The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

scientific article (publication date: 2010)

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata is …
instance of (P31):
scholarly articleQ13442814

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P8978DBLP publication IDjournals/nar/LioliosCMTHMK10
P356DOI10.1093/NAR/GKP848
P3181OpenCitations bibliographic resource ID2048617
P932PMC publication ID2808860
P698PubMed publication ID19914934
P5875ResearchGate publication ID38090897

P50authorNektarios TavernarakisQ20986533
Philip HugenholtzQ28219811
Victor MarkowitzQ28320562
Konstantinos LioliosQ28322523
Konstantinos MavromatisQ28324373
Nikos C. KyrpidesQ30348949
P2093author name stringI-Min A Chen
P2860cites workGenomes OnLine Database (GOLD 1.0): a monitor of complete and ongoing genome projects world-wideQ33875144
EMBL Nucleotide Sequence Database in 2006.Q38442424
Habitat-Lite: a GSC case study based on free text terms for environmental metadataQ38514043
Genomes OnLine Database (GOLD): a monitor of genome projects world-wideQ38662165
Fifteen years of microbial genomics: meeting the challenges and fulfilling the dreamQ39964486
GenBankQ79484297
CAMERA: a community resource for metagenomicsQ21145892
The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomesQ21284200
DDBJ in preparation for overview of research activities behind data submissions.Q25255926
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwideQ25257048
Prepublication data sharingQ26283296
The minimum information about a genome sequence (MIGS) specificationQ28279450
Meeting Report from the Genomic Standards Consortium (GSC) Workshops 6 and 7Q28743062
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadataQ28755618
IMG ER: a system for microbial genome annotation expert review and curationQ29616791
IMG/M: a data management and analysis system for metagenomesQ31132895
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensionsQ31132964
P433issueDatabase issue
P407language of work or nameEnglishQ1860
P921main subjectdatabaseQ8513
metadataQ180160
metagenomicsQ903778
P304page(s)D346-54
P577publication date2010-01-01
P1433published inNucleic Acids ResearchQ135122
P1476titleThe Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata
P478volume38

