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Data processing

 

Release cycle

An update of the GenomeRNAi database is performed every 3 - 6 months. Typically, pure data releases alternate with releases that also include new features to the website. For every release the data in GenomeRNAi is mapped to the latest NCBI gene annotation to ensure currency of the data.

 

Mapping procedures

When collecting RNAi phenotype data from the literature, the diversity of gene and /or reagent identifiers used by the respective authors represents a challenge. In order to be able to display and compare data from different screening experiments, a common reference gene identifier is needed. Therefore we attempt to map the author-provided gene/reagent identifiers to the Entrez database and use the Entrez Gene ID as the GenomeRNAi reference identifier.

Update of gene information

Before every release we download the latest NCBI gene table as well as the HomoloGene mappings. UniProt entries are updated according to the “idmapping” data files provided by the UniProt ftp site.

Reagent-to-gene mapping

We map RNAi reagent sequences to the latest gene annotation using the NEXT-RNAi software tool, which additionally provides quality assessments with respect to specificity and efficiency of RNAi reagents.

Phenotype mapping

Finally, we attempt to map all author-provided gene identifiers and / or gene symbols to Entrez Gene IDs and establish the gene – phenotype relationships. Reagent – phenotype relationships are directly extracted from the author-provided data



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