Repositories list

• rna-central-pipeline

  Public
  Import RNACentral IDs as 'external database ids' for all non-coding genes in RGD to generate links to RNACentral database.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

• RDO-Disease-Ontology

  Public
  semantic-webhumanowl+ 5diseaseobomodel-organismsrdoontology

  0•0•1•0•Updated Nov 26, 2024Nov 26, 2024

• RS-Rat-Strain-Ontology

  Public
  Rat strain ontology maintained by RGD

  nomenclaturesemantic-webowl+ 9ontologyratoboontologiessymbolstrainobofoundry+ 2

  2•0•0•1•Updated Nov 26, 2024Nov 26, 2024

• XCO-Experimental-Condition-Ontology

  Public
  Experimental Condition Ontology maintained by RGD

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

  2•2•0•1•Updated Nov 26, 2024Nov 26, 2024

• MMO-Measurement-Method-Ontology

  Public
  Measurement method ontology maintained by RGD

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

  2•1•0•1•Updated Nov 26, 2024Nov 26, 2024

• CMO-Clinical-Measurement-Ontology

  Public
  Clinical Measurement Ontology (CMO) maintained by RGD

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

  4•3•9•2•Updated Nov 26, 2024Nov 26, 2024

• fix-duplicate-ref-rgd_ids-pipeline

  Public
  Fixes the problem of duplicate PubMed ids for references

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

• text-mining-tools

  Public
  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

• 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 Nov 26, 2024Nov 26, 2024

• 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 Nov 26, 2024Nov 26, 2024

• rgd-core-library

  Public
  Domain layer and shared components

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

• misc-tools

  Public
  Miscellaneous tools, often one-off.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 25, 2024Nov 25, 2024

• rgd-annotation-files

  Public
  GO annotation files in GAF, GPAD and GPI format

  GNU General Public License v3.0

  •0•0•1•0•Updated Nov 23, 2024Nov 23, 2024

• ftp-file-extracts-pipeline

  Public
  Generate weekly files for RGD FTP site

  Java

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Nov 23, 2024Nov 23, 2024

• 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 Nov 22, 2024Nov 22, 2024

• expression-tpm-pipeline

  Public
  load the TPM data being generated for GEO expression samples

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 21, 2024Nov 21, 2024

• phenotype-annotation-pipeline

  Public
  Phenotype annotation pipeline, for mouse and human genes.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• clinvar-pipeline

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

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• cellosaurus-pipeline

  Public
  Pipeline to import cell lines from cellosaurus at Expasy

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• 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 Nov 18, 2024Nov 18, 2024

• gene-loci-pipeline

  Public
  Populates GENE_LOCI table used by Variant Visualizer tool.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• ontology-load-pipeline

  Public
  Load all ontologies used by RGD.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

• static-site-content

  Public
  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 14, 2024Nov 14, 2024

• 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 Nov 13, 2024Nov 13, 2024

• PW-Pathway-Ontology

  Public
  Pathway ontology developed by the Rat Genome Database

  networksemantic-webowl+ 6ontologyoboontologiespwpathwayobofoundry

  2•1•0•0•Updated Nov 12, 2024Nov 12, 2024

• ensembl-data-pipeline

  Public
  Load rat genes from Ensembl into RGD.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• go-rat-annotation-pipeline

  Public
  Imports GO annotation for rat from EBI

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• 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 Nov 12, 2024Nov 12, 2024

• marker-load-pipeline

  Public
  Load the marker data for new assembly

  GNU General Public License v3.0

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• omim-annotation-pipeline

  Public
  Loads OMIM ids and then creates OMIM disease annotations.

  Java

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Nov 11, 2024Nov 11, 2024