Reverse relations

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Q22064358Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460)
Q34559022Complete genome sequence of Desulfarculus baarsii type strain (2st14).
Q24623255Complete genome sequence of Desulfobulbus propionicus type strain (1pr3)
Q35037234Complete genome sequence of Desulfurococcus mucosus type strain (O7/1).
Q34559210Complete genome sequence of Ferrimonas balearica type strain (PAT).
Q22064382Complete genome sequence of Ferroglobus placidus AEDII12DO
Q36120757Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park
Q34558901Complete genome sequence of Geodermatophilus obscurus type strain (G-20)
Q34558720Complete genome sequence of Haliangium ochraceum type strain (SMP-2)
Q22064389Complete genome sequence of Haliscomenobacter hydrossis type strain (O)
Q36011726Complete genome sequence of Halopiger xanaduensis type strain (SH-6(T)).
Q22064364Complete genome sequence of Haloterrigena turkmenica type strain (4k)
Q36011787Complete genome sequence of Hirschia baltica type strain (IFAM 1418(T))
Q22064444Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1)
Q34559049Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1).
Q34559086Complete genome sequence of Intrasporangium calvum type strain (7 KIP).
Q34769037Complete genome sequence of Isosphaera pallida type strain (IS1B).
Q34558861Complete genome sequence of Kribbella flavida type strain (IFO 14399).
Q34176797Complete genome sequence of Leadbetterella byssophila type strain (4M15).
Q35165437Complete genome sequence of Mahella australiensis type strain (50-1 BON).
Q34558818Complete genome sequence of Meiothermus ruber type strain (21)
Q22064446Complete genome sequence of Meiothermus silvanus type strain (VI-R2)
Q35607924Complete genome sequence of Mycobacterium sp. strain (Spyr1) and reclassification to Mycobacterium gilvum Spyr1.
Q34558854Complete genome sequence of Nakamurella multipartita type strain (Y-104).
Q35165424Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1).
Q35037238Complete genome sequence of Oceanithermus profundus type strain (506)
Q35037219Complete genome sequence of Odoribacter splanchnicus type strain (1651/6).
Q34163434Complete genome sequence of Olsenella uli type strain (VPI D76D-27C)
Q34176805Complete genome sequence of Paludibacter propionicigenes type strain (WB4).
Q34558825Complete genome sequence of Planctomyces limnophilus type strain (Mü 290).
Q36011710Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1(T)).
Q34213010Complete genome sequence of Rhodospirillum rubrum type strain (S1).
Q35037229Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845).
Q57119328Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845T)
Q34558868Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300).
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Q22064385Complete genome sequence of Staphylothermus hellenicus P8
Q37102594Complete genome sequence of Streptococcus agalactiae strain SA20-06, a fish pathogen associated to meningoencephalitis outbreaks.
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Q35165441Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR).
Q57119265Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)
Q24629479Complete genome sequence of Thauera aminoaromatica strain MZ1T
Q34559064Complete genome sequence of Thermaerobacter marianensis type strain (7p75a)
Q34558953Complete genome sequence of Thermobispora bispora type strain (R51).
Q24629506Complete genome sequence of Thermocrinis albus type strain (HI 11/12)
Q34559242Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P)
Q22064361Complete genome sequence of Thermosphaera aggregans type strain (M11TL)
Q36011750Complete genome sequence of Thioalkalivibrio sp. K90mix
Q35607947Complete genome sequence of Tolumonas auensis type strain (TA 4)
Q41829348Complete genome sequence of Treponema pallidum strain DAL-1.
Q35165447Complete genome sequence of Treponema succinifaciens type strain (6091).
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Q36011736Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1(T)) from a deep-sea hydrothermal vent chimney
Q36070893Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T)).
Q35165416Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL)
Q36011775Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95(T)).
Q34105286Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).
Q35607942Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113)
Q57299635Complete genome sequence of the halophile bacterium X49, isolated from salt-fermented
Q36011766Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11(T)).
Q22064387Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A)
Q36601433Complete genome sequence of the motile actinomycete Actinoplanes missouriensis 431(T) (= NBRC 102363(T))
Q36605552Complete genome sequence of the plant-associated Serratia plymuthica strain AS13.
Q36011682Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9
Q36011701Complete genome sequence of the sulfur compounds oxidizing chemolithoautotroph Sulfuricurvum kujiense type strain (YK-1(T))
Q22064375Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812(T))
Q36011794Complete genome sequence of the thermophilic sulfur-reducer Desulfurobacterium thermolithotrophum type strain (BSA(T)) from a deep-sea hydrothermal vent
Q35165407Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2))
Q34105295Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and
Q34304571Complete genome sequence of the thermophilic, piezophilic, heterotrophic bacterium Marinitoga piezophila KA3
Q28834089Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost
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Q37274727Genome (re-)annotation and open-source annotation pipelines
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Q37214047Genome Sequence of Marine Bacterium Idiomarina sp. Strain 28-8, Isolated from Korean Ark Shells
Q37185511Genome Sequence of Saccharopolyspora erythraea D, a Hyperproducer of Erythromycin
Q37214052Genome Sequence of Streptococcus parauberis Strain KCTC11980, Isolated from Diseased Paralichthys olivaceus
Q24597640Genome Sequence of Weissella cibaria KACC 11862
Q41812134Genome sequence and description of the heavy metal tolerant bacterium Lysinibacillus sphaericus strain OT4b.31.
Q41990087Genome sequence and description of the mosquitocidal and heavy metal tolerant strain Lysinibacillus sphaericus CBAM5.
Q37498784Genome sequence and overview of Oligoflexus tunisiensis Shr3T in the eighth class Oligoflexia of the phylum Proteobacteria
Q35139683Genome sequence of Acinetobacter sp. strain P8-3-8, isolated from Fistularia commersonii in Vietnam
Q42706841Genome sequence of Lactobacillus animalis KCTC 3501
Q42582853Genome sequence of Lactobacillus coryniformis subsp. coryniformis KCTC 3167.
Q38285833Genome sequence of Lactobacillus cypricasei KCTC 13900.
Q41863101Genome sequence of Lactobacillus farciminis KCTC 3681.
Q42057306Genome sequence of Lactobacillus fructivorans KCTC 3543
Q38630998Genome sequence of Lactobacillus suebicus KCTC 3549.
Q38630860Genome sequence of Lactobacillus versmoldensis KCTC 3814.
Q41430872Genome sequence of Leuconostoc argentinum KCTC 3773.
Q38725086Genome sequence of Leuconostoc carnosum KCTC 3525
Q42141371Genome sequence of Leuconostoc fallax KCTC 3537.
Q42849937Genome sequence of Leuconostoc pseudomesenteroides KCTC 3652.
Q41889919Genome sequence of Peptoniphilus rhinitidis 1-13T, an anaerobic coccus strain isolated from clinical specimens
