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Международная инфраструктура для коллекций культур Василенко А.Н., Озерская С.М Всероссийская коллекция микроорганизмов ИБФМ РАН

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Presentation on theme: "Международная инфраструктура для коллекций культур Василенко А.Н., Озерская С.М Всероссийская коллекция микроорганизмов ИБФМ РАН"— Presentation transcript:

1 Международная инфраструктура для коллекций культур Василенко А.Н., Озерская С.М Всероссийская коллекция микроорганизмов ИБФМ РАН

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6 Ступарь Олег Сергеевич к.б.н. ВКМ ИБФМ РАН Московская обл Пущино, Проспект Науки 5

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26 Типовое описание поля RDS 1. Field's name 2. Short description of the content (one sentence) 3. Specification of the content 3.1. Detailed description of the content, difference from the other fields that may look similar 3.2. List of subfields and their descriptions 3.3. Specification of the coding for the field and subfields 3.4. The list of possible values (if short) or a reference to file with long list, or reference to thesaurus, or reference to ontology 3.5. Reference to a manual, which describes this field content 3.6. Reference to external standard used for this field 3.7. Samples of correct coding for this field.

27 The examination shows four factors that cuts the scope of the fields in possible request system and make the values inconsistent: (1) collections have some difference in selection of the fields, (2) Also some differences in understanding of the same fields are apparent, (3) different content while the understanding presumably is the same, (4) different typing for the same content is used. Factors (1) and (2) are specified by the standard, factors (3) and (4) aren't regulated, they are more difficult to classify, but we can give some examples.

28 Difference in typing (factor 4). Example: errors in a name EEE 1 EEE BKM 2 EER 3 ERE 4 ERR 5 REE 6 RER 7 RRE RRR 8 RRR

29 Factor 3: Differences in content. Example: One strain of Aspergillus brasiliensis Varga et al in four catalogues: Cultures: ATCC 9642 CBS DSM VKM F-1119

30 Results of comparison Organism type Name (Infrasubspecific names) Other names (Misapplied names) Previous names ATCC Subcollection: Fungi Aspergillus brasiliensis Varga et al. CBSF Aspergillus brasiliensis Varga, Frisvad & Samson Aspergillus brasiliensis; Aspergillus niger DSMZF Aspergillus brasiliensis Varga, Kocsube et al. VKMF Aspergillus brasiliensis Varga et al Aspergillus niger van Tieghem 1867

31 Results of comparison Accession number Other collection numbers ATCC9642 Australian Mycol. Panel series 26, CBS , DSM 63263, IFO 6342, IMI 91855, NRRL 3536, NRRL A- 5243, QM 386 CBS ATCC 9642;ATHUM 2856;CECT 2700;DSM 63263;IFO 6342;IHEM 3797;IMI ;IMI ;IMI ii;IMI iii;LCP ;MUCL 19001;NBRC ;NRRL 3536;NRRL A-5243;OECD 14;QM 386;VKM F1119 DSMZ63263 ATCC 9642, CBS , IFO 6342, IMI , NBRC 6342, NRRL 3536 VKMF-1119 ATCC 9642; CBS ; CCRC 31512; DSM 63263; FERM S-2; IFO 6342; IMI 91855; NRRL A-5243; NRRL A-3536; QM 386

32 Results of comparison History of depositDeposited as Strain Designation Depositors ATCC Aspergillus niger van Tieghem, anamorph SN 26WH Weston CBSQM, Jul 1965 DSMZ <- IMG, 4518 <- W. Kerner. [QM 386] Aspergillus niger VKM <-- INMI, VKM F <- ATCC, ATCC 9642 Aspergillus niger

33 Results of comparison Isolated fromIsolated by Geographic origin Additional geographic data ATCC wireless radio equipment New South Wales, Australia CBS radio equipment R.E. Klausmeier, Indiana, Crane Australia, New South Wales; Sydney Latitude, longitude coordinates where collected: ; DSMZRadio set VKMradio setAustralia, Sydney

34 Results of comparison Conditions for growth - Temperature Conditions for growth - MediumStorage methods ATCC 24.0°C ATCC medium: 336 Potato dextrose agar (PDA): Diced potatoes g; Glucose 20.0 g; Agar 5.0 g; Distilled water 1.0 L CBS DSMZ 30°C 129. POTATO DEXTROSE AGAR Infusion from potatoes (see below) ml Glucose 20.0 g; Agar 15.0 g; Potato infusion: Boil 200 g scrubbed and sliced potatoes in 1000 ml water for 1 hour. Pass through fine sieve. Avoid new potatoes. VKM 25 C Medium 12 (Medium CZAPEK MEDIUM (CZ): NaNO3 3.0 g; K2HPO4 1.0 g; KCl 0.5 g; MgSO4 x 7H2O 0.5 g; FeSO4 x 7H2O 0.01 g; Sucrose 30.0 g; Agar 20.0 g; Distilled water ml; pH 6.0; Sterilize at 121 C for 30 min) F-1, S-5, D-4

