Transcript Список сравниваемых стандартов:

Международная
инфраструктура для коллекций
культур
Василенко А.Н., Озерская С.М
Всероссийская коллекция микроорганизмов ИБФМ РАН
E-mail: [email protected]
Ступарь Олег Сергеевич
.
E-mail: [email protected]
ВКМ ИБФМ РАН
к.б.н
Московская обл. 142290
Пущино, Проспект Науки 5
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.
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.
Difference in typing (factor 4).
Example: errors in a name
E
E
E
1
2
3
B KM
4
5
6
7
R
R
R
8
E
E
E
E
R
R
R
R
E
E
R
R
E
E
R
R
E
R
E
R
E
R
E
R
Factor 3: Differences in content.
Example:
One strain of Aspergillus brasiliensis Varga et al. 2007
in four catalogues:
Cultures:
ATCC 9642
CBS 246.65
DSM 63263
VKM F-1119
Results of comparison
Organism
type
ATCC
CBS
Name
Other names
(Infrasubspecific
(Misapplied names)
names)
Aspergillus
Subcollection:
brasiliensis Varga et
Fungi
al.
Aspergillus
brasiliensis Varga,
F
Frisvad & Samson
DSMZ
F
VKM
F
Aspergillus
brasiliensis Varga,
Kocsube et al.
Aspergillus
Aspergillus niger
brasiliensis Varga et van Tieghem 1867
al. 2007
Previous
names
Aspergillus
brasiliensis;
Aspergillus
niger
Results of comparison
Accession
number
ATCC
9642
CBS
246.65
DSMZ
63263
VKM
F-1119
Other collection numbers
Australian Mycol. Panel series 26, CBS 246.65, DSM
63263, IFO 6342, IMI 91855, NRRL 3536, NRRL A5243, QM 386
ATCC 9642;ATHUM 2856;CECT 2700;DSM
63263;IFO 6342;IHEM 3797;IMI 149007;IMI
091855;IMI 091855ii;IMI 091855iii;LCP
74.2280;MUCL 19001;NBRC 105650;NRRL
3536;NRRL A-5243;OECD 14;QM 386;VKM F1119
ATCC 9642, CBS 246.65, IFO 6342, IMI 091855,
NBRC 6342, NRRL 3536
ATCC 9642; CBS 246.65; CCRC 31512; DSM 63263;
FERM S-2; IFO 6342; IMI 91855; NRRL A-5243;
NRRL A-3536; QM 386
Results of comparison
History of deposit Deposited as
ATCC
Aspergillus
niger van
Tieghem,
anamorph
CBS
<- IMG, 4518 <- W. Aspergillus
Kerner. [QM 386]
niger
<-- INMI, VKM FAspergillus
VKM
1119 <- ATCC,
niger
ATCC 9642
DSMZ
Strain
Designation
Depositors
SN 26
WH Weston
QM, Jul 1965
Results of comparison
Isolated from
ATCC
wireless radio
equipment
CBS
radio
equipment
DSMZ
VKM
Radio set
radio set
Isolated by
Geographic
origin
Additional
geographic
data
New South Wales,
Australia
Latitude,
longitude
Australia, New coordinates
R.E. Klausmeier,
South Wales; where
Indiana, Crane
Sydney
collected:
33.8833333;
151.2166667
Australia, Sydney
Results of comparison
Conditions for
growth Temperature
ATCC
24.0°C
CBS
DSMZ
30°C
VKM
25 C
Conditions for growth - Medium
Storage
methods
ATCC medium: 336 Potato dextrose agar (PDA):
Diced potatoes 300.0 g; Glucose 20.0 g;
Agar 5.0 g; Distilled water 1.0 L
129. POTATO DEXTROSE AGAR
Infusion from potatoes (see below) 1000.0 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.
