Abstract:
:This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://mibbi.org/.
journal_name
Stand Genomic Scijournal_title
Standards in genomic sciencesauthors
Kettner C,Field D,Sansone SA,Taylor C,Aerts J,Binns N,Blake A,Britten CM,de Marco A,Fostel J,Gaudet P,González-Beltrán A,Hardy N,Hellemans J,Hermjakob H,Juty N,Leebens-Mack J,Maguire E,Neumann S,Orchard S,Parkinsodoi
10.4056/sigs.147362subject
Has Abstractpub_date
2010-12-25 00:00:00pages
259-66issue
3issn
1944-3277journal_volume
3pub_type
杂志文章abstract::Cronobacter sakazakii is a Gram-negative opportunistic pathogen that causes life- threatening infantile infections, such as meningitis, septicemia, and necrotizing enterocolitis, as well as pneumonia, septicemia, and urinary tract and wound infections in adults. Here, we report 26 draft genome sequences of C. sakazaki...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-018-0339-6
更新日期:2018-11-29 00:00:00
abstract::Lutibacter profundi LP1T within the family Flavobacteriaceae was isolated from a biofilm growing on the surface of a black smoker chimney at the Loki's Castle vent field, located on the Arctic Mid-Ocean Ridge. The complete genome of L. profundi LP1T is the first genome to be published within the genus Lutibacter. L. p...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-016-0219-x
更新日期:2017-01-07 00:00:00
abstract::Streptobacillus moniliformis Levaditi et al. 1925 is the type and sole species of the genus Streptobacillus, and is of phylogenetic interest because of its isolated location in the sparsely populated and neither taxonomically nor genomically much accessed family 'Leptotrichiaceae' within the phylum Fusobacteria. The '...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.48727
更新日期:2009-12-30 00:00:00
abstract::Syntrophobacter fumaroxidans strain MPOB(T) is the best-studied species of the genus Syntrophobacter. The species is of interest because of its anaerobic syntrophic lifestyle, its involvement in the conversion of propionate to acetate, H2 and CO2 during the overall degradation of organic matter, and its release of pro...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.2996379
更新日期:2012-10-10 00:00:00
abstract::Methanoplanus petrolearius Ollivier et al. 1998 is the type strain of the genus Methanoplanus. The strain was originally isolated from an offshore oil field from the Gulf of Guinea. Members of the genus Methanoplanus are of interest because they play an important role in the carbon cycle and also because of their sign...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.1183143
更新日期:2010-10-27 00:00:00
abstract::Escherichia coli is the most abundant facultative anaerobic bacteria in the gastro-intestinal tract of mammals but can be responsible for intestinal infection due to acquisition of virulence factors. Genomes of pathogenic E. coli strains are widely described whereas those of bovine commensal E. coli strains are very s...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0272-0
更新日期:2017-10-10 00:00:00
abstract::Brachyspira murdochii Stanton et al. 1992 is a non-pathogenic, host-associated spirochete of the family Brachyspiraceae. Initially isolated from the intestinal content of a healthy swine, the 'group B spirochaetes' were first described as Serpulina murdochii. Members of the family Brachyspiraceae are of great phylogen...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.831993
更新日期:2010-06-15 00:00:00
abstract::Strain 3.5.1 was isolated from soils of the Republic of Tatarstan, Russia, on the basis of presence of a high phytate-degrading activity. Strains with such activities attract special interest because of its potential use as feed additives and natural manures. Strain 3.5.1 harbors a 99 % 16S rRNA nucleotide sequence si...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-015-0093-y
更新日期:2015-11-11 00:00:00
abstract::The tenacious association between strains of the heterotrophic alphaproteobacterial genus Acidiphilium and chemolithotrophic iron oxidizing bacteria has long been known. In this context the genome of the heterotroph Acidiphilium sp. JA12-A1, an isolate from an iron oxidizing mixed culture derived from a pilot plant fo...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/s40793-015-0040-y
更新日期:2015-08-19 00:00:00
abstract::Agromyces aureus AR33T is a Gram-positive, rod-shaped and motile bacterium belonging to the Microbacteriaceae family in the phylum Actinobacteria that was isolated from a former zinc/lead mining and processing site in Austria. In this study, the whole genome was sequenced and assembled combining sequences obtained fro...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-016-0217-z
更新日期:2017-01-05 00:00:00
abstract::Methylibium sp. strain T29 was isolated from a gasoline-contaminated aquifer and proved to have excellent capabilities in degrading some common fuel oxygenates like methyl tert-butyl ether, tert-amyl methyl ether and tert-butyl alcohol along with other organic compounds. Here, we report the draft genome sequence of M....