35 Results of comparison Applications ATCC bacterial resistance testing adhesives [21459]; degrades plastics [52928] fungus resistance testing [21552] [92556] [92557] [92558]; fungus resistance testing adhesives [21456]; fungus resistance testing airborne equipment [21535]; fungus resistance testing automotive components; fungus resistance testing cork; fungus resistance testing electrical insulation [21543]; fungus resistance testing leather ; fungus resistance testing polymers [21471]; fungus resistance testing varnish; fungus resistance testing wax [21551]; produces isopullulanase pullulan 4-glucanohydrolase [700]; produces lactoylglutathione glyoxalase I [1390]; testing antimicrobial agent [92595]; testing wood preservatives [55647] CBS Enzymes: amylase; isopullulanase; lipase Decomposition: plastics Testing: assay of wood preservative chemicals; testing fungus resistance of plastics DSMZ Assay of wood preservative chemicals (3693), assay of fungus resistance test (3732) VKM

36 Results of comparison CommentsGenotype ATCC This strain was recently re-named as Aspergillus brasiliensis according to the reference Varga et al [92930] CBS A novel species, Aspergillus brasiliensis sp. nov., is described within Aspergillus section Nigri. This species can be distinguished from other black aspergilli based on intergenic transcribed region, beta-tubulin and calmodulin gene sequences, by amplified fragment length polymorphism analysis and by extrolite profiles. A. brasiliensis isolates produced naphtho-gamma-pyrones, tensidol A and B and pyrophen in common with Aspergillus niger and Aspergillus tubingensis, but also several unique compounds, justifying their treatment as representing a separate species. None of the isolates were found to produce ochratoxin A, kotanins, funalenone or pyranonigrins. The novel species was most closely related to A. niger, and was isolated from soil from Brazil, Australia, USA and The Netherlands, and from grape berries from Portugal. The type strain of Aspergillus brasiliensis sp. nov. is CBS (T) (=IMI (T)=IBT 21946(T)). DNA sequence ITS rDNA: >gb|DQ900597|CBS |Aspergillus brasiliensis strain CBS internal transcribedspacer 1, partial sequence; 5.8S ribosomal RNA gene, completesequence; and internal transcribed spacer 2, partial sequence.| (length of sequence: 465) DNA sequence Beta tubuline: >gb|DQ900607|CBS |Aspergillus brasiliensis strain CBS beta-tubulin gene,partial cds.| (length of sequence: 355) DSMZ VKM

37 Results of comparison PricePermits/FormsKeyword(s)Restrictions ATCC$ In addition to the MTA mentioned above, other ATCC and/or regulatory permits may be required for the transfer of this ATCC material. Anyone purchasing ATCC material is ultimately responsible for obtaining the permits. Please click here for information regarding the specific requirements for shipment to your location. Biosafety Level: 1 CBS 155 EURO GENBANK/MB Aspergillus/*classification/ge netics/isolation & purification/metabolism DNA, Fungal/genetics DNA, Ribosomal Spacer/genetics Molecular Sequence Data Phylogeny Polymorphism, Restriction Fragment Length DSMZ65 EURO Risk group: 1 (classification according to German TRBA) VKM Risk group: 4

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39 Типовое описание поля RDS 1. Field's name 2. Short description of the content (one sentence) 3. Specification of the content 3.1. Detailed description of the content, difference from the other fields that may look similar 3.2. List of subfields and their descriptions 3.3. Specification of the coding for the field and subfields 3.4. The list of possible values (if short) or a reference to file with long list, or reference to thesaurus, or reference to ontology 3.5. Reference to a manual, which describes this field content 3.6. Reference to external standard used for this field 3.7. Samples of correct coding for this field.

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42 Their URLs: WFCC Nmbr AcronimCountry URL (dated ) 803RCDMArmeniahttp://wdcm.nig.ac.jp/catalogue/rcdm/rcdm.html 13ACMAustraliawww.babs.unsw.edu.au/files/babs_cultures_catalogue.pdf 532CCLM/CSIROAustraliahttp://www.csiro.au/places/Australian-National-Algae-Culture- Collection--ci_pageNo-1.html 839ACBRAustriahttp://www.acbr-database.at/BioloMICS.aspx 909BIMBelarushttp://www.mbio.bas-net.by/ 296BCCM/LMGBelgiumhttp://bccm.belspo.be/about/lmg.php 308BCCM/MUCLBelgiumhttp://bccm.belspo.be/about/mucl.php 642BCCM/IHEMBelgiumhttp://bccm.belspo.be/about/ihem.php 643BCCM/LMBPBelgiumhttp://bccm.belspo.be/about/lmbp.php 110IBSFBBrazilhttp://www.splink.org.br/index 364BRBrazilhttp://splink.cria.org.br/manager/detail?resource=BR&setlang=pt 575INCQSBrazilhttp://www.splink.org.br/index 604URMBrazilhttp://www.splink.org.br/index 712CGBrazilhttp://www.splink.org.br/index 731CLIOCBrazilhttp://www.splink.org.br/index 823CBMAIBrazilhttp://webdrm.cpqba.unicamp.br/cbmai/ 867CCGBBrazilhttp://splink.cria.org.br/manager/detail?resource=CCGB&setlang=pt 947IOCBrazilhttp://www.splink.org.br/index BGB, SinBiota, HUERS, CFAF Brazilhttp://www.splink.org.br/index

