Repositories list

• rgd-web-application

  Public
  Code used by the RGD web site and tools

  JavaScript

  •

  GNU General Public License v3.0

  •0•2•0•2•Updated Mar 4, 2026Mar 4, 2026

• RDO-Disease-Ontology

  Public
  semantic-webhumanowl+ 5

  semantic-webhumanowlontologydiseaseobomodel-organismsrdo

  0•0•1•0•Updated Mar 3, 2026Mar 3, 2026

• RS-Rat-Strain-Ontology

  Public
  Rat strain ontology maintained by RGD

  nomenclaturesemantic-webowl+ 9

  nomenclaturesemantic-webowlontologyratoboontologiessymbolstrainobofoundry+ 2

  2•0•0•1•Updated Mar 3, 2026Mar 3, 2026

• XCO-Experimental-Condition-Ontology

  Public
  Experimental Condition Ontology maintained by RGD

  laboratorysemantic-webhuman+ 8

  laboratorysemantic-webhumanowlontologyobomodel-organismsclinical-researchexperimental-conditionsobofoundry+ 1

  2•2•0•1•Updated Mar 3, 2026Mar 3, 2026

• MMO-Measurement-Method-Ontology

  Public
  Measurement method ontology maintained by RGD

  laboratorysemantic-webhuman+ 8

  laboratorysemantic-webhumanowlontologymmoobomodel-organismsclinical-researchobofoundry+ 1

  2•1•0•1•Updated Mar 3, 2026Mar 3, 2026

• CMO-Clinical-Measurement-Ontology

  Public
  Clinical Measurement Ontology (CMO) maintained by RGD

  semantic-webhumanowl+ 7

  semantic-webhumanowlontologyobomodel-organismscmoobofoundrylaboratory-measurementsclinical-measurements

  4•3•9•2•Updated Mar 3, 2026Mar 3, 2026

• alliance-submission-pipeline

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

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

• hrdp-variant-load-pipeline

  Public
  Load the HRDP Variants into variant visualizer

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

• rgd-core-library

  Public
  Domain layer and shared components

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

• elastic-search-indexer-pipeline

  Public
  Pipeline to create elastic search indexes.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

• pharmgkb-pipeline

  Public
  Imports PharmGKB external ids from files downloaded from PharmGKB website.

  Java

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Mar 3, 2026Mar 3, 2026

• update-objects-in-full-annot-pipeline

  Public
  Update names and symbols of genes/strains/qtls/variants in FULL_ANNOT, to keep them in sync with tables GENES, STRAINS, QTLS, VARIANTS

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 3, 2026Mar 3, 2026

• ontology-load-pipeline

  Public
  Load all ontologies used by RGD.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

• mouse-qtl-pipeline

  Public
  Load qtls for mouse, files from MGI FTP site.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

• hgnc-pipeline

  Public
  Handles obsolete HGNC IDs for human genes.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

• mouse-disease-annotation-pipeline

  Public
  Import disease annotations from MGI.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 2, 2026Mar 2, 2026

• rgd-annotation-files

  Public
  GO annotation files in GAF, GPAD and GPI format

  GNU General Public License v3.0

  •0•0•1•0•Updated Feb 28, 2026Feb 28, 2026

• gff3-pipeline

  Public
  Creates gff3 files to be loaded into RGD JBrowse instance.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 27, 2026Feb 27, 2026

• expression-tpm-pipeline

  Public
  load the TPM data being generated for GEO expression samples

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 26, 2026Feb 26, 2026

• goc-annotation-pipeline

  Public
  Generate GO annotation files in GAF format

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 24, 2026Feb 24, 2026

• text-mining-tools

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 23, 2026Feb 23, 2026

• omia-pipeline

  Public
  Create annotations from OMIA

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

• ncbi-gene-pipeline

  Public
  Load nucleotide and protein sequences for genes, all species, from NCBI.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

• eva-pipeline

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

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

• phenominer-annotation-index-pipeline

  Public
  Populate table populate table PHENOMINER_RECORD_IDS.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 19, 2026Feb 19, 2026

• php-site-content

  Public
  PHP

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 18, 2026Feb 18, 2026

• phenogen-pipeline

  Public
  Load external database ids to PhenoGen database at UC Denver.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 16, 2026Feb 16, 2026

• PW-Pathway-Ontology

  Public
  Pathway ontology developed by the Rat Genome Database

  networksemantic-webowl+ 6

  networksemantic-webowlontologyoboontologiespwpathwayobofoundry

  2•1•1•0•Updated Feb 16, 2026Feb 16, 2026

• transitive-annotation-pipeline

  Public
  Create transitive (ISO) annotations for all public species in RGD based on manual gene annotations.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 16, 2026Feb 16, 2026

• mutant-strain-annotation-pipeline

  Public
  Propagate disease and phenotype annotations from strains to alleles and genes.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 16, 2026Feb 16, 2026