rat-genome-database Goto Github PK
Name: Rat Genome Database
Type: Organization
Name: Rat Genome Database
Type: Organization
Generate and submit files for rat and human to the Alliance (https://www.alliancegenome.org/)
Import array ids with synergizer
Pipeline to import cell lines from cellosaurus at Expasy
Load chromosome and cytoband information.
Loads variants from ClinVar into RGD database. Creates disease annotations to variants and also for genes, based on orthology.
Clinical Measurement Ontology (CMO) maintained by RGD
Chinchilla sources ontology maintained by RGD
Imports chemical annotations from CTD database.
Load disease annotations to genes based on CTD FTP files.
General purpose qc reports on data integrity.
Load DB_SNP into db.
Pipeline to create elastic search indexes.
Load rat genes from Ensembl into RGD.
Downloads genes from Ensembl and compares them against genes in RGD.
Load rat, human, mouse and dog promoters from EPD (Eucaryotic Promoter Database)
Generate a XML file to send to Europe PMC
Load variants from EVA for Rat, Dog, Green Monkey, Mouse, and Pig.
Pipeline to load experiment values from expression atlas
Fixes the problem of duplicate PubMed ids for references
Generate weekly files for RGD FTP site
Updates FULL_ANNOT_INDEX table: big auxiliary table used to speed up many annotation queries used by RGD tools.
Precomputes summaries from experiment record data into FULL_RECORD_INDEX table for subsequent use by phenominer tool.
Generate gene descriptions for rat, mouse nad human based on automated gene synopses from AGR merged with automated gene synopses from RGD.
Loads gene models from NCBI
Populates GENE_LOCI table used by Variant Visualizer tool.
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