43 135NBIMCCBulgariahttp://www.nbimcc.org/cabricat/Main.php 6HERCanadahttp://www.phage.ulaval.ca/index.php?pageDemandee=search 73UAMHCanadahttp://www.devonian2.ualberta.ca/uamh/on-line_catalog.htm 338SGSCCanadahttp://people.ucalgary.ca/~kesander/catalogue.html 605CPCCCanadahttp://www.phycol.ca/search/node/ 582CICCChinahttp://www.china-cicc.org/English/english.html 65CCMCzechhttp://sci.muni.cz/ccm/index.html 130CNCTCCzechhttp://www.szu.cz/cnctc/a/uvod.php 486CAUPCzechhttp://botany.natur.cuni.cz/algo/caup-list.html 558CCBASCzechhttp://www.biomed.cas.cz/ccbas/fungi.htm 905CCALACzechhttp://www.butbn.cas.cz/ccala/index.php?page=se&st=as 935SCCAPDenmarkhttp://www.sccap.dk/search/ 926CELMSEstoniahttp://www.miccol.ut.ee/ VTTFinlandhttp://culturecollection.vtt.fi/ 779HAMBIFinlandhttp://www.mm.helsinki.fi/mmkem/hambi/ 639CFBPFrancehttp://www-intranet.angers.inra.fr/cfbp/recherche_e.php 759CRBIP/CIPFrancehttp://www.crbip.pasteur.fr/onglet.jsp?tab=bact 788CIRM-LevuresFrancehttp://genome.jouy.inra.fr/cirm/bdd/ 796ALGOBANKFrancehttp://www.unicaen.fr/ufr/ibfa/algobank/EN/catalogue/catalogue1.php 829RCCFrancehttp://www.sb- roscoff.fr/Phyto/RCC/index.php?option=com_dbquery&Itemid=34

44 879LeishCryo Bank Francehttp://www.parasitologie.univ-montp1.fr/catalogue_list.asp 917CIRM-BPFrancehttp://www.tours.inra.fr/cirm_bp_eng/commander_une_souche/le_catal ogue 918CIRM-BIAFrancehttp://jwsdp.jouy.inra.fr/Consult/exeRequete.jsp?cirm=gisilbia 192SAGGermanyhttp://sagdb.uni-goettingen.de/ 274DSMZGermanyhttp://www.dsmz.de/microorganisms/main.php?menu_id=2 807CCACGermanyhttp://www.ccac.uni-koeln.de/recherche.shtml 919FSUGermanyhttp://www.frc.uni-jena.de/stammsammlung.php 940CCCryoGermanyhttp://cccryo.fraunhofer.de/web/strains/ 485NCAIMHungaryhttp://web.uni-corvinus.hu:8089/NCAIM/frameset.jsp 3NCIMIndiahttp://www.ncl-india.org/ncim/catelogue.jsp?mid=29 773MTCCIndiahttp://mtcc.imtech.res.in/catalogue.php 945CRA-PAVItalyhttp://www.collezionedimicrorganismi.com/index.cfm?cis=1#strt 195HUTJapanhttp://home.hiroshima-u.ac.jp/hut/ 567JCMJapanhttp://www.jcm.riken.jp/JCM/catalogue.shtml 591NIESJapanhttp://mcc.nies.go.jp/ 637MAFFJapanhttp://www.gene.affrc.go.jp/databases-micro_search_en.php 825NBRC/IFOJapanhttp://www.nbrc.nite.go.jp/e/index.html 597KCTCKoreahttp://www.brc.re.kr/English/ekctc.aspx 806KACCKoreahttp://www.genebank.go.kr/ 903CFGRKoreahttp://genebank.riceblast.snu.ac.kr/ 500CDBBMexicohttp://micro500.cs.cinvestav.mx/ 817LIH-UAMMexicohttp://www.histoplas-mex.unam.mx/index_i.html 883CCMMMoroccohttp://www.ccmm.ma/catalogue.htm 133CBSNetherlandshttp://www.cbs.knaw.nl/databases/ 797NCCBNetherlandshttp://www.cbs.knaw.nl/databases/

45 589ICMPNew Zealand 212IAFBPolandhttp://kkp.ibprs.pl/ 914CCBAPolandhttp://pasat.ocean.univ.gda.pl/~ccba/ipl.php?id=ba-cya 816MUMPortugalhttp://www.micoteca.deb.uminho.pt/ 906ACOIPortugalhttp://acoi.ci.uc.pt/ 342VKMRussiahttp://www.vkm.ru 596IPPASRussiahttp://www.ippras.ru/cfc/ 768IEGMRussiahttp://www.iegm.ru/iegmcol/strains/index.html 836CCIBSORussiahttp://www.rbcar.ro/catalogues.htm 412CECTSpainhttp://www.cect.org/english/ 32CCUGSwedenhttp://www.ccug.se/ 603UPSCSwedenhttp://www-hotel.uu.se/evolmuseum/fytotek/ 651FCUGSwedenhttp://www2.dpes.gu.se/FCUGsrch.html 475VTT/CCTMSwitzerlandhttp://culturecollection.vtt.fi/ccdb/html?p=s 59BCRC/CCRCTaiwanhttp://www.ccrc.firdi.org.tw/ 383TISTRThailandhttp://www.biotec.or.th/tncc/tistr_dete.html 705BBPP/DOAThailandhttp://www.biotec.or.th/tncc/dbstore/DOAC_search.asp 707DMSTThailandhttp://www.biotec.or.th/tncc/ 783BCCThailandhttp://www.biotec.or.th/bcc/InternetSearch.asp 828RSKKTurkeyhttp://www.rshm.gov.tr/en/index.php?option=com_content&task=view& id=34&Itemid=61 126NCPPBUKhttp://www.ncppb.com/ncppbsearch.cfm 128FLYUKhttp://www.mba.ac.uk/culturecollection.php 134NCWRFUKhttp://www.bio-aware.com/cabi/Defaultinfo.aspx?Page=Home 137ECACCUKhttp://www.hpacultures.org.uk/collections/ecacc.jsp 154NCTCUKhttp://www.hpacultures.org.uk/collections/nctc.jsp