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 1000.0 ml; pH 6.0;
Sterilize at 121 C for 30 min)
F-1, S-5,
D-4
Results of comparison
Applications
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
ATCC
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
DSMZ
VKM
Enzymes: amylase; isopullulanase; lipase
Decomposition: plastics
Testing: assay of wood preservative chemicals; testing fungus resistance of
plastics
Assay of wood preservative chemicals (3693), assay of fungus resistance test
(3732)
Results of comparison
Comments
Genotype
This strain was recently re-named as Aspergillus brasiliensis
ATCC according to the reference Varga et al. 2007. [92930]
A novel species, Aspergillus brasiliensis sp. nov., is described DNA sequence ITS rDNA:
within Aspergillus section Nigri. This species can be
>gb|DQ900597|CBS
distinguished from other black aspergilli based on intergenic 246.65|Aspergillus brasiliensis
transcribed region, beta-tubulin and calmodulin gene
strain CBS 246.65 internal
sequences, by amplified fragment length polymorphism
transcribedspacer 1, partial
analysis and by extrolite profiles. A. brasiliensis isolates
sequence; 5.8S ribosomal RNA
produced naphtho-gamma-pyrones, tensidol A and B and
gene, completesequence; and
pyrophen in common with Aspergillus niger and Aspergillus internal transcribed spacer 2, partial
CBS tubingensis, but also several unique compounds, justifying sequence.| (length of sequence: 465)
their treatment as representing a separate species. None of the DNA sequence Beta tubuline:
isolates were found to produce ochratoxin A, kotanins,
>gb|DQ900607|CBS
funalenone or pyranonigrins. The novel species was most
246.65|Aspergillus brasiliensis
closely related to A. niger, and was isolated from soil from strain CBS 246.65 beta-tubulin
Brazil, Australia, USA and The Netherlands, and from grape gene,partial cds.| (length of
berries from Portugal. The type strain of Aspergillus
sequence: 355)
brasiliensis sp. nov. is CBS 101740(T) (=IMI 381727(T)=IBT
21946(T)).
DSMZ
VKM
Results of comparison
Permits/Forms
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
ATCC $155.00 material is ultimately responsible for
obtaining the permits. Please click here
for information regarding the specific
requirements for shipment to your
location.
CBS
Price
Keyword(s)
155
EURO
GENBANK/MB510581
Aspergillus/*classification/ge
netics/isolation &
purification/metabolism
DNA, Fungal/genetics DNA,
Ribosomal Spacer/genetics
Molecular Sequence Data
Phylogeny Polymorphism,
Restriction Fragment Length
DSMZ 65 EURO
VKM
Restrictions
Biosafety Level: 1
Risk group: 1
(classification
according to
German TRBA)
Risk group: 4
Organism type
Genus
Species
Name (Infrasubspecific names)
Accession number
Restrictions
Sexual state
Status
Other names (Misapplied names)
Literature
Other collection numbers
History of deposit
Isolated from
Identified by
Geographic origin
Conditions for growth - Temperature
Conditions for growth - Medium
Additional growth conditions - pH, light, O2,…
Conditions for sporulation
StorageMethods
MatingType
Mutant
Race
Serovar
Genotype
Images
Applications
Symbiosis
Description of morphology
Phylogeny
Comments
Form of supply
Price
EntryDate
0%
All
EMbaRC
GBRCN
Strainfo partners
20%
40%
60%
80%
100%
120%
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.
