Information platform to promote

Access and Benefit sharing of

Microbes under NP

——Global Catalogue of Microorganisms (GCM)

World Data Center for Microorganisms

Juncai Ma & Linhuan Wu

OUTLINES

1. Brief background of WDCM

2. An integrated information platform for Accessing ,Tracking,

monitoring and benefit sharing of microbial resources

CCINFO: Unique Identifier of CCs and Strains

Global Catalogue of Microorganisms: catalogue for accessing

Analyzer of Bio-resources citation: Tracking of utilization

Reference strain database: Commercial utilization of microbes

3. Some considerations

WFCC-MIRCEN WORLD DATA CENTRE FOR MICROORGANISMS

MICROBIAL

RESOURCES

CENTRES MIRCEN

UNESCO

An integrated information platform for Accessing ,

Tracking, monitoring and benefit sharing of microbial resources

Reference strain

database

ABC Data mining from

Publications, patents…

GCM, 29 countries

60 CCs, 288 190 strains

WDCM data warehouse

Big data of microorganisms

CCINFO

Metadata, GUID

Culture

Collections

Registration in WFCC and CCINFO

Online catalogue and data management system

Monitoring of strain transfer and utilization

National

Focal point

Academic and

industrial

users

GUID and Strain tracking system

By 2nd September, 2014

671 culture collections from 70 countries

CCINFO DATABASE——METADATA OF CC

Unique ID for Culture collection

Global Catalogue of Microorganisms

Microbial resources

Publication and patents Nucleotide, protein and genome

Bioinformatics tools

WFCC GLOBAL CATALOGUE OF MICROORGANISMS (GCM)

The objectives of the Global Catalogue of Microorganisms are

- to help all culture collections to get their data digitalized and

accessible online

Attractive for scientific use

- to connect these strain catalogue information with corresponding

nucleotide and protein sequences, as well as genome sequences and

reference citations.

- to create a comprehensive database and information retrieval, analysis

and visualization system for microbial resources. “Trust，April 2014”

What are the incentives for GCM users?

Now 60 CCs from 29 countries join GCM

Search GCM by Strain Name and Strain Number

Link back to original site

Exploring information about a strain

Advanced search interface

Search results

Filtering search result and customizing the output format

Formats to display the search results

Link to Species page

Display the search result in a list of culture collections

Display the table of isolation sources

Exploring information about a species

Publications related to the strains

Exploring information about a species

Publications related to this species

Species information

Patents related with this species explored by ABC

Adding your own comments

Display the Geographic origin of strains

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

DBMS for culture collections

Provides:

In-house data management

Homepage

Online Catalogue

Choose data items according to your own catalogue items

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 minimal 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

….

Import your data in EXCEL file

Export an EXCEL template for data management

http://gcm.wfcc.info/383

http://gcm.wfcc.info/TISTR

NAME CHECK FOR DATA QUALITY CONTROL

Organism type Species

Names Un-matched species

Name Percentage of Un-

match

Archaea 1399 32 2.30%

Microalgae 1457 360 24.70%

Fungi 20719 698 3.40%

Bacteria 12855 1098 8.50%

Total 36430 2188 6.00%

Linhuan, W.; Global catalogue of microorganisms (gcm): a comprehensive database

and information retrieval, analysis, and visualization system for microbial resources

http://abc.wdcm.org/

ABC – DATA RESOURCES

Dates

In Resource

Journal Paper Patent

Derwent Innovations IndexSM

1963~ --- --- >3 million

PubMed 1940~ >25,000 >22 million ---

Highwire 1953~ 1,774 >2 million ---

Web of science 1900~ ~10,000 >40 million ---

NEW FUNCTIONS IN ABC

--DYNAMIC STATISTICS FOR EACH

CULTURE COLLECTION

ABC

ABC

ABC – DATA RESOURCES

Derwent Innovations

IndexSM Patent database for potential commercial

use

PubMed & Highwire

Publication database for academic use

NCBI & PDB & KEGG Bioinformatics database for academic

use

Google

thomson reuters ?

Commercial use

国际标准化组织 ISO (International Organization for Standardization)

112

46

4

• ISO covers 162 countries and areas.

• Up to now, ISO developed 19,500 standards, 3,958 are in biological field.

• 350,000 companies are using ISO standards.

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

ISO/FDIS 13629-1

ANTIFUNGAL ACTIVITY TESTING METHOD

WDCM ID for ISO strains

ISO Standard Related to Microbiology

STATISTICS FROM WDCM

DATABASE AND WDCM

REPORTS

642 culture collections from 73 countries have registered in CCINFO. The ranked top six countries based the amount of culture collections are Brazil (64), Thailand (59), France (39), Australia (34), India (27) and China (25).

