Data

SynBioMine integrates data from a large number of sources into a single data warehouse. This page lists the data that are included in the current release. More data sets will be added in future releases, please contact us if there are any particular data you would like to see included.

Organisms

Unless otherwise specified, the following organisms are loaded for each data source below.

  • Bacillus amyloliquefaciens DSM 7 (taxon 692420)
  • Bacillus anthracis str. Ames (taxon 198094)
  • Bacillus anthracis str. Sterne (taxon 260799)
  • Bacillus atrophaeus 1942 (taxon 720555)
  • Bacillus atrophaeus subsp. globigii (taxon 1529886)
  • Bacillus cellulosilyticus DSM 2522 (taxon 649639)
  • Bacillus cereus ATCC 14579 (taxon 226900)
  • Bacillus clausii KSM-K16 (taxon 66692)
  • Bacillus coagulans 2-6 (taxon 941639)
  • Bacillus coagulans DSM 1 = ATCC 7050 (taxon 1121088)
  • Bacillus cytotoxicus NVH 391-98 (taxon 315749)
  • Bacillus endophyticus (taxon 135735)
  • Bacillus gobiensis (taxon 1441095)
  • Bacillus halodurans C-125 (taxon 272558)
  • Bacillus infantis NRRL B-14911 (taxon 1367477)
  • Bacillus lehensis G1 (taxon 1246626)
  • Bacillus licheniformis DSM 13 = ATCC 14580 (taxon 279010)
  • Bacillus megaterium NBRC 15308 = ATCC 14581 (taxon 1348623)
  • Bacillus methanolicus MGA3 (taxon 796606)
  • Bacillus mycoides (taxon 1405)
  • Bacillus oceanisediminis 2691 (taxon 1196031)
  • Bacillus pseudofirmus OF4 (taxon 398511)
  • Bacillus pumilus (taxon 1408)
  • Bacillus simplex (taxon 1478)
  • Bacillus smithii (taxon 1479)
  • Bacillus sp. 1NLA3E (taxon 666686)
  • Bacillus sp. FJAT-18017 (taxon 1705566)
  • Bacillus sp. FJAT-22090 (taxon 1581038)
  • Bacillus sp. OxB-1 (taxon 98228)
  • Bacillus sp. X1(2014) (taxon 1565991)
  • Bacillus subtilis subsp. subtilis str. 168 (taxon 224308)
  • Bacillus thuringiensis YBT-1518 (taxon 529122)
  • Bacillus velezensis FZB42 (taxon 326423)
  • Bacillus weihenstephanensis KBAB4 (taxon 315730)
  • Escherichia coli IAI39 (taxon 585057)
  • Escherichia coli O104:H4 str. 2011C-3493 (taxon 1133852)
  • Escherichia coli O157:H7 str. Sakai (taxon 386585)
  • Escherichia coli O83:H1 str. NRG 857C (taxon 685038)
  • Escherichia coli UMN026 (taxon 585056)
  • Escherichia coli str. K-12 substr. MG1655 (taxon 511145)
  • Geobacillus kaustophilus HTA426 (taxon 235909)
  • Geobacillus sp. C56-T3 (taxon 691437)
  • Geobacillus sp. WCH70 (taxon 471223)
  • Geobacillus sp. Y4.1MC1 (taxon 581103)
  • Geobacillus sp. Y412MC52 (taxon 550542)
  • Geobacillus sp. Y412MC61 (taxon 544556)
  • Geobacillus subterraneus (taxon 129338)
  • Geobacillus thermodenitrificans NG80-2 (taxon 420246)
  • Geobacillus thermoleovorans CCB_US3_UF5 (taxon 1111068)
  • [Bacillus thuringiensis] serovar konkukian str. 97-27 (taxon 281309)
  • [Bacillus] selenitireducens MLS10 (taxon 439292)

The following data are loaded in SynBioMine:


Type Source Organisms Version
Parts SynBIS n/a January 2017
Taxonomy NCBI Taxonomy All January 2017
Genome sequences NCBI Refseq All NCBI RefSeq Release 80 (Jan 2017)
Protein sequences and annotations UniProt All UniProt Release 2017_01 (Jan 2017)
Protein Gene Ontology annotations UniProt-GOA All UniProt-GOA Release 2017-01-18 (Jan 2017)
Protein domains InterPro All InterPro 60.0 (Nov 2016)
Gene Ontology Gene Ontology Consortium All Gene Ontology 2017-01-25 (Jan 2017)
Sequence Ontology The Sequence Ontology Project All 2.5 (June 2012)
Functional Classification EggNOG All v4.5 (Oct 2015)
Pathways Ecocyc from Keseler et al. (2013), "EcoCyc: fusing model organism databases with systems biology", Nucleic Acids Research 41: D605-12. Escherichia coli K-12 substr. MG1655 Version 20.5 (Dec 2016)
Reactions Path2Models from Buchel et al. (2013), "Path2Models: large-scale generation of computational models from biochemical pathway maps.", BMC Syst Biol. 2013 Nov 1;7:116. Escherichia coli K-12 substr. MG1655 r30 (November 2013)
Interactions BioGRID Escherichia coli K-12 substr. MG1655 Version 3.4.142 (Nov 2016)
Regulatory features (promoters, operons) DBTBS; Nicolas et al. (2012), "Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.", Science, 2012 Mar 2;335(6072):1103-6, PMID 22383849 Bacillus subtilis subsp. subtilis str. 168 DBTBS Release 5 (Sept 2007), Nicolas et al March 2012
Whole-genome expression - B. subtilis 168 GEO series data set GSE27219, Nicolas et al. (2012), "Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.", Science 2012 Mar 2;335(6072):1103-6. PMID: 22383849 Bacillus subtilis subsp. subtilis str. 168 Apr 2014
Whole-genome expression - E. coli K-12 MG1655 GEO series data set GSE6836, Faith et al (2007), "Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles", PLoS Biol 2007 Jan;5(1):e8. PMID: 17214507 (Large-Scale Mapping and Validation of E. coli Transcriptional Regulation from a Compendium of Expression Profiles) Escherichia coli str. K-12 substr. MG1655 Jan 2015
Orthologues OrthoDB, OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. EV Kriventseva, F Tegenfeldt, TJ Petty, RM Waterhouse, FA Simao, IA Pozdnyakov, P Ioannidis, and EM Zdobnov NAR, Jan 2015, PMID:23180791 Bacillus amyloliquefaciens subsp. plantarum str. FZB42, Bacillus anthracis str. Ames, Bacillus anthracis str. Sterne, Bacillus cereus ATCC 14579, Bacillus clausii KSM-K16, Bacillus cytotoxicus NVH 391-98, Bacillus halodurans C-125, Bacillus licheniformis DSM 13 = ATCC 14580, Bacillus pumilus SAFR-032, Bacillus subtilis subsp. subtilis str. 168, Bacillus thuringiensis serovar konkukian str. 97-27, Bacillus weihenstephanensis KBAB4, Escherichia coli IAI39, Escherichia coli UMN026, Escherichia coli str. K-12 substr. MG1655, Escherichia fergusonii ATCC 35469, Geobacillus kaustophilus HTA426, Geobacillus sp. WCH70, Geobacillus sp. Y412MC61, Geobacillus thermodenitrificans NG80-2 v9.1 (Oct 2016)
Publications NCBI PubMed All Jan 2017