Their URLs:
WFCC
Acronim
Nmbr
803 RCDM
13
ACM
532 CCLM/CSIRO
839
909
296
308
642
643
110
364
575
604
712
731
823
867
947
ACBR
BIM
BCCM/LMG
BCCM/MUCL
BCCM/IHEM
BCCM/LMBP
IBSFB
BR
INCQS
URM
CG
CLIOC
CBMAI
CCGB
IOC
BGB, SinBiota,
HUERS, CFAF
Country
URL (dated 18.09.2010)
Armenia http://wdcm.nig.ac.jp/catalogue/rcdm/rcdm.html
Australia www.babs.unsw.edu.au/files/babs_cultures_catalogue.pdf
Australia http://www.csiro.au/places/Australian-National-Algae-CultureCollection--ci_pageNo-1.html
Austria
http://www.acbr-database.at/BioloMICS.aspx
Belarus http://www.mbio.bas-net.by/
Belgium http://bccm.belspo.be/about/lmg.php
Belgium http://bccm.belspo.be/about/mucl.php
Belgium http://bccm.belspo.be/about/ihem.php
Belgium http://bccm.belspo.be/about/lmbp.php
Brazil
http://www.splink.org.br/index
Brazil
http://splink.cria.org.br/manager/detail?resource=BR&setlang=pt
Brazil
http://www.splink.org.br/index
Brazil
http://www.splink.org.br/index
Brazil
http://www.splink.org.br/index
Brazil
http://www.splink.org.br/index
Brazil
http://webdrm.cpqba.unicamp.br/cbmai/
Brazil
http://splink.cria.org.br/manager/detail?resource=CCGB&setlang=pt
Brazil
http://www.splink.org.br/index
Brazil
http://www.splink.org.br/index
135 NBIMCC
6
73
338
605
582
65
130
486
558
905
935
926
139
779
639
759
788
796
829
Bulgaria http://www.nbimcc.org/cabricat/Main.php
HER
Canada
http://www.phage.ulaval.ca/index.php?pageDemandee=search
UAMH
SGSC
CPCC
CICC
CCM
CNCTC
CAUP
CCBAS
CCALA
SCCAP
CELMS
VTT
HAMBI
CFBP
CRBIP/CIP
CIRM-Levures
ALGOBANK
RCC
Canada
Canada
Canada
China
Czech
Czech
Czech
Czech
Czech
Denmark
Estonia
Finland
Finland
France
France
France
France
France
http://www.devonian2.ualberta.ca/uamh/on-line_catalog.htm
http://people.ucalgary.ca/~kesander/catalogue.html
http://www.phycol.ca/search/node/
http://www.china-cicc.org/English/english.html
http://sci.muni.cz/ccm/index.html
http://www.szu.cz/cnctc/a/uvod.php
http://botany.natur.cuni.cz/algo/caup-list.html
http://www.biomed.cas.cz/ccbas/fungi.htm
http://www.butbn.cas.cz/ccala/index.php?page=se&st=as
http://www.sccap.dk/search/
http://www.miccol.ut.ee/385219
http://culturecollection.vtt.fi/
http://www.mm.helsinki.fi/mmkem/hambi/
http://www-intranet.angers.inra.fr/cfbp/recherche_e.php
http://www.crbip.pasteur.fr/onglet.jsp?tab=bact
http://genome.jouy.inra.fr/cirm/bdd/
http://www.unicaen.fr/ufr/ibfa/algobank/EN/catalogue/catalogue1.php
http://www.sbroscoff.fr/Phyto/RCC/index.php?option=com_dbquery&Itemid=34
879 LeishCryo France
Bank
917 CIRM-BP France
918
192
274
807
919
940
485
3
773
945
195
567
591
637
825
597
806
903
500
817
883
133
797
CIRM-BIA
SAG
DSMZ
CCAC
FSU
CCCryo
NCAIM
NCIM
MTCC
CRA-PAV
HUT
JCM
NIES
MAFF
NBRC/IFO
KCTC
KACC
CFGR
CDBB
LIH-UAM
CCMM
CBS
NCCB
http://www.parasitologie.univ-montp1.fr/catalogue_list.asp
http://www.tours.inra.fr/cirm_bp_eng/commander_une_souche/le_catal
ogue
France
http://jwsdp.jouy.inra.fr/Consult/exeRequete.jsp?cirm=gisilbia
Germany
http://sagdb.uni-goettingen.de/
Germany
http://www.dsmz.de/microorganisms/main.php?menu_id=2
Germany
http://www.ccac.uni-koeln.de/recherche.shtml
Germany
http://www.frc.uni-jena.de/stammsammlung.php
Germany
http://cccryo.fraunhofer.de/web/strains/
Hungary
http://web.uni-corvinus.hu:8089/NCAIM/frameset.jsp
India
http://www.ncl-india.org/ncim/catelogue.jsp?mid=29
India
http://mtcc.imtech.res.in/catalogue.php
Italy