46 169NCYCUKhttp://www.ncyc.co.uk/ 184NCPFUKhttp://www.hpacultures.org.uk/collections/ncpf.jsp 214IMIUKhttp://www.bio-aware.com/cabi/Defaultinfo.aspx?Page=Home 522CCAPUKhttp://www.ccap.ac.uk/ccap_search.php 653NCIMBUKhttp://www.ncimb.com/search.php?parent=culture 814NCPFUKhttp://www.hpacultures.org.uk/collections/ncpv.jsp 1ATCCUSAhttp://www.lgcstandards- atcc.org/ATCCCulturesandProducts/tabid/979/Default.aspx 2CCMPUSAhttps://ccmp.bigelow.org/search_strains 97NRRLUSAhttp://nrrl.ncaur.usda.gov/cgi-bin/usda/ 112ARSEFUSAhttp://arsef.fpsnl.cornell.edu/mycology/ARSEF_Culture_Collection.html# Catalogs 115FGSCUSAhttp://www.fgsc.net/scripts/catalog.asp 530LMSUSAhttp://www.carolina.com/ 573BGSCUSAhttp://www.bgsc.org/ 606UTEXUSAhttp://web.biosci.utexas.edu/utex/Search.aspx 827CGSCUSAhttp://cgsc.biology.yale.edu/ 849DSCUSAhttp://www.dictybase.org/StockCenter/StockCenter.html 888UCD-FSTUSAhttp://www.phaffcollection.org/ 933VTCCViet Namhttp://biotechvnu.edu.vn/vtcc/

47 Real fields names Geographic origin, History of deposit, Species, Accession number, Antagonism, Applications, Carbon source assimilation, Carbon source fermentation, Cell wall, Class, Clonal, Collected date, Collector, Collector number, Comments, Conditions for growth - Medium, Conditions for sporulation, Constructed by, Coordinate of Location, Country, Date of identification, Date of isolation, Date of isolation, Decomposes, Deposition date, Description of Location, Description of morphology, Deterioration abilites, Division, DNA-DNA relatedness, EditDate, EntryDate, Enzyme production, Family, Fatty acid profile, Filamentous Growth, Form of supply, G+C (Mol%)\GC, Genotype, Genus, Geographic origin, Growth in broth, Host, Identified by, Images, Infrasubspecific names, Isolate Number, Isolated by, Isolated from, Isolation method, Kingdom, light, Literature, MatingType, MaxMinTemperature, Metabolites, Misapplied names, Mutant, Mycoparasiitism, Name and taxonomy, National name, Numerical taxonomy, O2, Order, Organism type, Other collection numbers, Parents strain, Pathogenicity, pH, Phylum, Pigment, Plasmid, Polar lipid, Quinone, Race, Restrictions, Salt Tolerant, Sensitive to, Serotype, Serovar, Sexual state, Sole Sources of Nitrogen, Status, StorageMethods, Strip test, Synonyms, Temperature, Toxicity, Toxicity type, Toxicity value, Transformation, Veg. compatibility, Yeast physiological data

48 The data standards compared: - MINE Bacterial - MINE Fungal - CABRI / OECD MDS+RDS+FDS - Darwin Core - ABCD - Straininfo

49 MINE The Microbial Information Network Europe Sponsored by the CEC, MINE was established to coordinate, harmonize and integrate data on microbial cultures held in collections of 9 EC countries: Belgium, Germany, France, Greece, Italy, Netherlands, Portugal, Spain, U.K. In 1989 MINE consisted of 32 Culture Collections Database was planned separately in 9 national nodes. DEC VAX minicomputers (BASIS software) and microcomputers PC AT (ORACLE database). In 1989 there was on-line access to DSM, CMI, CBS, NCYC, LMG nodes via modem connection. Menu request system, search with AND/OR operators. Thesaurus files in BASIS aid in maintaining consistency during data entry. Integrated database was planned in DSM, and Responsible Committee was to make decisions on conflicting strain data.

50 Group of fields in MINE standard Field groupsFungalBacterial 1Name++ 2Strain Administration++ 3Status++ 4Environment and history++ 5Biological interactions++ 6Sexuality++ 7Properties cytology, biomolecular data morphological, cultural and chemota- xonomical data 8Genetics+- 9Mutants, Plasmids and Phages-+ 10Growth conditions++ 11Chemistry and enzymes++ 12Practical applications++

51 Fields in MINE Fungal A. Internal administration EDI Date of input. EDM Date of last update. SEC Security code. ID Typist's identification. OT Organism type. B = Bacteria, F = Filamentous Fungi, Y = Yeasts. B. Name SP Species name SSP Subspecies name VAR Variety name F Form name FSP Epithet of forma specialis RACE Race name, authors SERO Serotype, serovar MIS Misapplied name TAX Taxonomy. Contains names of suprageneric taxa MOR Morph: A = anamorph; T = teleomorph. ILL Illustrations TAXREM Taxonomic remarks LIT Taxonomic and other literature

52 C. Strain administration STN Strain number OCC Numbers in other collections EDA Date of accession EDR Date of receipt CORR Correspondence. Refers to letters SPINF Special information available REM General remarks. CHK Internal check of identity at collection. PRE Mode of preservation / storage PREREM Remarks on preservation RESTR Restrictions, care and precautions D. Status STAT Status: T = type strain; NT = neotype; PVRS = pathovar, etc.

