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INFORMATION SYSTEM THAT
MEET THE CHANGING DEMANDS
Traditional microbiology
Molecular biology
Gene and
Genome
Systematic
biology
Synthetic
biology
Microorganism Microbiome
mangrove soil South-East Asian stingless bee
highly acidic swamps in South-East Asia Sulfate soil of Vietnam
IMBALANCE OF INFORMATION
LEVEL
a large number of collections lag behind
in digitization, largely because of the
lack of facilities and human resources.
According to statistics presented by
CCINFO, of 708 registered culture
collections, only 60 of them have
published online catalogues and only 96
of them have their catalogue
computerized.
A desirable information system
For users
Feedback from a survey of 60 European
Culture Collections’ Organisation (ECCO)
culture collection curators and their users
carried out in Spring 2013
For culture collections
Improved and reliable metadata
Improvement in search range and detail
Improved interoperability between
databases
harmonization of Standard Operating
Procedures (SOPs), data
structures and software tools.
Reference
strain
ABC Data mining tools and database
GCM
Strain data retrieval, analysis, and
visualization system CCINFO Metadata,
Strain
number
and
species
name list
Culture
Collections
Publication Patent Genome Nucleotide sequence
Strain
Catalogue
Strain number species name
Strain number species name
Academic
and user
communitie
s
A system-level overview of the WDCM databases
OUTLINES
CCINFO
WDCM data standards
Global Catalogue of Microorganisms 1.0
Species Name Services
Analyzer of Bioresources Citation
Global Catalogue of Microorganisms 2.0
CCINFO
Improved and reliable metadata
The necessary process to become WFCC member collections
Unique ID for Culture
collection
The World Directory of Culture Collections
The total amount of strains in the 642 culture collections
all over the world is 2, 222, 463. Bacteria: 1, 004, 994;
Fungus: 607,129, Virus: 24,969; Cell line: 30,216.
45%
27%
2% 1%
25%
The distribution of global
inventory
bacteria
fungi
virus
Cell line
Ohters
NO. Country Culture
Collections Preserved
strains 1 Japan 25 246，343 2 U.S.A. 23 221，556 3 India 27 215，770 4 Brazil 64 166，629
5 Korea (Rep. of) 21 134，902
6 China 25 112，179 7 France 39 91，385
8 Netherlands 6 90，775
9 Denmark 3 88，566 10 U.K. 19 84，010 11 Australia 34 82，246 12 Canada 18 77，868 13 Taiwan 2 67，526
14 Russian Federation
22 60，281
15 Belgium 7 55，142 16 Sweden 3 52，700 17 Germany 13 52，151 18 Thailand 59 43，106
19 New Zealand 7 24，447
20 Armenia 1 17，805
Top 20 countries of microbial resources inventory
Status of culture collections: Holdings
WDCM data standards
Harmonization of data structures and software tools
JCM NBRC CBS DSMZ
WDCM Recommended datasets
Biochemistry
package
Environment
package
Application
package
Sequences information
package
Data format diversity in different culture collections
ATCC
JCM
NBRC
CBS
DSMZ
BCC
…
Strain number、Name、Organism type、 Date of deposition、History 、isolated from、Geographic origin、Condition for growth、
Other collection numbers、Application、Reference
WDCM minimum datasets
Indexing
System
Isolation
source
Original
Location Application
WDCM recommended datasets
Environment package
Application package
Sequence information package
Biochemical and Physiological package
OECD Guidelines
Darwin core
MCL
JSCC
ABRCN
EBRCN
CABRI
….
GCM integrated all the
standards and established a
new Minimum Data Sets
standard and Recommended
Data Sets.
A software package based on
the data sets was developed
and distributed freely to culture
collections.
Current progress
ISO TC 276 BIOTECHNOLOGY
Creation date: 2013
Secretariat: DIN
Participating Countries：30
Observing Countries：14
ISO standards under development: 16
WG Title
WG1 Terminology
WG2 Biobanks and Bio-Resources
WG3 Analytical methods
WG4 Bioprocessing
WG5 Data processing and integration
• WD 21710 Microbial resources data specification on data management and publication in microbial resources center (By Dr. Juncai MA)
OUTLINE OF THE MICROBIAL
STANDARD
Data management and publication in microbial resources
center
1 In-house data management
• Database management system
• Data management for deposition of microbial resources.