http://www.collezionedimicrorganismi.com/index.cfm?cis=1#strt
Japan
http://home.hiroshima-u.ac.jp/hut/
Japan
http://www.jcm.riken.jp/JCM/catalogue.shtml
Japan
http://mcc.nies.go.jp/
Japan
http://www.gene.affrc.go.jp/databases-micro_search_en.php
Japan
http://www.nbrc.nite.go.jp/e/index.html
Korea
http://www.brc.re.kr/English/ekctc.aspx
Korea
http://www.genebank.go.kr/
Korea
http://genebank.riceblast.snu.ac.kr/
Mexico
http://micro500.cs.cinvestav.mx/
Mexico
http://www.histoplas-mex.unam.mx/index_i.html
Morocco
http://www.ccmm.ma/catalogue.htm
Netherlands http://www.cbs.knaw.nl/databases/
Netherlands http://www.cbs.knaw.nl/databases/
589 ICMP
New
Zealand
212 IAFB
Poland
914 CCBA
Poland
816 MUM
Portugal
906 ACOI
Portugal
342 VKM
Russia
596 IPPAS
Russia
768 IEGM
Russia
836 CCIBSO
Russia
412 CECT
Spain
32 CCUG
Sweden
603 UPSC
Sweden
651 FCUG
Sweden
475 VTT/CCTM Switzerland
59 BCRC/CCRC Taiwan
383 TISTR
Thailand
705 BBPP/DOA
Thailand
707 DMST
Thailand
783 BCC
Thailand
828 RSKK
Turkey
http://nzfungi.landcareresearch.co.nz/icmp/search_cultures.asp
126
128
134
137
154
http://kkp.ibprs.pl/
http://pasat.ocean.univ.gda.pl/~ccba/ipl.php?id=ba-cya
http://www.micoteca.deb.uminho.pt/
http://acoi.ci.uc.pt/
http://www.vkm.ru
http://www.ippras.ru/cfc/
http://www.iegm.ru/iegmcol/strains/index.html
http://www.rbcar.ro/catalogues.htm
http://www.cect.org/english/
http://www.ccug.se/
http://www-hotel.uu.se/evolmuseum/fytotek/
http://www2.dpes.gu.se/FCUGsrch.html
http://culturecollection.vtt.fi/ccdb/html?p=s
http://www.ccrc.firdi.org.tw/
http://www.biotec.or.th/tncc/tistr_dete.html
http://www.biotec.or.th/tncc/dbstore/DOAC_search.asp
http://www.biotec.or.th/tncc/
http://www.biotec.or.th/bcc/InternetSearch.asp
http://www.rshm.gov.tr/en/index.php?option=com_content&task=view&
id=34&Itemid=61
http://www.ncppb.com/ncppbsearch.cfm
http://www.mba.ac.uk/culturecollection.php
http://www.bio-aware.com/cabi/Defaultinfo.aspx?Page=Home
http://www.hpacultures.org.uk/collections/ecacc.jsp
http://www.hpacultures.org.uk/collections/nctc.jsp
NCPPB
FLY
NCWRF
ECACC
NCTC
UK
UK
UK
UK
UK
169
184
214
522
653
814
1
2
97
112
115
530
573
606
827
849
888
933
NCYC
NCPF
IMI
CCAP
NCIMB
NCPF
ATCC
UK
UK
UK
UK
UK
UK
USA
http://www.ncyc.co.uk/
http://www.hpacultures.org.uk/collections/ncpf.jsp
http://www.bio-aware.com/cabi/Defaultinfo.aspx?Page=Home
http://www.ccap.ac.uk/ccap_search.php
http://www.ncimb.com/search.php?parent=culture
http://www.hpacultures.org.uk/collections/ncpv.jsp
http://www.lgcstandardsatcc.org/ATCCCulturesandProducts/tabid/979/Default.aspx
CCMP
USA
https://ccmp.bigelow.org/search_strains
NRRL
USA
http://nrrl.ncaur.usda.gov/cgi-bin/usda/
ARSEF
USA
http://arsef.fpsnl.cornell.edu/mycology/ARSEF_Culture_Collection.html#
Catalogs
FGSC
USA
http://www.fgsc.net/scripts/catalog.asp
LMS
USA
http://www.carolina.com/
BGSC
USA
http://www.bgsc.org/
UTEX
USA
http://web.biosci.utexas.edu/utex/Search.aspx
CGSC
USA
http://cgsc.biology.yale.edu/
DSC
USA
http://www.dictybase.org/StockCenter/StockCenter.html
UCD-FST USA
http://www.phaffcollection.org/
VTCC
Viet Nam http://biotechvnu.edu.vn/vtcc/
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
The data standards compared:
- MINE Bacterial
- MINE Fungal
- CABRI / OECD MDS+RDS+FDS
- Darwin Core
- ABCD
- Straininfo
MINE
The Microbial Information Network Europe
1985 - 1993
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.
