Share bioinformatics database

[Miachol]

Configuration file: db_main.toml
Description: miRDB is an online database for miRNA target prediction and functional annotations.

[db_mirdb]
source_url = "http://mirdb.org/download/miRDB_v{{version}}_prediction_result.txt.gz"
version_avaliable = ["5.0", "4.0", "3.0", "2.0", "1.0"]

[Miachol]

Configuration file: db_main.toml
Description: As a database, miRTarBase has accumulated more than three hundred and sixty thousand miRNA-target interactions (MTIs), which are collected by manually surveying pertinent literature after NLP of the text systematically to filter research articles related to functional studies of miRNAs.

[db_mirtarbase]
source_url = "http://mirtarbase.mbc.nctu.edu.tw/cache/download/{{version}}/miRTarBase_MTI.xlsx"
version_avaliable = ["7.0"]

[Miachol]

Configuration file: db_main.toml
Description: miRNEST is an integrative collection of animal, plant and virus microRNA data.

[db_mirnest]
source_url = "http://rhesus.amu.edu.pl/mirnest/copy/downloads/{{version}}.gz"
version_avaliable = ["mirnest_EST_predictions", "mirnest_targets", "mirnest_deep_predictions", 
                                  "mirnest_degradomes", "mirnest_mirtrons", "mirnest_mirna_gene_structure"]

[Miachol]

Configuration file: db_main.toml
Description: RBPDB, the database of RNA-binding protein specificities

[db_rbpdb]
source_url = "http://rbpdb.ccbr.utoronto.ca/downloads/{{version}}"
version_avaliable = ["RBPDB_v1.3.1_2012-11-21.sql", "RBPDB_v1.3.1_2012-11-21_TDT.zip", 
                                  "RBPDB_v1.3.1_2012-11-21_CSV.zip"]

[Miachol]

Configuration file: db_main.toml
Description: APPRIS, annotating principal splice isoforms

[db_appris]
source_url = "http://apprisws.bioinfo.cnio.es/pub/current_release/datafiles/homo_sapiens/{{version}}/appris_data.principal.txt"
version_avaliable = ["GRCh38", "rs108v26", "up201703v26", "a1v26", "GRCh37", "rs105v24", "g12v24"]

[Miachol]

Configuration file: db_main.toml
Description: LNCipedia is a public database for long non-coding RNA (lncRNA) sequence and annotation. The current release contains 127,802 transcripts and 56,946 genes.

[db_lncipedia]
source_url = "https://lncipedia.org/downloads/lncipedia_{{version}}"
version_avaliable = ["5_1_hg19.bed", "5_1_hg38.bed", "5_1_hc_hg19.bed", "5_1_hc_hg38.bed", 
                                  "5_1.fasta", "5_1_hc.fasta", "5_1_hg19.gff", "5_1_hg38.gff", "5_1_hc_hg19.gff", 
                                  "5_1_hc_hg38.gff", "5_1_hg19.gtf", "5_1_hg38.gtf", "5_1_hc_hg19.gtf", 
                                  "5_1_hc_hg38.gtf"]

[Miachol]

Configuration file: db_main.toml
Description: MSigDB (Molecular Signatures Database), The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software.

[db_msigdb]
source_url = "http://bioinfo.rjh.com.cn/download/bioinstaller/msigdb/{{version}}"
version_avaliable = ["c1.all.v6.2.entrez.gmt", "c1.all.v6.2.symbols.gmt", "c2.all.v6.2.entrez.gmt", "c2.all.v6.2.symbols.gmt", "c2.cgp.v6.2.entrez.gmt", "c2.cgp.v6.2.symbols.gmt", "c2.cp.biocarta.v6.2.entrez.gmt", "c2.cp.biocarta.v6.2.symbols.gmt", "c2.cp.kegg.v6.2.entrez.gmt", "c2.cp.kegg.v6.2.symbols.gmt", "c2.cp.reactome.v6.2.entrez.gmt", "c2.cp.reactome.v6.2.symbols.gmt", "c2.cp.v6.2.entrez.gmt", "c2.cp.v6.2.symbols.gmt", "c3.all.v6.2.entrez.gmt", "c3.all.v6.2.symbols.gmt", "c3.mir.v6.2.entrez.gmt", "c3.mir.v6.2.symbols.gmt", "c3.tft.v6.2.entrez.gmt", "c3.tft.v6.2.symbols.gmt", "c4.all.v6.2.entrez.gmt", "c4.all.v6.2.symbols.gmt", "c4.cgn.v6.2.entrez.gmt", "c4.cgn.v6.2.symbols.gmt", "c4.cm.v6.2.entrez.gmt", "c4.cm.v6.2.symbols.gmt", "c5.all.v6.2.entrez.gmt", "c5.all.v6.2.symbols.gmt", "c5.bp.v6.2.entrez.gmt", "c5.bp.v6.2.symbols.gmt", "c5.cc.v6.2.entrez.gmt", "c5.cc.v6.2.symbols.gmt", "c5.mf.v6.2.entrez.gmt", "c5.mf.v6.2.symbols.gmt", "c6.all.v6.2.entrez.gmt", "c6.all.v6.2.symbols.gmt", "c7.all.v6.2.entrez.gmt", "c7.all.v6.2.symbols.gmt", "msigdb.v6.2.entrez.gmt", "msigdb.v6.2.symbols.gmt", "msigdb_v3.0.zip", "msigdb_v3.1.zip", "msigdb_v4.0.zip", "msigdb_v5.0.zip", "msigdb_v5.1.zip", "msigdb_v5.1_chip.zip", "msigdb_v5.2.zip", "msigdb_v5.2_chip.zip", "msigdb_v6.0.zip", "msigdb_v6.0_chip.zip", "msigdb_v6.1.zip", "msigdb_v6.1_chip.zip", "msigdb_v6.2.xml", "msigdb_v6.2.zip"]

[Miachol]

Configuration file: db_main.toml
Description: miRCancer provides comprehensive collection of microRNA (miRNA) expression profiles in various human cancers which are automatically extracted from published literatures in PubMed. It utilizes text mining techniques for information collection. Manual revision is applied after auto-extraction to provide 100% precision.

