GeneticsKP Reference Ingest Guide¶
Source Information¶
InfoRes ID: infores:geneticskp
Description: GeneticsKP is a Translator Knowledge Provider that surfaces gene-disease and gene-phenotype associations derived from genome-wide association study (GWAS) data. Associations are computed using MAGMA (Multi-marker Analysis of GenoMic Annotation), a gene-level statistical method that aggregates variant-level GWAS summary statistics into gene-based association scores. GeneticsKP packages these MAGMA-derived associations as a KGX knowledge graph, providing statistically grounded genetic evidence linking genes to diseases and phenotypic traits that can be combined with other knowledge sources in Translator. This ingest is a passthrough of the pre-computed GeneticsKP KGX graph, validating and re-serializing its nodes and edges to Biolink Model form.
Data Access Locations: - Data is provided as a pre-computed KGX tar.gz file (genetics_magma.tar.gz) sourced from GeneticsKP
Data Provision Mechanisms: file_download
Data Formats: kgx
Data Versioning and Releases: Static, pre-computed release based on a single MAGMA analysis; not versioned on a fixed schedule.
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¶
Edge Types¶
| Subject Categories | Predicate | Object Categories | Knowledge Level | Agent Type | UI Explanation |
|---|---|---|---|---|---|
| biolink:Gene | biolink:Disease, biolink:PhenotypicFeature | statistical_association | computational_model | This edge asserts that genetic variation in the subject gene is statistically associated with the object disease or phenotypic feature. The association is derived from MAGMA (Multi-marker Analysis of GenoMic Annotation), which aggregates variant-level GWAS summary statistics into a gene-level association score. Because the knowledge is produced by a statistical model rather than manual curation, these edges carry a knowledge level of 'statistical_association' and an agent type of 'computational_model'. This ingest passes the pre-computed GeneticsKP KGX edges through with minimal transformation, attributing infores:geneticskp as the primary knowledge source. |
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