Group of fields in MINE standard
Field groups
Fungal
Bacterial
1
2
Name
Strain Administration
+
+
+
+
3
4
Status
Environment and history
+
+
+
+
5
6
7
Biological interactions
Sexuality
Properties
8
9
10
11
Genetics
Mutants, Plasmids and Phages
Growth conditions
Chemistry and enzymes
12
Practical applications
+
+
+
+
cytology,
morphological,
biomolecular cultural and chemotadata
xonomical data
+
+
+
+
+
+
+
+
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
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.
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
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
SEXST
Sexual behaviour
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
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
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
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
Fields in MINE Bacterial
A. Internal Administration
OT
EDI
EDM
ID
SEC
Organism type. B = bacteria; F = fungi; P = plasmids; Y = yeasts
Date of input
Date of latest update
Typist identification
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
C. Strain Administration
STN
Strain number in collection
OCC
Other collections numbers
EDR
Date of receipt
EDA
Date of accession
CORR Correspondence
SPINF Special information
CHK
Collection check
PRE
Preservation type
PREREM Remarks on preservation
PRELIT Literature on preservation
RESTR Precautions and restrictions
SUPPLY Form of supply
ADMREM Administrative remarks
D. Environment and History
HABI
ISOFR
LOC
Specific habitat. Indicates restrictions to substrates
Isolated from
Geographic location
COLL
Collector of sample
ISOL
Isolated by
ISOM
Isolation method
DET
Identified by
DEP
Depositor
HIS
History
NAMCH Name changes
ENHISLIT Literature on environment and history
ENHISREM Remarks on environment and history
E. Properties (morphological, cultural and chemotax-onomical data)
FSTR
WCONS
CINC
CHTAX
GRAM
KOH
AMPEP
STAIN
CELL
MOT
PIGM
GRWTHL
GRWTHS
Fine structure data
Cell wall constituents
Cell inclusions
Chemotaxonomical markers
Gram behaviour
KOH test
Aminopeptidase test
Staining reactions
Shape, arrangement and size of cell
Motility
Pigments
Growth characteristics in liquid media
Growth characteristics on solid media
QUADGER
Quantitative data on growth
RESTST Resting 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
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
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
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
I. Biological Interactions
SYMB
Symbiosis or synthrophy
PATH
Pathogenicity and virulence
ALLER
Allergenicity
TOX
Toxicity
ANT
Antagonistic activity
BINTLIT Literature on biological interactions
BINTREM Remarks on biological interactions
J. Practical Applications
APPL
TEST
CTR
PATENT
APLIT
APREM
General and industrial application
Applications in testing and assays
Procedures for control
Patent
Literature on applications, patents
Remarks on applications and patents
Example of field specification in MINE
Name
SUGC
Contents
Descriptions
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
Sugar
containing the values are separated by ",". If a
concentration 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
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
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
Accession number
Other collection numbers
Restrictions
Organism type
Name
Race
Status
Misapplied names/Other names
History of deposit
Conditions for growth
Form of supply
Isolated from
Geographic origin
Mutant
Sexual state
Literature
Infrasubspecific names
Serovar
Genotype
Pathogenicity
Enzyme_production
Metabolite_production
Applications
Remarks
Price_code
Catalogue_entry
Plasmids
FY
FY
FY
FY
FY
FY
FY
FY
FY
FY
FY
FY
FY
FY
FY
FY
M
M
M
M
M
R
M
R
M
M
M
R
R
R
R
R
FY
FY
FY
FY
FY
FY
FY
F
F
F
F
R
F
F
AcB
AcB
AcB
AcB
AcB
M
M
M
M
M
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
AcB
M
R
M
M
M
R
R
R
F
R
M
R
R
F
F
F
F
F
F
F
F
M
M
M
M
M
R
M
R
M
M
M
R
M
R
R
R
R
R
F
F
F
F
F
F
F
Darwin Core
http://rs.tdwg.org/dwc/, 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 http://rs.tdwg.org/dwc/terms/simple/index.htm
Darwin Core Terms: A quick reference guide http://rs.tdwg.org/dwc/terms/
Darwin Core (versions DwC 1.21, DwC 1.3 and DwC 1.4) makes a part of TDWG
group of standards.