• Data management for preservation of microbial resources
• Data management for distribution of microbial resources
• Data quality control
2 Online catalogue
• Unique identifier of microbial resources
• Minimum and recommended data fields of online catalogue
Standard Operating Procedure for the World Data Centre for Microorganisms Reference Strain Catalogue
7. Dissemination of data
6. Maintenance and update
5. Entry into catalogue
4. Allocation of WDCM strain number
3. Authorisation
2. Details checked
1. Request received by WDCM Bacterial or fungal strains to be considered for inclusion
in the WDCM database must have been deposited in at least two collections with Affiliate status with the WFCC
Nominations for new strains will only be received from ISO, member bodies of or constituent bodies of the IUMS
Any WFCC Affiliate Collection member may nominate strains that are proven lines of strains already existing in the WDCM reference strain database to be included in a database entry. It is the responsibility of the Affiliate Collection member to ensure that the characteristics of the proposed strain from their collection agree with those of the strains already listed.
New strain linkages i.e. culture collection strains that are linked to existing entries in the database require approval by the WDCM RSSG.
Unique WDCM strain numbers will be allocated through by the WDCM and will generally be allocated sequentially as the strains are authorised for inclusion.
Contents Page
Foreword iv
Introduction v
1. Scope 1
2. Normative reference 1
3. Terms and definitions 1
4. Principle 2
5. Safety precaution 2
6. Reference fungi 3
7. Apparatus 3
8. Reagents and culture media 5
9. Fungus preservation and use 8
10. Spore suspension 9
11. Preparing ATP calibration curve 12
12. Testing method 13
13. Measurement of luminescence
intensity 15
14. Calculation 17
15. Test report 18
Annex A 19
Annex B 20
Bibliography 21
ANTIFUNGAL ACTIVITY TESTING
METHOD
ISO/FDIS 13629-1
ISO/FDIS 13629-1 ANTIFUNGAL ACTIVITY TESTING METHOD
WDCM number Species Preservation No.
00144 Aspergillus niger
ATCC 6275 UMIP 2475.98 DSM 1957 NBRC 105649
00189 Penicillium citrinum
ATCC 9849 NBRC 6352
00190 Cladosporium cladosporioides
ATCC 11277 NBRC 6368 NBRC 6348
00191 Trichophyton mentagrophytes
NBRC 32409 NBRC 32412
The utilization of WDCM reference strains according to ISO standards
count total
Food manufacture and security 25 Milk and milk products 55 157 Microbiology of food and animal feeding stuffs 77 Biological evaluation of medical devices 2 Dentistry 1 Washer-disinfectors 12 Sterilization of health care products 26 Surgical drapes, gowns and clean air suits, used as medical devices 6 99 Retrieval and analysis of surgical implants 1 Optics and optical instrument 10 Medical laboratories 5 Clinical laboratory testing and in vitro diagnostic test systems 28 Modification of the isolation media and the haemolysis test 6 Cleanrooms and associated controlled environments 2 Water quality 57 57 Textiles 10 Lubricants, industrial oils and related products 3 Chemical analysis of refractory products by XRF 1 32 Plastics 17 Safety of machinery 1 Cosmetics 22 22 Indoor air 11 Soil quality 4 15
26%
4% 41%
15%
8% 6%
medical devices and health
environments
Foodstuffs
Water quality
industrial production
Cosmetics
WDCM Reference Strain Catalogue
OUTLINES
CCINFO
WDCM data standards
Global Catalogue of Microorganisms 1.0
Species Name Services
Analyzer of Bioresources Citation
Global Catalogue of Microorganisms 1.0
Improvement of resources accessing
Search GCM by Strain Name and Strain Number
Filtering search result and customizing the output format
Search results
Link to Species page
Formats to display the search results
Link back to original site
GCM Strain Page: Exploring global knowledge about a strain
Exploring information about a species
Publications related to the strains
Exploring information about a species
Publications related to this species
Advanced search interface
Display the table of isolation sources
Display the Geographic origin of strains
Advanced search interface
Searching results of sequence similarity
Searching strains by publications and patents
128,914 papers in paper database now, 1 M papers will be available soon
Searching results by publications and patents
The original isolation places of the strains in GCM
Asia: 44 Africa: 46 Europe: 42
North America:17 Oceania:9 South America:13
Total: 171 countries and regions
Global access to GCM
Login from
GCM site
http://gcm.wfcc.info/
Statistic summary could be displayed after
catalogue information uploaded
Automatic ABC (Analysis of Bioresources Citation) data mining results, data
could be further refined after catalogue information uploaded
Strain catalogue information could be added and edited here
Strain catalogue information could be added here one by one or imported on batch
Sub user accounts could be created here for editing or viewing the data
Create Excel Template
Species Name check services
Improvement of data quality
Analyzer of Bioresource Citation
How the resources were used?
Analyzer of Bio-resources Citation
How many Papers, Patents, Sequences, Genomes are
published worldwide using my microbial strains?
BRCs distribute many microbial strains per year.
It is our great contributions from WFCC collections.
