge sources | N | While ChEA3 paper cited, specific source attribution for individual TF-gene relationships not provided |
| Edges deduplication | N | No documentation of deduplication strategies for redundant TF-target associations across ChIP-seq studies |
| Triples source details | N | RDF/semantic specifications for edge relationships not documented; Neo4j schema not formally published |
| Edge type schema | N | Relationship types (e.g., 'targets', 'binds_to') not formally specified with ontology mappings |
Section Score: 0/7
Documented standards, schema, construction
| Question | Answer | Comment |
|---|---|---|
| Biological usable data | Y | ChIP-seq derived TF-gene relationships provide actionable insights for gene regulation and transcriptional control research |
| Resolvable IDs | Y | Uses standard HGNC gene symbols and documented TF identifiers resolvable through external databases |
| Construction documentation | N | ETL process and quality control steps not documented; only high-level description of ChEA3 integration available |
| Transformation documentation | N | No documentation of ChIP-seq data preprocessing, filtering thresholds, or binding site calling parameters used |
| Schema used | N | Neo4j property graph schema not formally documented; no RDF/OWL schema available for semantic integration |
Section Score: 2/5
Update frequency and versioning
| Question | Answer | Comment |
|---|---|---|
| Stable versions | Y | GitHub releases available at github.com/MaayanLab/chea-kg providing tagged stable versions for reproducibility |
| Public tracker information | Y | GitHub issues tracker active; Ma'ayan Lab maintains responsive maintenance of systems biology tools |
| Knowledge graph contact information | Y | Contact available through Ma'ayan Lab (avi.maayan@mssm.edu) and GitHub organization; active development team |
| Updated annually | Y | Part of continuously maintained Ma'ayan Lab ecosystem; repository shows recent commits and updates |
| Prior versions access | Y | Full Git history available; prior versions accessible through GitHub releases and commits for reproducibility |
Section Score: 5/5
Evaluation - Metrics and Fitness for Purpose
| Question | Answer | Comment |
|---|---|---|
| Use case provided | Y | Clear use case: identify transcription factor targets for functional enrichment and regulatory network analysis |
| Evaluation against other models | N | No comparison with other TF-target databases (ENCODE, ReMap, or similar); no benchmarking studies published |
| Defined scope | Y | Well-defined scope: ChIP-seq derived transcription factor binding to gene regulatory elements |
| Multiple evaluation methods | N | No validation against independent experimental data (e.g., CRISPR screening, reporter assays) |
| Accuracy metrics | N | No sensitivity, specificity, or positive predictive value reported; no quantitative validation metrics available |
Section Score: 2/5
License Information
| Question | Answer | Comment |
|---|---|---|
| License |