User:ProteinBoxBot/Gene-disease links

Introduction

This bot is part of a family of bots to capture and maintain Genes, Diseases and Drugs in Wikidata. The objective of this sub-bot is to insert and maintain information about relationships between genes and diseases.

Properties

For all of these properties, the domain is a gene and the range is a disease. If you stick Gene A in front and Disease B behind the relation it should almost form a sentence. In case its not clear, \ in front of term means it has children, + means it does not yet.

\--geneDiseaseAssociation
    \--alteredExpressionAssociation
        +--decreased expression in
        +--increased expression in
    +--altered regulation leads to
    \--genetic association
        \--mutationAssociation
            +--gene deletion association with
            +--gene duplication association with
            +--gene insertion association with
            +--gene inversion association with
            +--gene substitution association with
    +--posttranslational modification association with

Examples for modeling

genetic association

According to OMIM:

endothelin receptor type B has a genetic association with ABCD syndrome

endothelin receptor type B has a genetic association with Waardenburg syndrome

More complex examples of gene-drug-disease relationships

1. deletion mutation in a human gene that causes a disease (Q19888172)
2. genetic association between a human gene and a disease from [Phenocarta](http://chibi.ubc.ca/Gemma/neurocartaStatistics.html):

Data Source: GWAS_Catalog Gene NCBI: 4477 Gene Symbol: MSMB Taxon: human Phenotype Names: prostate cancer Phenotype URIs: http://purl.obolibrary.org/obo/DOID_10283 Pubmeds: 24753544 Web Link: http://www.genome.gov/gwastudies/index.cfm?gene=MSMB Is Negative: No Note: Disease/Trait: Prostate cancer; Initial Sample Description: 1,146 European ancestry cases, 1,804 European ancestry controls; Replication Sample Description: 1,854 European ancestry cases, 1,437 European ancestry controls; Strongest SNP-Risk Allele: rs10993994-T; SNPs: rs10993994; Context: nearGene-5; Risk Allele Frequency: NR; p-Value: 3E-26; OR or beta: .40; Platform [SNPs passing QC]: Illumina [514,432] (Imputed)

Data source

• [Clinvar]
• [Phenotype]