Repositories list

• RDO-Disease-Ontology

  Public
  semantic-webhumanowl+ 5diseaseobomodel-organismsrdoontology

  0•0•1•0•Updated Feb 11, 2025Feb 11, 2025

• RS-Rat-Strain-Ontology

  Public
  Rat strain ontology maintained by RGD

  nomenclaturesemantic-webowl+ 9ontologyratoboontologiessymbolstrainobofoundry+ 2

  2•0•0•1•Updated Feb 11, 2025Feb 11, 2025

• XCO-Experimental-Condition-Ontology

  Public
  Experimental Condition Ontology maintained by RGD

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

  2•2•0•1•Updated Feb 11, 2025Feb 11, 2025

• CMO-Clinical-Measurement-Ontology

  Public
  Clinical Measurement Ontology (CMO) maintained by RGD

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

  4•3•9•2•Updated Feb 11, 2025Feb 11, 2025

• rgd-core-library

  Public
  Domain layer and shared components

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 11, 2025Feb 11, 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 Feb 11, 2025Feb 11, 2025

• elastic-search-indexer-pipeline

  Public
  Pipeline to create elastic search indexes.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 11, 2025Feb 11, 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 Feb 11, 2025Feb 11, 2025

• pubmed-crawler2

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

• ctd-disease-annotation-pipeline

  Public
  Load disease annotations to genes based on CTD FTP files.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 10, 2025Feb 10, 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 Feb 8, 2025Feb 8, 2025

• variant-load-pipeline

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

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• 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 Feb 6, 2025Feb 6, 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 Feb 6, 2025Feb 6, 2025

• php-site-content

  Public
  PHP

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Feb 5, 2025Feb 5, 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 Feb 4, 2025Feb 4, 2025

• ontology-load-pipeline

  Public
  Load all ontologies used by RGD.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

• hrdp-variant-load-pipeline

  Public
  Load the HRDP Variants into variant visualizer

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

• rna-seq-pipeline

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 29, 2025Jan 29, 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 28, 2025Jan 28, 2025

• hgnc-pipeline

  Public
  Handles obsolete HGNC IDs for human genes.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 27, 2025Jan 27, 2025

• chromosome-pipeline

  Public
  Load chromosome and cytoband information.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 27, 2025Jan 27, 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 Jan 24, 2025Jan 24, 2025

• spring-ai-chat-rag

  Public
  A Spring Boot application leveraging OpenAI embeddings and PostgreSQL vector store for efficient document retrieval and question answering through RAG (Retrieval Augmented Generation). Enables document uploads, semantic search, and context-aware responses.

  Java

  •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

• static-site-content

  Public
  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• perpetuate-nomenclature-to-strain-pipeline

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• MMO-Measurement-Method-Ontology

  Public
  Measurement method ontology maintained by RGD

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

  2•1•0•1•Updated Jan 22, 2025Jan 22, 2025

• qtl-rso-annotation-pipeline

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•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

• 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