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.
http://www.tdwg.org/activities/abcd/
1305 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
http://wiki.tdwg.org/twiki/bin/view/ABCD/AbcdConcepts.
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, E-mails, 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, 2002. Maps to Darwin Core 2: Longitude.
Example Value: 0762510W
Straininfo MCL 2.1 (2011)
http://www.straininfo.net/projects/mcl/reference.
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 http://www.straininfo.net/projects/mcl/reference
and http://www.straininfo.net/projects/mcl/ are quite sufficient for this job.
Comparison of the standards.
Fragment of the table
ABCD
.../Serovar
.../MycologicalLiveStage
.../Temperature
0
1
1
0
0
0
0
1
0
MINE F
SERO
SERO
SEX
NSOR
STAT
PRE
TKIT
>CONDL
<TOX
MINE B
1
1
1
1
1
1
1
1
1
SVAR
NSOR
STAT
PRE
TKIT
<TOX
Real
0
1
0
1
1
1
1
0
1
Darwin Core
Serotype
Serovar
Sexual state
lifeStage
Sole Sources of Nitrogen
Status
typeStatus
StorageMethods
Strip test
Temperature
Toxicity
0
0
1
0
1
0
0
0
0
Comparison of the standards.
Final results
ABCD
MINE B
MINE F
OECD
DwC
Straininfo
Compliance with Real
24(252)
26%
71
76%
81
87%
50
54%
31
33%
20
22%
Related to CC
19%
55%
72%
100%
17%
19%
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
Results of comparison
ABCD
MINE B
MINE F
OECD
DwC
Straininfo
Combined
Compliance with Real
24(252)
26%
71
76%
81
87%
50
54%
31
33%
20
22%
93
100%
Related to CC
19%
55%
72%
100%
17%
19%
100%
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
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
Genetic data standards
The International Nucleotide Sequence Database Collaboration (INSDC,
http://www.insdc.org) includes:
- GenBank - the National Center for Biotechnology Information - NCBI, USA
http://www.ncbi.nlm.nih.gov/genbank/
- EMBL-Bank at the European Molecular Biology Laboratory
http://www.ebi.ac.uk/embl/
- DDBJ - the DNA Data Bank of Japan, Japan http://www.ddbj.nig.ac.jp/
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
http://gensc.org/gc_wiki/index.php/Main_Page) in 2008 - 2011 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)
In the project "MIGS/MIMS Structured Comment" GSC is also working with
INSDC to develop a way to submit these data standards to DDBJ/EMBLBank/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, humanoral, 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.
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
15%
and Hygiene (ICFMH-WPCM).
8%
6%
26%
41%
medical devices and health
environments
Foodstuffs
Water quality
industrial production
Cosmetics
4%
DB for Microorganisms in Extreme Environment
Volcanic
Hot spring
Volcanic salt and alkali lakes
DB for Microorganisms in Extreme Environment
Physiological
and
biochemical
properties
Isolation
•
•
•
•
•
•
Temperature
Humidity
PH value
Elevation
Vegetation
Date
Data
base
Application
• Usage
• Industry use
• Medium
• Culture
conditions
• Biochemical
reactions
• Metabolites
Sequences
•
•
•
•
Information sharing to resources sharing
Get benefits according to CBD
Strains even outside of CCs
For both scientific and industry users
• Sequence
• Genome
• Annotation
中国科学院微生物研究所
• CODATA Task Group on Advancing Informatics
for Microbiology (TG-AIM)
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
Участник
Страна
DSMZ
DE
CABI
UK
IP
FR
SPP-PS
BE
KNAW/CBS
NL
UGOT
SE
UVEG-CECT
ES
UGENT
BE
INRA-CIRM
FR
JacobsUni
DE
UMinho-MUM
PT
MUT
IT
CSIC-IMEDEA
ES
VKM
RU
IAFB-CCIM
PL
USMI
IT
Благодарю за внимание
Василенко Александр
[email protected]