Rat Genome Database

CMO-Clinical-Measurement-Ontology

Clinical Measurement Ontology (CMO) maintained by RGD

omim-annotation-pipeline

Loads OMIM ids and then creates OMIM disease annotations.

pharmgkb-pipeline

Imports PharmGKB external ids from files downloaded from PharmGKB website.

PW-Pathway-Ontology

Pathway ontology developed by the Rat Genome Database

rgd-annotation-files

GO annotation files in GAF, GPAD and GPI format

rgd-core-library

Domain layer and shared components

rgd-web-application

Code used by the RGD web site and tools

rgd-web-services

Swagger implementation

transitive-ortholog-pipeline

Generate transitive orthologs for all species based on HUMAN orthologs.

XCO-Experimental-Condition-Ontology

Experimental Condition Ontology maintained by RGD

rat-genome-database/CMO-Clinical-Measurement-Ontology

Clinical Measurement Ontology (CMO) maintained by RGD

rat-genome-database/omim-annotation-pipeline

Loads OMIM ids and then creates OMIM disease annotations.

rat-genome-database/XCO-Experimental-Condition-Ontology

Experimental Condition Ontology maintained by RGD

rat-genome-database/ftp-file-extracts-pipeline

Generate weekly files for RGD FTP site

rat-genome-database/MMO-Measurement-Method-Ontology

Measurement method ontology maintained by RGD

rat-genome-database/PW-Pathway-Ontology

Pathway ontology developed by the Rat Genome Database

rat-genome-database/rgd-web-application

Code used by the RGD web site and tools

rat-genome-database/RS-Rat-Strain-Ontology

Rat strain ontology maintained by RGD

rat-genome-database/clinvar-pipeline

Loads variants from ClinVar into RGD database. Creates disease annotations to variants and also for genes, based on orthology.

rat-genome-database/eva-pipeline

Load variants from EVA for Rat, Dog, Green Monkey, Mouse, and Pig.

rat-genome-database/gff3-pipeline

Creates gff3 files to be loaded into RGD JBrowse instance.

rat-genome-database/rgd-annotation-files

GO annotation files in GAF, GPAD and GPI format

rat-genome-database/rgd-core-library

Domain layer and shared components

rat-genome-database/alliance-submission-pipeline

Generate and submit files for rat and human to the Alliance (https://www.alliancegenome.org/)

rat-genome-database/cellosaurus-pipeline

Pipeline to import cell lines from cellosaurus at Expasy

rat-genome-database/ensembl-data-pipeline

Load rat genes from Ensembl into RGD.

rat-genome-database/expression-tpm-pipeline

load the TPM data being generated for GEO expression samples

rat-genome-database/fix-duplicate-ref-rgd_ids-pipeline

Fixes the problem of duplicate PubMed ids for references

rat-genome-database/gene-loci-pipeline

Populates GENE_LOCI table used by Variant Visualizer tool.

rat-genome-database/go-rat-annotation-pipeline

Imports GO annotation for rat from EBI

rat-genome-database/marker-load-pipeline

Load the marker data for new assembly

rat-genome-database/mouse-qtl-pipeline

Load qtls for mouse, files from MGI FTP site.

rat-genome-database/ontology-load-pipeline

Load all ontologies used by RGD.

rat-genome-database/orthology-paf-pipeline

Generate PAF files for Jbrowse2 based on orthology

rat-genome-database/phenotype-annotation-pipeline

Phenotype annotation pipeline, for mouse and human genes.

rat-genome-database/RDO-Disease-Ontology

rat-genome-database/static-site-content

rat-genome-database/synteny-load-pipeline

Pipeline to create synteny blocks for all species

rat-genome-database/synteny-paf-pipeline

Generate synteny paf files for jbrowse2

rat-genome-database/variant-load-pipeline

Load rat strain data from VCF files into RGD database and precomputes data for use by Variant Visualizer tool