Repositories list

• europe-pmc-pipeline

  Public
  Generate a XML file to send to Europe PMC

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 22, 2025Aug 22, 2025

• update-terms-in-full-annot-pipeline

  Public
  Internal QC pipeline for FULL_ANNOT table: updates term names and aspects.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 22, 2025Aug 22, 2025

• ortholog-pipeline

  Public
  Load orthologs.

  Java

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Aug 22, 2025Aug 22, 2025

• 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 Aug 22, 2025Aug 22, 2025

• uniprot-pipeline

  Public
  Imports external db ids, protein objects and sequences from UniProtKB.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 22, 2025Aug 22, 2025

• ftp-file-extracts-pipeline

  Public
  Generate weekly files for RGD FTP site

  Java

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Aug 22, 2025Aug 22, 2025

• rgd-core-library

  Public
  Domain layer and shared components

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 20, 2025Aug 20, 2025

• gene-loading-pipeline

  Public
  Loads gene models from NCBI

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• elastic-search-indexer-pipeline

  Public
  Pipeline to create elastic search indexes.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• statistics-archiver-pipeline

  Public
  Generate comprehensive statistics for objects in RGD database and store it; run weekly.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• ontology-load-pipeline

  Public
  Load all ontologies used by RGD.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• ontomate-query-builder

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• RDO-Disease-Ontology

  Public
  semantic-webhumanowl+ 5diseaseobomodel-organismsrdoontology

  0•0•1•0•Updated Aug 19, 2025Aug 19, 2025

• RS-Rat-Strain-Ontology

  Public
  Rat strain ontology maintained by RGD

  nomenclaturesemantic-webowl+ 9ontologyratoboontologiessymbolstrainobofoundry+ 2

  2•0•0•1•Updated Aug 19, 2025Aug 19, 2025

• XCO-Experimental-Condition-Ontology

  Public
  Experimental Condition Ontology maintained by RGD

  laboratorysemantic-webhuman+ 8owlontologyobomodel-organismsclinical-researchexperimental-conditionsobofoundry+ 1

  2•2•0•1•Updated Aug 19, 2025Aug 19, 2025

• MMO-Measurement-Method-Ontology

  Public
  Measurement method ontology maintained by RGD

  laboratorysemantic-webhuman+ 8owlontologymmoobomodel-organismsclinical-researchobofoundry+ 1

  2•1•0•1•Updated Aug 19, 2025Aug 19, 2025

• CMO-Clinical-Measurement-Ontology

  Public
  Clinical Measurement Ontology (CMO) maintained by RGD

  semantic-webhumanowl+ 7ontologyobomodel-organismscmoobofoundrylaboratory-measurementsclinical-measurements

  4•3•9•2•Updated Aug 19, 2025Aug 19, 2025

• solr-conf

  Public
  OntoMate solr config

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• epd-pipeline

  Public
  Load rat, human, mouse and dog promoters from EPD (Eucaryotic Promoter Database)

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• rna-seq-pipeline

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 19, 2025Aug 19, 2025

• strain-synonym-fix-pipeline

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 18, 2025Aug 18, 2025

• themes

  Public
  Wordpress themes

  PHP

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 18, 2025Aug 18, 2025

• 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 Aug 18, 2025Aug 18, 2025

• transitive-ortholog-pipeline

  Public
  Generate transitive orthologs for all species based on HUMAN orthologs.

  Java

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Aug 18, 2025Aug 18, 2025

• rgd-annotation-files

  Public
  GO annotation files in GAF, GPAD and GPI format

  GNU General Public License v3.0

  •0•0•1•0•Updated Aug 16, 2025Aug 16, 2025

• 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 Aug 15, 2025Aug 15, 2025

• RGD_RNAseq_workflows

  Public
  workflows for processing GEO RNAseq data

  Shell

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 15, 2025Aug 15, 2025

• 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 Aug 15, 2025Aug 15, 2025

• static-site-content

  Public
  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 14, 2025Aug 14, 2025

• strain-files-pipeline

  Public
  Sends an email with strain files from the past week

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 11, 2025Aug 11, 2025