53 E. Environment and history SUSP Substratum specificity SSTR Original substratum HAB Habitat (original biotope) LOC Origin / location of original material (country, locality). COLL Collector. HERB Herbarium where specimen is deposited ISOL Isolated by. Name of isolator, original number of isolate, date. ISOM Source and method of isolation DET Identified by DEP Depositor. HIS History (between isolation and deposit) NAMCH Name changes / previous names ECOLIT Literature on ecology ECOREM Remarks on ecology and environment

54 F. Biological interactions SYMB Symbiosis MPAR Mycoparasitism PATH Pathogenicity ALLER Allergenicity TOX Toxicity to other organisms ANT Antagonistic activities against other organisms PATHLIT Literature on biological interactions PATHREM Remarks on pathogenicity G. Sexuality SEX Sexual behaviour SEXST Sexual state H. Properties (cytology, biorolecular data) NUCL Number of nuclei FSTR Fine structure data WCONS Wall constituents CCONT Cell contents COO Coenzyme-Q system STAIN Staining reactions PIGMENT Pigment production and autofluorescence. GRWTH Growth characteristics TKIT Results of test-kit PROPLIT Literature on morphological, taxonomic, fine structure characteristics

55 I. Genetics GENOT Genotype GC Guanine-cytosine content of DNA DNAD Hybridization DNA-DNA with other strains DNAR Hybridization DNA-r.RNA with other strains RNAD Hybridization r.RNA-DNA with other strains MUT Mutants MUTMET Method by which mutation was induced HYBR Hybrids PLS Plasmid out/in the host KIL Killer properties of yeast GENREM Remarks on genetics, DNA data, mutations, plasmids GENLIT Literature on genetics and mutants J. Growth conditions CONDS Conditions for growth and maintenance on solid media CONDL Conditions for growth in liquid media CONDSP Conditions for fruiting or sporulation CONDGER Conditions for germination CSOR Carbon sources that have been tested for growth

56 NSOR Nitrogen sources that have been tested for growth CNSOR Single compounds tested as sole carbon and nitrogen source for growth NUGR Nutritional requirements and growth factors required DEF Deficiencies TOL Tolerances and sensitivities TEMPR Temperature relationships for growths TEGR Cardinal temperatures for growth TESP Temperature optimum range for sporulation HEATR Heat resistance PHR pH requirements for growth PHC pH conditions ETHC Ethanol conditions SALR Salinity requirements for growth SALC NaCl concentration SUGC Optimum and maximum sugar concentrations OSM Osmophily and xerophily WATC Conditions of water activity LC Light conditions

57 K. Chemistry and enzymes ENZ Enzymes produced DEC Decomposition and deteriorating capacities MET Metabolites produced BIOTR Biotransformations CHREM Remarks on chemical data CHLIT Literature on the impact of chemical and physical factors L. Practical applications APPL Industrial and general applications TEST Applications in testing (assay). BIOM Production of biomass, edibility PATENT Patent(s) CTR Control of the microorganism in question APLIT Literature on application, patents, etc

58 Fields in MINE Bacterial A. Internal Administration OT Organism type. B = bacteria; F = fungi; P = plasmids; Y = yeasts EDI Date of input EDM Date of latest update ID Typist identification SEC Security code B. Name SP Species name SSP Subspecies name PVAR Pathovar name VAR Infrasubspecific names SVAR Serovar OTHNAM Other names STAT Status: T = type strain; NT = neotype; PVRS = pathovar TAX Taxonomy. Names of suprageneric taxa TAXREM Taxonomic remarks TAXLIT Taxonomic literature ILL Illustration REM General remarks LIT General references

59 C. Strain Administration STNStrain number in collection OCCOther collections numbers EDRDate of receipt EDADate of accession CORRCorrespondence SPINFSpecial information CHKCollection check PREPreservation type PREREMRemarks on preservation PRELITLiterature on preservation RESTRPrecautions and restrictions SUPPLY Form of supply ADMREM Administrative remarks D. Environment and History HABISpecific habitat. Indicates restrictions to substrates ISOFRIsolated from LOCGeographic location

60 COLLCollector of sample ISOLIsolated by ISOMIsolation method DETIdentified by DEPDepositor HISHistory NAMCHName changes ENHISLIT Literature on environment and history ENHISREM Remarks on environment and history E. Properties (morphological, cultural and chemotax-onomical data) FSTRFine structure data WCONSCell wall constituents CINCCell inclusions CHTAXChemotaxonomical markers GRAMGram behaviour KOHKOH test AMPEPAminopeptidase test STAINStaining reactions CELLShape, arrangement and size of cell MOTMotility PIGMPigments GRWTHLGrowth characteristics in liquid media GRWTHSGrowth characteristics on solid media

61 QUADGERQuantitative data on growth RESTSTResting structures. C = cyst, ENS = endospore, EXS = exospore, MS = myxospore, F = fruiting body GC Guanine-cytosine content of DNA DNAD Hybridization DNA-DNA with other strains DNAR Hybridization DNA-r.RNA with other strains RNAD Hybridization r.RNA-DNA with other strains DNASQ DNA sequences RNASQ RNA sequences PHYLO Other phylogenetic data TKIT Result of testkit PROPLIT Literature on properties PROPREM Remarks on properties

