GCM 2.0 Type Strain Sequencing Project - World Data Centre ... WDCM updates new.pdf · GCM-10K type...

The 8th WDCM Symposium on

GCM 2.0 Type Strain Sequencing Project

November 21-22, Beijing, China

Program

1. Keynote speech

2. Culture collection activities

3. Roadmap of the GCM 2.0

4. CBD, IP & legal issue

5. SOPs

6. Data annotation, data publication and

data platform

The past, now and future

WFCC – WDCM

Juncai MA Institute of Microbiology, Chinese Academy of Sciences

The Global Catalogue of Microorganisms(GCM)

United Nations Educational，Scientific

and Cultural Organization International Union of

Biological Sciences International Union of

Microbiological Societies

MICROBIAL

RESOURCES CENTRES

MIRCEN UNESCO

The culture collections Worldwide

Collections: 763

Countries/Regions: 76

Staffs: 6,189

Online catalogues: 336 According to WDCM CCINFO Database on November 20, 2018

WDCM Catalogues

Global Catalogue of Microorganisms

in 2012

Started

The first collection in GCM is

Joined on January 30, 2012

Japan Collection of Microorganisms(JCM)

Global Catalogue of Microorganisms 1.0

Strains：426,210 Species : 52,960

Culture Collections：125

Countries and regions：47

The Great Contributions from 124 collections

Papers: 75,574

Patents: 61,114

Sequences: 272,206

Genome: 3,298

Global Catalogue of Microorganisms(GCM)

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

GCM can help to

access microorganisms and

its global knowledge

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

GCM can provide

the value added services

for the different data providers

Vietnam Type Culture Collection

1,000 strains

GCM make unavailable strains

accessible

Create Excel Template

Strains data management Strains data search

40 collections created their online catalogues

International Name databases:

• Species 2000

• NCBI Taxonomy

• LPSN

• MycoBank

• DMSZ

WDCM Data Quality Check for Scientific Names

GCM helps culture collections

Monitoring the utilization of

their microorganisms

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

Genome info species taxonomy Nucleotide Sequence

KEGG Gene

KEGG Metabolic PATHWAYS

Enzyme Reaction Data

Publications Patents Data

CDS info

Pfam PDB GO

EC

Strain Catalogue

WDCM Big Data System

Japan Collection of Microorganisms(JCM)

Paper

WDCM GCM is a open network

Global access to GCM

GCM provide services

for CBD national focal points

COP 12 in Korea, Sep 2014

A global information platform for accessing, tracking, monitoring and benefit

sharing of microbial resources

Pandemic Influenza Preparedness

Framework for the sharing of

influenza viruses and access to

vaccines and other benefits

194 Member States joined

The WHO PIP Framework

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 Bioresources

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)

WDCM Symposiums and workshops

WDCM 1 in 2011

WDCM 5 in 2015

WDCM 2 in 2012 WDCM 3 in 2013

WDCM 50th Anniversary in 2016

WDCM 4 in 2014

WDCM 7 in 2017 WDCM in 2018

WDCM Training Course

2012 in Beijing 2013 in Malaysia 2011 in Beijing 2014 in Beijing 2014 in Thailand

2016 in Beijing 2015 in Indonesia UNESCO 2017 in Thailand 2017 in Beijing

The Participants for WDCM training courses

The great supports for training from Chinese Academy of Science

Participants: >100

Countries: 26

WDCM Global Nodes System

BCC in Thailand VKM in Russia TISTR in Thailand UPM in Malaysia Minho in Portugal

LIPI in Indonesia

• European CC organization

• Korean Network for RRC

• Thailand BRC

• Chile Network for CCs

• Kansas State University

(KSU)

The MOUs with regional and national networks

BGI WFCC ECCO MIRRI ISO276 DOE JGI CODATA

WDCM 50 Years Anniversary

September 6-8, 2016, Beijing

References of GCM

IF 4.04

Nucleic Acids Research 2019 Nucleic Acids Research 2017

BMC Genomics

GCM-10K type strain genome sequencing project

GCM I S C O M I N G

China cover the costs for sequencing services, database system and data analysis

Raw data and analysis results are published online for free access.

