Table 2.
A list of external data resources for the Rat Genome Database.
| Imported data type | Resource |
|---|---|
| Gene (GO) annotations | Gene Ontology Consortium (human and mouse) (The Gene Ontology Consortium 2021) and UniProt-GOA (rat) (The Gene Ontology Consortium 2019), Mouse Genome Informatics (MGI) (mouse) (BLAKE et al. 2021), and European Bioinformatics Institute (EBI) (human, 13-lined ground squirrel, chinchilla, naked mole-rat, dog, pig, African green monkey/vervet, and bonobo) (Cantelli et al. 2022) |
| Mammalian phenotype (MP) annotations | MGI (mouse) (Blake et al. 2021) and Online Mendelian Inheritance in Animals (OMIA) (dog) (Nicholas 2021) |
| Disease (DO) annotations | Online Mendelian Inheritance in Man (OMIM) (human) (Amberger and Hamosh 2017), MGI (human and mouse), OMIA (dog and pig), ClinVar (human) (Landrum et al. 2020), and Comparative Toxicogenomics Database (CTD) (human) (Davis et al. 2019) |
| Gene–chemical interaction (ChEBI) annotations | CTD (human) (Davis et al. 2019) |
| Human phenotype (HP) annotations | Human Phenotype Ontology group (Köhler et al. 2021) and ClinVar (human) (Landrum et al. 2020) |
| Pathway (PW) annotations | Small Molecule Pathway Database (SMPDB) (human) (Jewison et al. 2014) |
| RNA-Seq expression data | Gene Expression Omnibus (GEO) (rat and human) (Clough and Barrett 2016), Expression Atlas (rat, mouse, human dog, African green monkey, pig) (Moreno et al. 2022), and Genotype-Tissue Expression (GTEx) (human) (GTEx Consortium 2020) |
| Predicted protein structures | AlphaFold (all RGD species) (Jumper et al. 2021) |
| miRNA | mRNA targets—miRGate (all RGD species) (Andrés-Leó et al. 2015) |
| Variants | Genome-wide association studies (GWAS) Catalog (human) (Sollis et al. 2022), European Variation Archive (EVA) (rat, dog, African green monkey, mouse, and pig) (Cezard et al. 2022), and Dog10K genomes project (Ostrander et al. 2019) |
| Gene records, gene positions, gene model definitions (the intron/exon structures for the genes) | NCBI (Brown et al. 2015) and Ensembl (Cunningham et al. 2022) |
| Gene nomenclature | The primary sources: HGNC (human), MGI (mouse), and VGNC (other RGD species; https://vertebrate.genenames.org/) (Bruford et al. 2020); the secondary sources if primary unavailable—NCBI and Ensembl |
| Retired/archived data | From resources that are no longer freely accessible, such as the Pathway Interaction Database (Schaefer et al. 2009), Kyoto Encyclopedia of Genes and Genomes (KEGG) for pathway annotations (Kanehisa and Goto 2000), and the Genetic Association Database (GAD) (Becker et al. 2004) |