62 F. Mutants, Plasmids and Phages MUT Mutant MUTMET Method of mutation MUTREM Remarks on genetics, mutations, DNA data MUTLIT Literature on genetics and mutants GENOT Genotype, chromosomal marker SEXST Sexual state HYBR Hybrid PLS Plasmids info PHAGE Phage PLPREM Remarks on plasmids and phages PLPLIT Literature on plasmids and phages

63 G. Growth Conditions CONDS Conditions for growth on solid media CONDL Conditions for growth on liquid media CONDGER Conditions for germination NUGR Nutritional requirements and growth factors TOL Tolerances and sensitivities DEF Deficiencies METY Metabolic type CNUT Carbon nutrition type CSOR Single carbon sources tested for growth NSOR Single nitrogen sources tested for growth CNSOR Single compounds tested as C and N source for growth OXR Oxygen relationships GAS Gas phase. Percentage of gases TEMPR Temperature relationships TEGR Cardinal temperatures for growth HEATR Heat resistance PHR pH relationships PHC pH conditions LC Light conditions SALR Salinity relationships SALC Salinity conditions SUGC Sugar concentration WATC Conditions of water activity

64 ELDO Electron donor ENERS Energy source ELAC Special electron acceptors CONDREM Remarks on growth conditions CONDLIT Literature on growth conditions H. Chemistry and Enzymes ENZ Enzymes produced DEC Decomposition, degradation and utilization capacities DETER Biodeterioration MET Metabolites LEACH Leaching BIOLUM Bioluminescence HAEMOL Haemolysis MISPROP Miscellaneous properties CHREM Remarks on chemical data and metabolic properties CHLIT Literature on chemical data and metabolic properties

65 I. Biological Interactions SYMBSymbiosis or synthrophy PATHPathogenicity and virulence ALLER Allergenicity TOX Toxicity ANT Antagonistic activity BINTLIT Literature on biological interactions BINTREM Remarks on biological interactions J. Practical Applications APPLGeneral and industrial application TESTApplications in testing and assays CTRProcedures for control PATENT Patent APLITLiterature on applications, patents APREMRemarks on applications and patents

66 Example of field specification in MINE NameContentsDescriptions SUGC Sugar concentration Sugar concentration. In STR. Names of sugars and optimum and maximum concentration (in that order) in % (without "%", but with indication w/w, v/v, w/v, where "w" is weight and "v" is volume). The subfields containing the name of a sugar and the values of the concentrations are separated by ";". Subsubfields containing the values are separated by ",". If a subsubfield contains no data, care must be taken that the comma which terminates this empty subfield is entered. If growth has been tested for a particular sugar at a particular concentration without establishing the range, name and concentration are indicated with the growth response ( +,-,v). Examples: saccharose, 20, v/v; glucose 3-5,20; glycerol 22-25, w/w

67 CABRI / OECD MDS+RDS+FDS -OECD Best Practice Guidelines for Biological Resource Centres. OECD, 2007, 115 p. - CABRI (http://www.cabri.org/guidelines.html) CABRI: MDS+RDS+FDS for Bacteria and Archea, Fungi, Yeast, Plasmids, Phages, Animal and Human Cells, DNA probes, Plant Cells, Plant Viruses OECD: MDS+RDS for Microbial Accessions (Filamentous fungi, Yeasts, Microalgae, Bacteria, Cyanobacteria, Archaea, Plasmids, Protozoa, Phages, Viruses), DNA, tissues and isolated cells, cell line, primary cultured cells, transformed cells

68 1Accession numberFYMAcBMM 2Other collection numbersFYMAcBMM 3RestrictionsFYMAcBMM 4Organism typeFYMAcBMM 5NameFYMAcBMM 6RaceFYRR 7StatusFYMAcBMM 8Misapplied names/Other namesFYRAcBRR 9History of depositFYMAcBMM 10Conditions for growthFYMAcBMM 11Form of supplyFYMAcBMM 12Isolated fromFYRAcBRR 13Geographic originFYRAcBRM 14MutantFYRAcBRR 15Sexual stateFYRAcBFR 16LiteratureFYRAcBRR 17Infrasubspecific namesAcBM- 18SerovarAcBRR 19GenotypeFYFAcBRR 20PathogenicityFYFAcBF 21Enzyme_productionFYFAcBFF 22Metabolite_productionFYFAcBFF 23ApplicationsFYRAcBFF 24RemarksFYFAcBFF 25Price_codeFYFAcBFF 26Catalogue_entryAcBFF 27PlasmidsAcBFF

69 Darwin Core 184 fields The Darwin Core standard was originally conceived to facilitate the discovery, retrieval, and integration of information about modern biological specimens, their spatiotemporal occurrence, and their supporting evidence housed in collections Keeps expanded list of geographical and geological fields and fields for taxonomy. We did not find the fields: Restrictions, Toxicity, Identification, Deposition and Isolation data, Conditions for growth, Storage Methods, Race, Mutant, Serovar, Kind of relationship, Applications, group of fields Phenotype. Simple Darwin Core Darwin Core Terms: A quick reference guide Darwin Core (versions DwC 1.21, DwC 1.3 and DwC 1.4) makes a part of TDWG group of standards.