Status of culture collections: distribution

Data was generated from CCINFO, May 21, 2013

0

10

20

30

40

50

60

70

Arg

entina

Austr

alia

Bela

rus

Bra

zil

Ca

nad

a

Ch

ina

Cu

ba

De

nm

ark

Egypt

Fin

land

Germ

any

Ho

ng K

on

g

India

Iran

Isra

el

Japa

n

Kore

a (

Re

p. o

f)

Ma

laysia

Mo

ngo

lia

Ne

therl

and

s

Nig

eri

a

Pakis

tan

Phili

ppin

es

Port

ug

al

Ru

ssia

n F

ed

era

tion

Sin

gapo

re

Slo

ven

ia

Spain

Sw

ede

n

Taiw

an

Turk

ey

U.S

.A.

Ukra

ine

Vene

zu

ela

Yugo

sla

via

Brazil

France Australia

India

Thailand

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

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)

0

5000

10000

15000

20000

25000

30000

The amount of strains found in published papers in different countries

The countries ranking according to the amount of strain resources

found in published papers. Top five are USA, Japan, Belgium, Germany

and England; China is ranked 18th with a total of 1561 strains.

U.S.A

Japan

Belgium U.K Germany

Unpublished data (Permission required)

Data was generated from ABC, May 21, 2013

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

COUNTRY COVERAGE

OF PATENTS

PLATFORM FOR SERVICES

PLATFORM FOR COOPERATION

Academic and industrial users

Large collections

Small collections

Integrated Knowledge base of

Microorganisms

Flexible and user-friendly search

interface

Database management system

Lists of publications and statistic reports

Training courses and symposium

WDCM Global Nodes System

September 14, 2012 MOU with BCC in Thailand

June 19 , 2013 MOU with VKM in Russia

January 13, 2012 MOU with TISTR in Thailand

September 30, 2013 MOU with UNiCC in Malaysia

WDCM Symposiums

and Training Course

WDCM Symposiums

WDCM 1: May 17-18, 2011

WDCM Workshop May 23-25, 2013

WDCM 2: June 7-8， 2012

WDCM 3: September 26, 2013

WDCM Training Course on Management and Application of Microbial Data

(Every year)

Hosted By:

WFCC-MIRCEN World Data Center for Microorganisms (WDCM)

Organized By:

World Federation for Culture Collections (WFCC)

United Nations Educational, Scientific and Cultural Organization(UNESCO)

Asian Consortium for Conservation and Sustainable Use of Microbial Resources (ACM)

Asian Network for Research Resource Centers(ANRRC)

Biological Resources Center, Institute of Microbiology, CAS(IMCAS)

Research Network for Applied Microbiology, Chinese Academy of Sciences (RNAM)

Supported By:

Bureau of International Cooperation, Chinese Academy of Sciences(BICCAS)

The Committee on Data for Science and Technology (CODATA)

WDCM Symposiums and Training Course on Sep 1-15, 2014

19 trainees from 8 countries

14 teachers from 5 countries

WDCM Training courses With UNiCC in Malaysia，2013

WDCM Training courses with TISTR in Thailand，2014

36 participants from domestic universities and organizations

WDCM databases and databases management system for culture collections

Presentations, demonstration and practice

Training courses 2014 in Beijing .

Asia: 8 Africa: 4 Europe: 1

North America:1 South America:3

Total: 21 trainees from 17 countries

SEVERAL CONSIDERATIONS

Efficiently monitoring the utilization of genetic resources (Article 17)

To create a viable, cost-effectiveness, and expeditious system (Article 8)

The best way to achieve ABS with effective socio-economic profit is to build on

existing procedures, to make the appropriate linkages between the various actors,

provide the necessary incentives to the users so that ABS is effectively more

beneficial to all and does not require coercive measures or penalties.

Recommended by “Trust 2014 April”

Deploy one or several prototype tracking systems to validate underlying concepts

and refine critical elements that will be needed in a fully operational system.

Recommended by “Studies on Monitoring and Tracking Genetic Resources by G.M.

Garrity et at.

SOME IDEAS ON CONNECTING WITH CHM

Developing and utilizing GUID of

Microorganisms in WDCM system

Prototype of information system of

Microorganisms

Links to CHM and National focal point

Culture

Collection B

Culture

Collection A

Country A Country B

National Focal Point

ABS-CHM

1

2

5

1. A IRCC is issued by National Focal point to the sampling

2. When organisms are identified and deposited to a registered culture collection, a IRCC number is necessary to be

filled in the accession form.

3. At the same time, a GUID is to be obtained from Global Catalogue of Microorganisms(GCM)

4. GCM will send the information to the NCA along with its IRCC number , and with a copy to the ABS CHM.

5. The GCM would publish the microorganisms with GUID and other necessary information, which allow the further

tracking of the transfer and utilization of the microorganisms.

5

3

4

4

A Persistent identifier system could be used for GUID which allow unique

identification of microorganisms and also their related documents

(PIC,MAT)

Possible solution

GCM

WDCM WOULD LIKE TO PROVIDE

Investment in hardware and maintenance of servers and

computers

Utilization of publication and patent databases

Maintenance on the Persistent identifiers system for GUID

Software development and database management

Organizing workshop and expert working group

Necessary training for ICT staff

Thanks for your attention!