Call for strains and samples from culture collections and scientists with a targets for a

specific subject researches.

• 10,000 bacteria, archaea and fungi type strains

• 1,000 Microbiome samples

The 7th WDCM Workshop October 12-13, 2017, Beijing

Organized by:

Institute of Microbiology, CAS

World Federation for Culture Collections (WFCC)

European Commission

Supported by:

Bureau of Science & Technology for Development, CAS

Department of General Administration, CAS

Bureau of International Co-operation, CAS

National Science and Tech Infrastructure Center, MOST

• ATCC, USA

• BCCM/LMG, Belgium

• BCRC, Chinese Taipei

• CAIM, Mexico

• CBS, Netherland

• CCM, Czech

• CCUG, Sweden

• CECT, Spain

• CICC, China

• CIP, France

• CGMCC, China

• FGSC, USA

• ICMP, Netherland

CULTURE COLLECTIONS CONFIRMED

• JCM, Japan

• KCTC, Korea

• KMM, Russia

• MUM, Portugal

• NCTC, UK

• NBRC, Japan

• NCAIM, Portugal

• PCU, Thailand

• TBRC, Thailand

• TISTR, Thailand

• UCD-FST, USA

• VKM, Russia

The collections can

provide DNA or cultured

cell sample

The 25 collections from 16 countries and regions

More than 300 species were sequenced

WORKING GROUPS

1. Bacteria Selection

2. Fungi Selection

3. SOPs

4. Database

5. Intellectual Property Right and Legal Issue

Standard data analysis pipeline MOU & MTA template

SOP for Sample preparation and submission

Prof. Martin Blaser from New

York University:

It is a very good place to start, a

very worthwhile project.

PROJECT PROGRESS

Science News 1445-1446, 30 March 2018 • VOL 359 ISSUE 6383

22 March 2018 online

New Global Cooperation Mechanisms

Sequencing platform

Data sharing platform

Global Network

Resources

Providers Scientists

WDCM

Sequencing Capacity

Sequencers(295+)

BGISeq-500 Illumina/HiSeq Illumina/MiSeq AB/3730xi Roche/454

PacBio RSⅡ Sequel Bionano Irys System Life Tech/Ion Torrent

Sequencing Capacity：>30 Tb / day

BGI has the largest sequencing capacity in the world.

Dr. Linhuan WU

2017 WDS Data Stewardship Award International Data Week 2018 (IDW 2018) on Nov 7, 2018

CAS Microbiome Project

3 Banks:

Sample Bank\Strain Bank\Data Bank

Data analysis

Data standards

Data Management

• Metadata description

• SOP

• Data quality control

• Data storage services

• Data management and

publication

• Data submission

• Reference databases

• Algorithm and model

• Analysis pipelines

综合信息平台

Genetic Bio-Resource

Biodiversity monitoring

network Herbarium Botanical

Garden

Laboratory Animal 6,728,055 120,096 25,538 1,367 15,832

CAS Biological Resources Service Network

Near 7 million data online

Big Earth Data Science Engineering Project

USD 230 M

2018：25 CCs in GCM 2.0 today!

2017：GCM 2.0 started!

2016：100 CCs in GCM 1.0

2015：GCM for CBD workshop

2014：GCM side event in CBD COP 12

2013：ABC started!

2012：GCM 1.0 started, 36 CCs!

2011：Inauguration ceremony

2010：IMCAS became new host of WDCM

The milestone of WDCM in China

1.Great international supports & Cooperation

2.Financial supports from multiple sources

3.Flexible human resources

4.Enough working space: server room & office

Great Operating Mechanism

Great Operating Mechanism

11 floor, 30,000 M2

• Bridge

• Forum

• Knowledge base

• Match the needs from different users

• GCM for microbiological Laboratories

The future of WDCM

Acknowledgement

• The great contributions from WFCC and culture collections worldwide

• The strong supports from CAS and MOST etc

• The hard works of my team

The 124 culture collections in GCM