11- Database sources
Bioplanet
https://tripod.nih.gov/bioplanet/download/pathway.csv
Comparative Toxicogenomics Database
http://ctdbase.org/reports/CTD_chem_gene_ixns.csv.gz
Disgenet
https://www.disgenet.org/static/disgenet_ap1/files/downloads/curated_gene_disease_associations.tsv.gz
DoRothEA
https://github.com/saezlab/dorothea/raw/master/data/dorothea_hs.rda
https://github.com/saezlab/dorothea/raw/master/data/dorothea_mm.rda
https://github.com/saezlab/dorothea/tree/master/data (mus_musculus, homo_sapiens)
EBI
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz
EPIC
https://webdata.illumina.com/downloads/productfiles/methylationEPIC/infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip
Ensembl
ftp://ftp.ensembl.org/pub/current_gtf (canis_lupus_familiaris, bos_taurus, caenorhabditis_elegans, danio_rerio, drosophila_melanogaster, gallus_gallus, homo_sapiens, mus_musculus, rattus_norvegicus, sus_scrofa)
EnsemblGenomes
ftp://ftp.ensemblgenomes.org/pub/bacteria/current/species_EnsemblBacteria.txt
ftp://ftp.ensemblgenomes.org/pub/bacteria/current/gtf (escherichia_coli_str_k_12_substr_mg1655_gca_000005845)
ftp://ftp.ensemblgenomes.org/pub/fungi/current/gtf (aspergillus_nidulans, saccharomyces_cerevisiae, candida_albicans_sc5314_gca_000784635)
ftp://ftp.ensemblgenomes.org/pub/plants/current/gtf (arabidopsis_thaliana, oryza_sativa)
Gene Ontology
http://purl.obolibrary.org/obo/go.obo
http://geneontology.org/data/sars-cov-2_targets.gaf
http://current.geneontology.org/annotations/ (all organisms)
Human Phenotype Ontology
https://ci.monarchinitiative.org/view/hpo/job/hpo.annotations/lastSuccessfulBuild/artifact/rare-diseases/util/annotation/genes_to_phenotype.txt
Human microRNA Disease Database
http://www.cuilab.cn/static/hmdd3/data/alldata.xlsx
Infinium MethylationEPIC
http://webdata.illumina.com.s3-website-us-east-1.amazonaws.com/downloads/productfiles/methylationEPIC/infinium-methylationepic-v-1-0-b5-manifest-file-csv.zip
KEGG
https://www.kegg.jp/kegg/rest/keggapi.html
LINCS
https://clue.io/touchstone
Mammalian ncRNA-Disease Repository
https://www.rna-society.org/mndr/download/miRNA-disease%20information.zip
Mouse Genome Informatics
http://www.informatics.jax.org/downloads/reports/HOM_AllOrganism.rpt
http://www.informatics.jax.org/downloads/reports/VOC_MammalianPhenotype.rpt
http://www.informatics.jax.org/downloads/reports/MRK_ENSEMBL.rpt
http://www.informatics.jax.org/downloads/reports/MGI_PhenoGenoMP.rpt
NCBI
https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz
ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz
ftp://ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen
ftp://ftp.ncbi.nlm.nih.gov/pub/medgen/NAMES.RRF.gz
ftp://ftp.ncbi.nih.gov/gene/DATA/gene_refseq_uniprotkb_collab.gz
ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2ensembl.gz
https://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip
Panther
ftp://ftp.pantherdb.org/pathway/current_release
PharmGKB
https://s3.pgkb.org/data/drugs.zip
https://api.pharmgkb.org/v1/download/file/data/genes.zip
https://api.pharmgkb.org/v1/download/file/data/relationships.zip
Reactome
https://reactome.org/download/current/NCBI2Reactome_All_Levels.txt
TAM2
http://www.lirmed.com/tam2/Public/static/data/mirset_v9.txt
WikiPathways
http://data.wikipathways.org/current/gmt/ (Arabidopsis_thaliana, Bos_taurus, Caenorhabditis_elegans, Canis_familiaris, Danio_rerio, Drosophila_melanogaster, Gallus_gallus, Homo_sapiens, Mus_musculus, Oryza_sativa, Rattus_norvegicus, Saccharomyces_cerevisiae, Sus_scrofa)
miRBase
https://www.mirbase.org/ftp/CURRENT/miRNA.xls.zip
miRTarBase
https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2019/cache/download/8.0/miRTarBase_SE_WR.xls