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monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza
https://monarchinitiative.org
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IMPC ingest #67

Closed putmantime closed 1 year ago

putmantime commented 3 years ago

The International Mouse Phenotyping Consortium (IMPC) is generating a knockout mouse strain for every protein coding gene by using the embryonic stem cell resource generated by the International Knockout Mouse Consortium (IKMC). Systematic broad-based phenotyping is performed by each IMPC center using standardized procedures found within the International Mouse Phenotyping Resource of Standardised Screens (IMPReSS) resource. Gene-to-phenotype associations are made by a versioned statistical analysis.

How do we use it? We use the allele-phenotype associations recorded by the consortium. In addition, we map their allele+zygosity+background to MGI genotype identifiers. Where they do not map to MGI genotype identifiers, we create temporary identifiers for navigation purposes. Download RDF

Ingested files: ftp://ftp.ebi.ac.uk/pub/databases/impc/all-data-releases/release-12.0/results/genotype-phenotype-assertions-ALL.csv.tgz.md5 ftp://ftp.ebi.ac.uk/pub/databases/impc/all-data-releases/release-12.0/results/genotype-phenotype-assertions-ALL.csv.tgz https://archive.monarchinitiative.org/DipperCache/impc/impc_evidence_stable_key.tsv Monarch Ingest Date: 2020-12-16 License information from the (Re)usable Data Project

putmantime commented 1 year ago

Archived as part of legacy monarch graph but not core 2.0 graph. Will revisit when use cases arise.