70 ABCD Access to Biological Collections Data Standard This schema is a common data specification for biological collection units, including living and preserved specimens, along with field observations that did not produce voucher specimens. It is intended to support the exchange and integration of detailed primary collection and observation data fields in version 2.06, including containers, makes a part of TDWG group of standards. Based on BioCASE software. Description of fields is given on

71 The biggest group of items is DataSets/DataSet/Units/Unit/Gathering/ (423 fields) - the elements describing the event and site of collecting a microbial unit - description of the place, geographical data (even bigger than in Darwin Core). ABCD presents a very big list of fields with contact data: for institutions and people, which keep the database or the records, or acquired microorganisms – names, phones, s, etc. – in various formats. Also pictures, property fields (including IPR), bibliography and comments. Ruther short opportunities for most of other types of data in microbial CC. We didn’t find the fields Pathogenicity, Race, Price code, the field Applications is specified but with no definition inside. Standard is very difficult in use. Example from this description Identifier: DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLa tLong/LongitudeDecimal Documentation: The longitude of the gathering site, expressed in decimal degrees. Content: The longitude of the gathering site, expressed in decimal degrees. Degrees (3 digits), minutes (2 digits), and seconds (2 digits) followed by E (East) or W (West). Every missing digit (minutes or seconds) should be indicated with a hyphen. Leading zeros are required. A FAO/IPGRI multi-crop passport descriptor (MCPD), description and examples taken from EURISCO descriptor list dated July 3, Maps to Darwin Core 2: Longitude. Example Value: W

72 Straininfo MCL 2.1 (2011) MCL presents Strainifo database content in XML format. 103 fields Fields structure, descriptions, recommended values, references to external data standards: MINE, DCMI Metadata, PRISM, WGS84 Any microbial culture collection that has programmer and sufficiently good catalogue presentation in Internet, can become Straininfo partner and upload its catalogue into Straininfo database. The collection catalogue is to be converted to XLM file according to MCL specification. Examples presented on pages and are quite sufficient for this job.

73 Comparison of the standards. Fragment of the table

74 Compliance with RealRelated to CC ABCD24(252)26%19% MINE B7176%55%55% MINE F8187%72%72% OECD5054%100% DwC3133%17% Straininfo2022%19% Comparison of the standards. Final results

75 Combined list of fields LocationEng, Depositor, AuthoritySp, Strain nmbr, Antagonism, Applications, Carbon source assimilation, Carbon source fermentation, Cell wall, Class (-), Clonal, Collected date, Collector, Sample number, General remarcs, StrainComments, GrowthMedium liquid, Conditions for sporulation, Constructed by, decimalLatitude (?), countryCode (- ), IdentificateDate, Date of isolation, IsolationDate, Degradation, ReceivedDate, AreaDetail, CellMorphology, Deterioration abilites, Division (-), DNA-DNA relatedness, EditDate, EntryDate, Enzyme production, family (-), Fatty acid profile, Filamentous Growth, Supply, G+C (Mol%)\GC, Genotype, Genus, stateProvince, Growth in broth, associatedTaxa, IdentificateByEng, Images, AuthoritySubSp, IsolateNumber, IsolatedBy, IsolatedFrom, Isolation method, kingdom (-), Light conditions, References, MatingType, Sexual state, MaxMinTemperature, Metabolites, OtherName, Mutant, Mycoparasiitism, originalNameUsage (?), Taxcomments, ColonyMorphology, Oxygen relationships, order (-), Subcollection, OtherCol, Parents strain, Pathogenicity, pH relationships, phylum (-), Pigment, Plasmid, Polar lipid, Quinone, Race, PhytopatogenLevel, Salt Tolerant, Tolerances and sensitivities, Serotype, Serovar, State, Sole Sources of Nitrogen, Type, StorageMethods, Results of test-kit, Synonym, IncubationTempLiquid, Toxicity, Toxicity type, Toxicity value, Transformation, Veg. compatibility, Yeast physiological data

76 Results of comparison Compliance with RealRelated to CC ABCD24(252)26%19% MINE B7176%55%55% MINE F8187%72%72% OECD5054%100% DwC3133%17% Straininfo2022%19% Combined93100%

77 Combined standard Taxonomy CCname, Organism type, Genus, Species, Authors of species, date, Subspecies, Variant, Authors of variant, date, Forma, FormaSpecies, Pathovar, Serotype, Serovar, Race, Synonym, Misapplied name, Name changes, Type strain, Strain nmbr, IdentificationComments, IdentificationReferences, IdentificateDate, IdentificateBy, Taxlit, Taxcomments History of strain, Sample, Ecology Correspondence, ReceivedDate, Date of accession, Depositor, History, OtherCol, IsolateNumber, IsolationDate, Isolation method, IsolatedBy, IsolatedFrom, Collector, Sample number, CountryCode, Country, Height, DecimalLatitude, DecimalLongitude, Altitude, MaximumDepthInMeters (?), MinimumDepthInMeters (?), NamedArea, AreaDetail, Geographic location, Island, Habitat, associatedTaxa, Ecollit, Ecol comments Growth and maintenance conditions GrowthMedium solid, GrowthMedium liquid, Remarks on growth conditions, Growth in liquid, Growth on solid, Filamentous Growth, Carbon nutrition type, Carbon source assimilation, Carbon source fermentation, Energy source, Sugar concentration, Sole Sources of Nitrogen, Oxygen relationships, Percentage of gases, Ethanol condition, Growth factors, Conditions of water activity, MaxMinTemperature, Temperature relationships, Light conditions, pH conditions, pH relationships, Quantitative data on growth, Growth conditions lit, Temperature for sporulation, Conditions for sporulation, Conditions for germination, StorageMethods, Storage Comments, Data of storage, Storage Lit