Q37543617Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis
Q33774403Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens
Q31067959Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment
Q34177049Genome sequence of the Spinosyns-producing bacterium Saccharopolyspora spinosa NRRL 18395
Q34107846Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8(T.).
Q36011760Genome sequence of the filamentous, gliding Thiothrix nivea neotype strain (JP2(T))
Q36066551Genome sequence of the haloarchaeon Haloterrigena jeotgali type strain A29(T) isolated from salt-fermented food.
Q36601404Genome sequence of the halotolerant bacterium Corynebacterium halotolerans type strain YIM 70093(T) (= DSM 44683(T)).
Q37544193Genome sequence of the marine bacterium Corynebacterium maris type strain Coryn-1(T) (= DSM 45190(T)).
Q37102561Genome sequence of the moderately halophilic bacterium Salinicoccus carnicancri type strain Crm(T) (= DSM 23852(T)).
Q22064380Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10)
Q36070917Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314(T)).
Q36070907Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15(T))
Q35878470Genome sequence of the soil bacterium Corynebacterium callunae type strain DSM 20147(T)
Q36070902Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128(T)).
Q34108094Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11(T) (= DSM 44721(T)).
Q31114294Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools
Q42178119Genome-based studies of marine microorganisms to maximize the diversity of natural products discovery for medical treatments
Q28818088Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements
Q34107956Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project
Q33801702Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes
Q34367952Genomic repertoires of DNA-binding transcription factors across the tree of life
Q28661848Genomics of microalgae, fuel for the future?
Q60909682Global genomic similarity and core genome sequence diversity of the genus as a toolkit to identify closely related bacterial species in complex environments
Q33918160Going deeper: metagenome of a hadopelagic microbial community
Q34456566GreenPhylDB v2.0: comparative and functional genomics in plants.
Q35110559Hierarchical partitioning of metazoan protein conservation profiles provides new functional insights
Q64927575High precision protein functional site detection using 3D convolutional neural networks.
Q42034279High quality draft genome sequence of Segniliparus rugosus CDC 945(T)= (ATCC BAA-974(T)).
Q36274211High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1.
Q30983716High-quality draft genome sequences of five anaerobic oral bacteria and description of Peptoanaerobacter stomatis gen. nov., sp. nov., a new member of the family Peptostreptococcaceae
Q28253050IMG/M: the integrated metagenome data management and comparative analysis system
Q24620517IMG: the Integrated Microbial Genomes database and comparative analysis system
Q39704771Improving reverse vaccinology with a machine learning approach.
Q33766790In vitro homology search array comprehensively reveals highly conserved genes and their functional characteristics in non-sequenced species
Q36973573Integrated protein function prediction by mining function associations, sequences, and protein-protein and gene-gene interaction networks
Q90196597Loci Encoding Compounds Potentially Active against Drug-Resistant Pathogens amidst a Decreasing Pool of Novel Antibiotics
Q33650402MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
Q28743027Meeting Report from the Genomic Standards Consortium (GSC) Workshop 10
Q28743022Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9
Q28743033Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010
Q28743031Meeting report: GSC M5 roundtable at the 13th International Society for Microbial Ecology meeting in Seattle, WA, USA August 22-27, 2010
Q35606594Meeting report: the 2 annual argonne soils workshop, argonne national laboratory, chicago illinois, USA, october 6-8, 2010
Q33621959MetaBar - a tool for consistent contextual data acquisition and standards compliant submission
Q58743081MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources
Q35468435Misannotations of rRNA can now generate 90% false positive protein matches in metatranscriptomic studies.
Q33786825Mutation detection with next-generation resequencing through a mediator genome
Q34105291Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).
Q34559090Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3).
Q35037253Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139).
Q37544226Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4
Q35607962Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20).
Q30503641Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli
Q30155435Pattern of amino acid substitutions in transmembrane domains of β-barrel membrane proteins for detecting remote homologs in bacteria and mitochondria
Q24629612Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207)
Q41877586PhyleasProg: a user-oriented web server for wide evolutionary analyses.
Q38502841PlaNet: combined sequence and expression comparisons across plant networks derived from seven species
Q36670863Predicting antigenicity of proteins in a bacterial proteome; a protein microarray and naïve Bayes classification approach
Q45944894ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network.
Q24622828ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins
Q37830004Proteogenomics
Q41866689QuartetS: a fast and accurate algorithm for large-scale orthology detection
Q33533663Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0.
Q33987523Recombination and population structure in Salmonella enterica.
Q33584880SOBA: sequence ontology bioinformatics analysis
Q34192167Safeguarding bacterial resources promotes biotechnological innovation
Q34105299Solving the Problem: Genome Annotation Standards before the Data Deluge
Q28539782Standardized metadata for human pathogen/vector genomic sequences
Q35579194Standards in Genomic Sciences: New beginnings to reflect the association between the journal and BMC.
Q24608697TADB: a web-based resource for Type 2 toxin-antitoxin loci in bacteria and archaea
Q56891626The EBI Metagenomics Archive, Integration and Analysis Resource
Q24621641The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
Q34445059The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification.
Q28743400The Genomic Standards Consortium
Q28709370The Metadata Coverage Index (MCI): A standardized metric for quantifying database metadata richness
Q51731205The Nothoaspis amazoniensis Complete Mitogenome: A Comparative and Phylogenetic Analysis.
Q57730588The State of Standards in Genomic Sciences
Q34388083The complete genome sequence of Natrinema sp. J7-2, a haloarchaeon capable of growth on synthetic media without amino acid supplements
Q58577479The complete genomic sequence of a novel cold-adapted bacterium, Y42, isolated from crude oil-contaminated soil
Q35630989The genome portal of the Department of Energy Joint Genome Institute
Q21296848The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments
Q36011165The state of standards in genomic sciences
Q27027251The use of evolutionary patterns in protein annotation
Q52841700Thermodynamics of writhe in DNA minicircles from molecular dynamics simulations.
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