——
-- An data mining tools to trace and explore utilization of microbes
Global contributions from the collection
Web service
Solr
Patent Journals Genome Nucleotide
sequence
Remove false positive
Information Crawling
Regular expression（Acronym of culture collection） +
number／Species name
GCM data provider
Remove duplication
Figure 3: ABC data mining working flow
Japan Collection of Microorganisms(JCM)
Paper
Patents
China - Japan MOST joint cooperation project in 2015
0
10000
20000
30000
40000
50000
60000
70000
The amount of papers about preserved strains in different countries
The countries ranking based on the amount of journals published related to the utilization of strain resources. Top five are USA, Japan, England, France and Brazil; China is ranked 25th with a total of 1273 papers. This indicates that China still need to improve the research of microbial resource utilization compared with its holdings
U.S.A
U.K Japan France Braz
il
Unpublished data (Permission required)
The amount of patents for preserved strains in different countries
The ranking based on the amount of patents for utilizing strain resources. Top five are USA, China, Korea, Japan and Germany. China is ranked second with a total amount of 2125 journals which demonstrates China’s capability in this field.
0
1000
2000
3000
4000
5000
6000
U.S.A
Japan
China
Korea(Rep.of
) Germany
Unpublished data (Permission required)
ANNUAL INCREASES OF PATENTS
OF THE TOP 4 COUNTRIES
The most popular strains in the world
Strain Name
TotalIF Patents Nucleotide Paper Count
ATCC 13032 1345.16 298.00 1.00 408.00
ATCC 6538 752.69 177.00 5.00 421.00
ATCC 13869 166.30 129.00 0.00 53.00
ATCC 6633 2467.50 120.00 38.00 857.00
ATCC 29213 4365.55 104.00 5.00 1118.00
ATCC 14067 112.54 102.00 0.00 53.00
ATCC 25922 6986.14 100.00 2.00 2297.00
ATCC 10231 673.78 90.00 23.00 352.00
DSM 5715 6.99 77.00 0.00 2.00
ATCC 8739 536.53 76.00 7.00 211.00
ATCC 25923 3221.92 63.00 4.00 1289.00
ATCC 13870 3.83 58.00 0.00 1.00
ATCC 6872 112.88 57.00 13.00 49.00
ATCC 9027 500.57 57.00 3.00 187.00
NCIMB 40771
8.60 53.00 0.00 2.00
ATCC 14020 10.42 53.00 0.00 5.00
ATCC 21 65.09 52.00 0.00 15.00
ATCC 27853 3518.58 52.00 10.00 1220.00
ATCC 43504 984.34 50.00 5.00 271.00
ATCC 6538P 390.59 48.00 0.00 136.00
Patents
Strain Name
TotalIF Paper Count
Nucleotide Patents
ATCC 25922 6986.14 2297.00 2.00 100.00
ATCC 25923 3221.92 1289.00 4.00 63.00
ATCC 27853 3518.58 1220.00 10.00 52.00
ATCC 29213 4365.55 1118.00 5.00 104.00
ATCC 6633 2467.50 857.00 38.00 120.00
ATCC 29212 2523.79 746.00 1.00 41.00
ATCC 6538 752.69 421.00 5.00 177.00
NCTC 11168 1411.63 413.00 0.00 7.00
ATCC 824 1428.81 410.00 0.00 28.00
ATCC 13032 1345.16 408.00 1.00 298.00
ATCC 49619 1749.11 408.00 7.00 29.00
ATCC 14579 1312.54 380.00 6.00 13.00
ATCC 33277 986.61 355.00 0.00 23.00
ATCC 10231 673.78 352.00 23.00 90.00
NCTC 8325 1325.19 351.00 0.00 7.00
ATCC 9341 1173.19 346.00 0.00 23.00
MUT 3 1441.84 338.00 0.00 8.00
NCTC 11637 730.44 320.00 0.00 13.00
ATCC 22019 1281.85 315.00 5.00 6.00
NCTC 109 1819.05 302.00 0.00 3.00
Papers
Global catalogue of Microorganisms 2.0
From Catalogue data to Omics data
LIST OF TYPE SPECIES AND TYPE STRAINS
LIST OF TYPE SPECIES AND TYPE STRAINS
LIST OF TYPE SPECIES AND TYPE STRAINS
Cooperation through a international
network
WDCM International partners
泰国BCC 俄罗斯VKM 泰国TISTR
马来西亚UPM 葡萄牙Minho 印度尼西亚LIPI
WDCM training courses
Beijing, 2012 Beijing, 2014
Malysia, 2013 Thailand, 2014
3 training courses, more than 100 participants all over the world
ACKNOWLEDGEMENT
WFCC board members
Culture collections and international network
International colleagues
The team of WDCM
