The 8 th WDCM Symposium on GCM 2.0 Type Strain Sequencing Project November 21-22, Beijing, China
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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
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