Repositories list

• hgnc-pipeline

  Public
  Handles obsolete HGNC IDs for human genes.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 20, 2025Jan 20, 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 Jan 18, 2025Jan 18, 2025

• elastic-search-indexer-pipeline

  Public
  Pipeline to create elastic search indexes.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• 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 Jan 17, 2025Jan 17, 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 Jan 16, 2025Jan 16, 2025

• qtl-rso-annotation-pipeline

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• RDO-Disease-Ontology

  Public
  semantic-webhumanowl+ 5diseaseobomodel-organismsrdoontology

  0•0•1•0•Updated Jan 14, 2025Jan 14, 2025

• RS-Rat-Strain-Ontology

  Public
  Rat strain ontology maintained by RGD

  nomenclaturesemantic-webowl+ 9ontologyratoboontologiessymbolstrainobofoundry+ 2

  2•0•0•1•Updated Jan 14, 2025Jan 14, 2025

• XCO-Experimental-Condition-Ontology

  Public
  Experimental Condition Ontology maintained by RGD

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

  2•2•0•1•Updated Jan 14, 2025Jan 14, 2025

• MMO-Measurement-Method-Ontology

  Public
  Measurement method ontology maintained by RGD

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

  2•1•0•1•Updated Jan 14, 2025Jan 14, 2025

• CMO-Clinical-Measurement-Ontology

  Public
  Clinical Measurement Ontology (CMO) maintained by RGD

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

  4•3•9•2•Updated Jan 14, 2025Jan 14, 2025

• human-proteome-map-pipeline

  Public
  Load Human Proteome Map ids for human genes

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• pubmed-crawler2

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• ensembl-data-pipeline

  Public
  Load rat genes from Ensembl into RGD.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• rgd-core-library

  Public
  Domain layer and shared components

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• 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 Jan 13, 2025Jan 13, 2025

• gtex-pipeline

  Public
  Java

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jan 13, 2025Jan 13, 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 Jan 13, 2025Jan 13, 2025

• PW-Pathway-Ontology

  Public
  Pathway ontology developed by the Rat Genome Database

  networksemantic-webowl+ 6ontologyoboontologiespwpathwayobofoundry

  2•1•0•0•Updated Jan 13, 2025Jan 13, 2025

• rna-seq-pipeline

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• omia-pipeline

  Public
  Create annotations from OMIA

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• object-mapper-pipeline

  Public
  Calculates/Updates assembly map positions for strains, qtls and markers.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• ontology-load-pipeline

  Public
  Load all ontologies used by RGD.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• php-site-content

  Public
  PHP

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• marker-load-pipeline

  Public
  Load the marker data for new assembly

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

• static-site-content

  Public
  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 9, 2025Jan 9, 2025

• chromosome-pipeline

  Public
  Load chromosome and cytoband information.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 8, 2025Jan 8, 2025

• rgd-web-application

  Public
  Code used by the RGD web site and tools

  JavaScript

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jan 8, 2025Jan 8, 2025

• phenominer-load-pipeline

  Public
  Load data into phenominer tool.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 7, 2025Jan 7, 2025

• notification-pipeline

  Public
  Send notification email to watchers

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 7, 2025Jan 7, 2025