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/s40793-015-0023-z
更新日期:2015-07-19 00:00:00
abstract::The family Hyphomonadaceae within the Alphaproteobacteria is largely comprised of bacteria isolated from marine environments with striking morphologies and an unusual mode of cell growth. Here, we report the complete genome sequence Hirschia baltica, which is only the second a member of the Hyphomonadaceae with a publ...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.2205004
更新日期:2011-12-31 00:00:00
abstract::Alistipes obesi sp. nov. strain ph8(T) is the type strain of A. obesi, a new species within the genus Alistipes. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. A. obesi is an obligately anaerobic rod. Here we describe the features of...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.3336746
更新日期:2013-02-25 00:00:00
abstract::Litoreibacter arenae Kim et al. 2012 is a member of the genomically well-characterized Rhodobacteraceae clade within the Roseobacter clade. Representatives of this clade are known to be metabolically versatile and involved in marine carbon-producing and biogeochemical processes. They form a physiologically heterogeneo...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.4258318
更新日期:2013-10-01 00:00:00
abstract::Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range of annual Medicago (medic) species. Strain WSM419 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially ...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.43526
更新日期:2010-01-28 00:00:00
abstract::Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile bacterium that was isolated from the Geysir geothermal area, Iceland. Like other thermophiles, Thermus species are often used as model organisms to understand the mechanism of action of extremozymes, especially focusing on their...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0225-7
更新日期:2017-02-03 00:00:00
abstract::Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.1784330
更新日期:2011-04-29 00:00:00
abstract::Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a hyperthermophilic, anaerobic chemolithoautotroph, but it can also use a variety of...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.2225018
更新日期:2011-10-15 00:00:00
abstract::Candidatus Arsenophonus lipopteni (Enterobacteriaceae, Gammaproteobacteria) is an obligate intracellular symbiont of the blood feeding deer ked, Lipoptena cervi (Diptera: Hippoboscidae). The bacteria reside in specialized cells derived from host gut epithelia (bacteriocytes) forming a compact symbiotic organ (bacterio...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-016-0195-1
更新日期:2016-09-17 00:00:00
abstract::Microvirga lupini LUT6(T) is an aerobic, non-motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Lupinus texensis. LUT6(T) was isolated in 2006 from a nodule recovered from the roots of the annual L. texensis growing in Travis Co., Texas. LUT6(T) forms a hig...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.5249382
更新日期:2014-03-01 00:00:00
abstract::Staphylococcus cohnii subsp. cohnii belongs to the family Staphylococcaceae in the order Bacillales, class Bacilli and phylum Firmicutes. The increasing relevance of S. cohnii to human health prompted us to determine the genomic sequence of Staphylococcus cohnii subsp. cohnii strain hu-01, a multidrug-resistant isolat...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.5429581
更新日期:2014-03-15 00:00:00
abstract::At present, Joostella marina Quan et al. 2008 is the sole species with a validly published name in the genus Joostella, family Flavobacteriacae, phylum Bacteriodetes. It is a yellow-pigmented, aerobic, marine organism about which little has been reported other than the chemotaxonomic features required for initial taxo...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.3537045
更新日期:2013-04-15 00:00:00
abstract::Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus Hydrogenobacter. H. thermophilus was the first obligate autotrophic organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6(T) is of interest because of the unusually efficient hydrogen-oxidizing ability of this strain,...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.1463589
更新日期:2011-04-29 00:00:00
abstract::We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists of a circular chromosome of 2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755 p...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/s40793-015-0098-6
更新日期:2015-11-20 00:00:00
abstract::Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1(T) is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest because it represents a subspecies with cosmopolitan and ubiquitous distribution in standing freshwater systems...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.4056/sigs.2395367
更新日期:2012-03-19 00:00:00
abstract::Thiobacillus thioparus DSM 505T is one of first two isolated strains of inorganic sulfur-oxidising Bacteria. The original strain of T. thioparus was lost almost 100 years ago and the working type strain is Culture CT (=DSM 505T = ATCC 8158T) isolated by Starkey in 1934 from agricultural soil at Rutgers University, New...
journal_title:Standards in genomic sciences
pub_type:
doi:10.1186/s40793-017-0229-3
更新日期:2017-01-19 00:00:00
abstract::Enterobacter mori strain 5-4 is a Gram-negative, motile, rod shaped, and facultatively anaerobic bacterium, which was isolated from a mixture of formation water (also known as oil-reservior water) and crude-oil in Karamay oilfield, China. To date, there is only one E. mori genome has been sequenced and very little kno...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/1944-3277-10-9
更新日期:2015-02-27 00:00:00
abstract::Flavihumibacter solisilvae 3-3(T) (= KACC 17917(T) = JCM 19891(T)) represents a type strain of the genus Flavihumibacter within the family Chitinophagaceae. This strain can use various sole carbon sources, making it applicable in industry and bioremediation. In this study, the draft genomic information of F. solisilva...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/s40793-015-0037-6
更新日期:2015-09-19 00:00:00
abstract::Brachymonas chironomi strain AIMA4(T) (Halpern et al., 2009) is a Gram-negative, non-motile, aerobic, chemoorganotroph bacterium. B. chironomi is a member of the Comamonadaceae, a family within the class Betaproteobacteria. This species was isolated from a chironomid (Diptera; Chironomidae) egg mass, sampled from a wa...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/s40793-015-0010-4
更新日期:2015-05-27 00:00:00
abstract::Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and p...
journal_title:Standards in genomic sciences
pub_type: 杂志文章
doi:10.1186/1944-3277-10-17
更新日期:2015-03-19 00:00:00