WFCC Global Catalogue of Microorganisms (GCM) Introduction. World Data Center of Microorganisms(WDCM)

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1 WFCC Global Catalogue of Microorganisms (GCM) Introduction World Data Center of Microorganisms(WDCM)

2 Outlines 1 Rectangle graphics Part 1: GCM: mission, functional architecture and progress Part 2: Minimum and Recommended Data Sets Part 3: GCM for the data users Part 4: GCM for the culture collections

3 WFCC Global Catalogue of Microorganisms (GCM) An initiative launched by the World Data Center for Micro-organisms For culture collections: a reliable and user-friendly system to help culture collections to manage, disseminate and share the information related to their holdings. For scientific and industrial data users: supports them by integrated database and tools with a simple and flexible user interface.

4 Microbial Cloud CCINFO WFCC Global Catalogue of Microorganisms (GCM) ABC datamining Research community: SNS/Video conference Microbial Resources Data Warehouse Common Data standards ABC DBMS Literature Sequenc e Patents ISO Training Collections Regional network Collections

5 Contributions and benefits of CCs Contributions Benefits Catalogue information in XML, Excel, Mysql file. Further cooperate with WFCC WDCM for industrial application of microbial resources WFCC Global Catalogue Promote visibility Provide online catalogue for CC Provide data management services for small CC Provide platform for data and resource exchanges Benefits from industrial application of strains Training

6 Homepage: gcm.wfcc.info

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8 Overview 1 Rectangle graphics Part 1: GCM: mission, functional architecture and progress Part 2: Minimum and Recommended Data Sets Part 2: GCM for the data users Part 3: GCM for the culture collections

9 WDCM MDS is composed of 15 fields. The input files could be either EXCEL or XML.

10 Overview 1 Rectangle graphics Part 1: GCM: mission, functional architecture and progress Part 2: Minimum and Recommended Data Sets Part 3: GCM for the data users Part 4: GCM for the culture collections

11 eoffice Solution Planning strain number/name Advanced Search By Culture collection By strain number/name On Google map By isolation sources Search options Display format Filter Homology search Search literature Browse taxonomy tree Organism type Location Temperature Strain Page Species Page Further analysis

12 Search GCM by Strain Name and Strain Number

13 Formats to display the search results Search results Link to Species page Filtering search result and customizing the output format

14 Display the search result in a list of culture collections

15 Display the table of isolation sources

16 Display the Geographic origin of strains

17 Advanced search interface

18 Advanced search interface

19 Searching results of sequence similarity

20 Searching strains by publications and patents

21 Searching results by publications and patents

22 List of culture collections in the search result Link out to CCINFO database

23 Exploring information about a strain Catalogue information from collections Link back to original site Publications explored by Analyzer of Bio-resources Citations(ABC)

24 Detailed information of Strains Patents explored by ABC Choose sequences to execute bioinformatics analysis Sequences explored by ABC

25 Exploring information about a species

26 Exploring information about a species

27 Exploring information about a species Publications related to this species Publications related to the strains

28 Species information Patents related with this species explored by ABC

29 Adding your own comments

30 What users can do for the strain information? Bioinformatics Analysis Exchange of strains with collections Communicate with others on this platform

31 Choose sequences to execute bioinformatics analysis

32 Multiple Alignment of selected sequences

33 Order strains online

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35 Users can add comments on species page

36 Overview 1 Rectangle graphics Part 1: GCM: mission, functional architecture and progress Part 2: Minimum and Recommended Data Sets Part 3: GCM for the data users Part 4: GCM for the culture collections

37 Workflow Register in CCINFO Join in GCM Publish online Catalogue WDCM Number and Acronym Strain Number and Name Provide the DBMS Provide ABC and Name check results

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40 DBMS for culture collections Provides: In-house data management Homepage Online Catalogue

41 Choose data items according to your own catalogue items

42 Import your data in EXCEL file Export an EXCEL template for data management

43 Managing your data in EXCEL file

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46 Submit your data through EXCEL template directly

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48 Manage and add new accounts

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51 Name check for Data quality control

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53 Organism type Species Names Un-matched species Name Percentage of Un-match Archaea % Microalgae % Fungi % Bacteria % Total %

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56 Manage and add new accounts

57 European Consortium of Microbial Resources Centres (EMbaRC) Cooperation with EMbaRC EMbaRC CCs join GCM together WDCM develop EMbaRC catalogue page EMbaRC homepage links EMbaRC catalogue in GCM Cooperation with Russia collections Jointly develop data standards WDCM provide data platform Join GCM

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59 Android version of Global Catalogue ipad version will be Available soon

60 Statistics from WDCM database and WDCM reports

61 Contents Global Reports Status of culture collections: distribution, holdings, services Utilizations of microbial resources Isolation efforts of regions and countries Research status in the field of microbiology and applied microbiology Country report: case study in China

62 Status of culture collections: distribution 70 Data was generated from CCINFO, May 21, Brazil Thailand Australia France India 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).

63 Status of culture collections: Holdings Top 20 countries of microbial resources inventory 1% 2% The distribution of global 25% 27% inventory 45% bacteria fungi virus Cell line Ohters 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. NO. Country Culture Preserved Collections strains 1 Japan ,343 2 U.S.A ,556 3 India ,770 4 Brazil ,629 5 Korea (Rep. of) ,902 6 China ,179 7 France 39 91,385 8 Netherlands 6 90,775 9 Denmark 3 88, U.K , Australia 34 82, Canada 18 77, Taiwan 2 67, Russian Federation 22 60, Belgium 7 55, Sweden 3 52, Germany 13 52, Thailand 59 43, New Zealand 7 24, Armenia 1 17,805

64 The amount of papers about preserved strains in different countries U.S.A Braz il France Japan U.K 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 25 th with a total of 1273 papers. This indicates that China still need to improve the research of microbial resource utilization compared with its holdings Unpublished data (Permission required)

65 The amount of strains found in published papers in different countries Data was generated from ABC, May 21, U.S.A Belgium Germany Japan U.K 0 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 18 th with a total of 1561 strains. Unpublished data (Permission required)

66 The amount of patents for preserved strains in different countries U.S.A China Japan Germany Korea(Rep.of) 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. Unpublished data (Permission required)

67 Annual increases of patents of the top 4 countries

68 Country coverage of patents

69 The amount of genomes for preserved strains in different countries U.S.A Germany France Japan Netherlands The ranking based on the amount of genomes for utilizing strain resources. Top five are USA, Germany, Japan, Holland and France. China is ranked 9 th with a total amount of 7 genomes which indicates a big gap between China and developed countries in this area. Unpublished data (Permission required)

70 The ranking based on the amount of nucleotide sequence for utilizing strain resources. Top five are USA, Holland, Japan, Taiwan and England. China is ranked 10 th with a total amount of 6129 nucleotide sequences. However, comparing to USA (410,000), the big difference could be seen on the bar chart. The amount of nucleotide sequences for preserved strains in different countries U.S.A Japan Netherlands Taiwan U.K

71 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 Unpublished data (Permission required)

72 Isolation efforts of regions and countries Unpublished data (Permission required)

73 Thanks for your attention!