GeneticsKP Reference Ingest Guide¶
Source Information¶
InfoRes ID: infores:geneticskp
Description: GeneticsKP provides gene-disease associations derived from GWAS data using MAGMA analysis. It integrates genetic evidence from genome-wide association studies to identify genes associated with various diseases and traits.
Data Access Locations: - Data is provided as a checked-in tar.gz file in the translator-ingests repository
Data Provision Mechanisms: file_download
Data Formats: kgx
Data Versioning and Releases: Static version based on MAGMA analysis
Ingest Information¶
Ingest Categories: translator_knowledge_creator
Utility: GeneticsKP provides gene-disease associations based on GWAS data analyzed with MAGMA, offering genetic evidence for disease associations that can be integrated with other knowledge sources in Translator.
Scope: Gene-disease associations derived from GWAS data using MAGMA statistical analysis.
Relevant Files¶
| File Name | Location | Description |
|---|---|---|
| genetics_magma.tar.gz | translator-ingests repository | KGX files containing nodes and edges from MAGMA analysis |
Included Content¶
| File Name | Included Records | Fields Used |
|---|---|---|
| edges_geneticsKP_magma.jsonl | Gene-disease associations from MAGMA analysis | Gene identifiers, disease identifiers, association scores, p-values |
| nodes_geneticsKP_magma.jsonl | Gene and disease nodes referenced in the edges | Node identifiers, labels, categories |
Target Information¶
Target InfoRes ID: infores:translator-geneticskp-kgx
Edge Types¶
| Subject Categories | Predicate | Object Categories | Knowledge Level | Agent Type | UI Explanation |
|---|---|---|---|---|---|
| biolink:Gene | biolink:Disease, biolink:PhenotypicFeature | statistical_association | computational_model | The 'genetically_associated_with' predicate indicates that genetic variation in this gene is statistically associated with the disease or phenotype based on MAGMA analysis of GWAS data. |
Node Types¶
| Node Category | Source Identifier Types | Additional Notes |
|---|---|---|
| biolink:Gene | NCBI Gene ID, HGNC ID | |
| biolink:Disease | MONDO ID, EFO ID | |
| biolink:PhenotypicFeature | HP ID, EFO ID |
Provenance Information¶
Contributors: - GeneticsKP team - MAGMA analysis and KGX generation - Translator team - ingest implementation