[db_mircancer]
source_url = "http://mircancer.ecu.edu/downloads/{{version}}.txt"
version_avaliable = ["miRCancerOctober2017", "miRCancerMarch2017", "miRCancerDecember2016", "miRCancerSeptember2016", "miRCancerJune2016", "miRCancerMarch2016", "miRCancerDecember2015", "miRCancerSeptember2015", "miRCancerJune2015", "miRCancerMarch2015", "miRCancerDecember2014", "miRCancerSeptember2014", "miRCancerJune2014", "miRCancerMarch2014", "miRCancerDecember2013", "miRCancerSeptember2013", "miRCancerJune2013", "miRCancerMarch2013", "miRCancerNovember2012"]

[Miachol]

Configuration file: db_main.toml
Description: DCDB (Drug Combination Database), Accumulating scientific and clinical evidences have suggested the use of drug combinations as a safe and effective approach, to treat complicated and refractory diseases. The Drug Combination Database (DCDB) is devoted to the research and development of multi-component drugs. The current version of DCDB collected 1363 drug combinations (330 approved and 1033 investigational, including 237 unsuccessful usages), involving 904 individual drugs, 805 targets.

[db_dcdb]
source_url = "http://www.cls.zju.edu.cn/dcdb/downloadfile/{{version}}.zip"
version_avaliable = ["DCDB2_plaintxt", "DCDB2.sql", "targets", "Drug_combinations", 
                                  "components_identifier"]

[Miachol]

Configuration file: db_main.toml
Description: OncomiRDB, aiming at annotating the experimentally verified oncogenic and tumor-suppressive miRNAs from literature.

[db_oncomirdb]
source_url = "http://lifeome.net/database/oncomirdb/oncomirdb.v-{{version}}_download.txt"
version_avaliable = "1.1-20131217"

[Miachol]

Configuration file: db_main.toml
Description: IslandViewer, This web site was developed so that researchers could easily view and download genomic islands for all published sequenced bacterial and archaeal genomes that have been predicted using the the currently most accurate GI prediction methods.

[db_islandviewer]
source_url = "http://www.pathogenomics.sfu.ca/islandviewer/download/datasets/all_gis_{{version}}.txt.tar.gz"
version_avaliable = ["islandviewer_iv4", "islandpick_iv4", "islandpath_dimob_iv4", 
                                  "sigi_hmm_iv4", "islander_iv4"]

[Miachol]

Configuration file: db_main.toml
Description: hPDI (Human Protein-DNA Interactome), The hPDI database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The current release of hPDI contains 17,718 protein-DNA interactions for 1013 human DNA-binding proteins. These DNA-binding proteins include 493 human transcription factors (TFs) and 520 unconventional DNA binding proteins (uDBPs).

[db_hpdi]
source_url = "http://bioinfo.wilmer.jhu.edu/PDI/{{version}}"
version_avaliable = ["protein_chip_full_seq.csv", "protein_annotation.txt", 
                                  "pro2motif.txt", "DNA_motifs.txt", "motif2protein.txt", 
                                  "all_pwm.zip", "all_gpr_files.zip", "supplemental.pdf"]

[Miachol]

Configuration file: db_main.toml
Description: dbSNO, Protein S-nitrosylation (SNO) is a reversible post-translational modification (PTM) and involves the covalent attachment of nitric oxide (NO) to the thiol group of cysteine (Cys) residues. Given the increasing number of proteins reported to be regulated by this modification, S-nitrosylation is considered to act, in a manner analogous to phosphorylation, as a pleiotropic regulator that elicits dual effects to regulate diverse pathophysiological processes by altering protein function, stability, and conformation change in various cancers and human disorders.

[db_dbsno]
source_url = "http://140.138.144.145/~dbSNO/download/dbSNO{{version}}_all_data.txt.gz"
version_available = "v2"

[Miachol]

Configuration file: db_main.toml
Description: PhosphoNetworks, a combined bioinformatics and protein microarray-based strategy to construct a high-resolution map of the human phosphorylation networks.

[db_phosphonetworks]
soource_url = "http://www.phosphonetworks.org/download/{{version}}"
version_available = ["rawKSI.csv", "refKSI.csv", "comKSI.csv", "motifSite.csv", 
                                  "motifMatrix.csv",  "motifLogo.tar", "highResolutionNetwork.csv", 
                                  "supplemental.pdf"]

[Miachol]

Configuration file: db_main.toml
Description: ConsensusPathDB, ConsensusPathDB-human integrates interaction networks in Homo sapiens including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways.

[db_consensuspathdb]
source_url = "http://cpdb.molgen.mpg.de/download/ConsensusPathDB_{{version}}.gz"
version_available = ["human_PPI", "human_PPI.psi25"]