78 Strain properties Fine structure data, CellMorphology, Cell wall, Cell contents, ColonyMorphology, MatingType, Sexual state, Morph, Resting structures, Motility, Images, Gram stain, Staining reactions, Deficiencies, Heat resistance, Salinity relationships, Salt Tolerance, Osmophily and xerophily, Bioluminescence, Coenzyme-Q, Haemolysis, Killer properties, Metabolic type, Pigment, Tolerances and sensitivities, Results of test-kit, Aminopeptidase test, Electron donor, Special electron acceptors, Propertieslit, Remarks on properties, Allergen, Pathogenicity, Risk group, Restrictions, Toxicity, PhytopatogenLevel, Pathcomments, Interactions type, Interactions lit, Parasitism, Symbiosis, Antagonism, Chemical control, Chemlit, Metabolites, MetabolComments, TestSystems, Biofertilizer, Biopesticide, Bioremediation, Transformation, Degradation, Deterioration abilites, Enzyme production, Applications, Applicationslit, Miscellaneous properties, Production of biomass, Patent, Remarks on applications, References, General remarks, StrainComments Genetic characteristics of strain Hybrids, Plasmidslit, Mutant, Plasmid, Gencomments, Remarks on plasmids and phages, Phage, DNA sequences, DNA-DNA relatedness, G+C (Mol%)\GC, Genotype, Hybridization DNA-r.RNA, Hybridization r.RNA-DNA, GenMitlit, Other phylogenetic data, RNA sequences Processing data Curator, Security code, Supply, Category, EditDate, EntryDate, Date of last check, Date of last transfer

79 Genetic data standards The International Nucleotide Sequence Database Collaboration (INSDC, includes: - GenBank - the National Center for Biotechnology Information - NCBI, USA - EMBL-Bank at the European Molecular Biology Laboratory - DDBJ - the DNA Data Bank of Japan, Japan Each of these databases is daily updated at the expense of interchanging the new DNA sequences submitted to any one of them. These three organizations have slightly different submit procedures for new genetic data, but according their exchange data procedure we can speak of the unified data base DDBJ/EMBL-Bank/GenBank and, accordingly, one unified data standard. Genomic Standards Consortium (GSC in prepared new standards - "minimum information" checklists: - MIGS/MIMS - The reporting of genomes and metagenomes (http://gensc.org/gc_wiki/index.php/MIGS/MIMS) - MIMARKS - The reporting of environmental sequencing including ribosomal genes (http://gensc.org/gc_wiki/index.php/MIMARKS)

80 In the project "MIGS/MIMS Structured Comment" GSC is also working with INSDC to develop a way to submit these data standards to DDBJ/EMBL- Bank/GenBank In project BRIO we communicate with MIGS/MIMS component. MIGS/MIMS specification in XLS file has two worksheets: - MIGS_MIMS checklist with 47 standard fields presenting common data, and - environmental packages with 653 fields presenting features of the 14 types of microbial source: air, host-associated, human-associated, human-gut, human- oral, human-skin, human-vaginal, microbial mat/biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater/sludge, water. 193 fields from this list are unique. 19 fields from MIGS_MIMS checklist have or may have some compliance with usual CC catalogue data, the main problem - there is no microorganism name in this list. 193 fields of environmental packages present detailed (mostly chemical) information on the source (habitat), that potentially can be compliant to the properties of microorganisms extracted, but this is the subject of additional study.

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83 WDCM Reference Strain Catalogue This catalogue was produced to enable broader and easier access to the reference strains listed by the ISO TC 34 SC 9 Joint Working Group 5 and by the Working Party on Culture Media of the International Committee on Food Microbiology and Hygiene (ICFMH-WPCM).

84 DB for Microorganisms in Extreme Environment Hot spring Volcanic Volcanic salt and alkali lakes

85 中国科学院微生物研究所 Isolation Temperature Humidity PH value Elevation Vegetation Date Application Usage Industry use Physiological and biochemical properties Medium Culture conditions Biochemical reactions Metabolites Sequences Sequence Genome Annotation Information sharing to resources sharing Get benefits according to CBD Strains even outside of CCs For both scientific and industry users Data base DB for Microorganisms in Extreme Environment

86 CODATA Task Group on Advancing Informatics for Microbiology (TG-AIM)

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88 Общие требования включают: гарантии устойчивого функционирования в течение длительного времени (с указанием источников финансирования); наличие квалифицированного персонала; обязательства по выполнению своих функций (в строгом соответствии с национальной нормативно-правовой базой): прием и хранение первичного образца, поддержание образцов (консервация, проверка идентичности) и др.; обязательства по ведению документооборота; ведение компьютерной базы данных с описанием депонированного биологического материала и его происхождения, доступной через Интернет; обязательства по использованию стандартных сред и реагентов для поддержания коллекций; обеспечение контроля качества биологического материала, проверки его на безопасность (или проверки соответствия декларированному уровню биологической опасности) ISO 2000, ISO 9001, ISO 14001, ISO 14004, ISO 14010, ISO 14012, ISO 19011

89 УчастникСтрана DSMZDE CABIUK IPFR SPP-PSBE KNAW/CBSNL UGOTSE UVEG-CECTES UGENTBE INRA-CIRMFR JacobsUniDE UMinho-MUMPT MUTIT CSIC-IMEDEAES VKMRU IAFB-CCIMPL USMIIT

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91 Благодарю за внимание Василенко Александр


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