μsicol and SIColNet management and dynamic integration of microbial data

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1 μsicol and SIColNet management and dynamic integration of microbial data Sidnei de Souza ICCC-12 Conference 2010 Biological Resource Centers: gateway to biodiversity and services for innovation in biotechnology Florianópolis, October 2010

2 The (Reference Center on Environmental Information) is a not-for-profit, non-government organization. Its aim is to contribute towards a more sustainable use of Brazil's biodiversity through the dissemination of high quality information and education. Through research projects in partnership with the scientific community, dissemination of data and information generated by the scientific community,

3 Agenda μsicol status online catalogues SIColNet

4 What is μsicol? μsicol is a microbial collection management system being developed by Centro de Referência em Informação Ambiental, CRIA since 2005 with the support from the Ministry of Science and Technology. Its goal is to support best management practices and documentation of processes and products ensuring traceability and facilitating free and open access to data through the internet (specieslink, SIColNet, catalogues).

5 μsicol main characteristics Based on CABRI* guidelines and customizable to attend specific needs and requirements. Based on web technology and runs on different platforms. Provides both free text and controlled vocabulary fields. Provides mechanisms for internal references to documents, bibliography, and scientific names previously registered. Multilingual for both navigation and content. Provides a robust security schema for access to the registered information in different levels (user, group and record level). * Common Access to Biological Resources and Information, CABRI

6 μsicol components Collection documentation (archea, bacteria, filamentous fungi, yeast and protozoa) Strains (general, collect, isolation, identification, deposit, growth, characteristics, properties, stock) Taxa (configurable) Institutions People Documents (pictures, media, DNA sequences, etc.) Bibliographic References Documentation of processes Preservation + Stock maps Distribution Quality Control Stock Control (mininum stock alert) External access catalogue Integration with SIColNet and specieslink (DarwinCore2 + microbial extension)

DarwinCore2 μsicol components CONFIG USERS GROUPS ACCESS CONTROL INSTITUTIONS TAXA GENERAL COLLECT PEOPLE DOCUMENTS PROPS CHARS STRAINS ISOLATION IDENT

7 DarwinCore2 μsicol components CONFIG USERS GROUPS ACCESS CONTROL INSTITUTIONS TAXA GENERAL COLLECT PEOPLE DOCUMENTS PROPS CHARS STRAINS ISOLATION IDENT REFERENCES STOCK MAP STOCK GROWTH DEPOSIT QC ADVANCED SEARCH & REPORTS PRESERVATION DISTRIBUTION REPORTS ON TRACEABILITY + microbial USER S MANUAL ON-LINE CATALOG

8 μsicol installation examples single user installation Local Network with a shared server

μsicol culture collections 15 collections CLIOC Leishmania Collection Fiocruz RJ CBMAI Coleção de Culturas de Microrganismos de Ambiente e Indústria Unicamp CCBS Bacterial Culture Collection of

9 μsicol culture collections 15 collections CLIOC Leishmania Collection Fiocruz RJ CBMAI Coleção de Culturas de Microrganismos de Ambiente e Indústria Unicamp CCBS Bacterial Culture Collection of Health Importance Fiocruz - RJ Fiocruz - RJ Collection of Listeria CLIST Fiocruz - RJ Collection of Campylobacter CCAMP Fiocruz - RJ Culture Collection of Hospital Bacteria CCBH Fiocruz - RJ Collection of Enteropathogenic Bacteria CENT CCFF Culture Collection of Filamentous Fungi Fiocruz - RJ CCGB Culture Collection of Bacillus and Related Genera Fiocruz - RJ CMT Mycological Collection of Trichocomaceae Fiocruz - RJ ColTryp Collection of Trypanossoma from Wild and Domestic Mammals and Vectors Fiocruz - RJ CBAM Collection of Bacteria from Amazon Fiocruz - AM CFAM Collection of Fungi from Amazon Fiocruz - AM CBMA Bacteria Collection of the Atlantic Forest Fiocruz - RJ CFP Collection of Pathogenic Fungi Fiocruz - RJ INCQS Coleção de Microrganismos de Referência do Instituto Nacional de Controle de Qualidade em Saúde Fiocruz - RJ

10 μsicol strains list

11 μsicol strains general info

12 μsicol strains collect info

13 μsicol strains deposit info

14 μsicol strains characteristics

15 μsicol strains internal link to images

16 μsicol strains internal link to documents

17 μsicol strains quality control tests

18 μsicol preservation list

19 μsicol preservation details

20 μsicol preservation stock map

21 μsicol strains stock list

22 μsicol security

23 μsicol taxa data input

24 μsicol reports (next steps) Advanced search producing basic and customized reports and graphics Reports on traceability Continuous improvements on existing modules based on user feedbacks

25 Agenda μsicol status online catalogues SIColNet

26 coltryp.fiocruz.br cmt.fiocruz.br ccff.fiocruz.br ccgb.fiocruz.br clioc.fiocruz.br cbma.fiocruz.br cbam.fiocruz.br cfp.fiocruz.br cfam.fiocruz.br Fiocruz collections web sites

27 ccbs.fiocruz.br Fiocruz sub-collections web sites ccbs.fiocruz.br/ccbh ccbs.fiocruz.br/clist ccbs.fiocruz.br/cent ccbs.fiocruz.br/ccamp

28 μsicol catalogues integrated to web sites μsicol CLIOC website CLIOC collection catalogue available

29 μsicol catalogues integrated to web sites μsicol CMT website CMT collection catalogue available

30 Unicamp collection web sites

31 μsicol catalogues integrated to web sites μsicol CBMAI website CBMAI collection catalogue available

32 agenda μsicol status online catalogues SIColNet

33 global networks specieslink is a distributed information system that integrates primary data from biological collections. The development was funded by FAPESP, GBIF, JRS Foundation, MCT, CNPq, FINEP and CRIA. It uses Tapir and DiGIR as Information Retrieval Protocol and DarwinCore2 as its data model. 195 collections and sub-collections, 3,838,237 on-line records of all taxonomic groups Net SIColNet is a distributed information system that integrates primary data from microbial collections. The development was funded by MCT, FINEP and CRIA. It uses Tapir as Information Retrieval Protocol and DarwinCore2 + microbial extension as its data model. 10 collections, on-line records of bacteria, filamentous fungi, yeasts and protozoa. SIColNet uses the same technology developed for specieslink

34 data model DarwinCore2 and extensions DarwinCore2 Microbial extension

35 retrieval protocol TAPIR TAPIR (TDWG* Access protocol for Information Retrieval) specifies a standardized, stateless, HTTP transmittable, XML-based request and response protocol for accessing structured data that may be stored on any number of distributed databases of varied physical and logical structure TAPIR was developed for use with biodiversity and natural science collection data but is a generic tool applicable to other domains database database database TAPIR Biodiversity Information Standards (TDWG) is a not for profit scientific and educational association that is affiliated with the International Union of Biological Sciences.

36 the pieces put together CENT CCBH CLIST CCAMP CCBS ColTryp CBMA μsicol CMT CFP INCQS CCFF CCGB CLIOC Fiocruz - RJ TAPIRLink

the pieces put together CBAM μsicol CFAM CBMAI μsicol Unicamp - SP Fiocruz - AM CENT CCBH CLIST CCAMP CCBS ColTryp CBMA μsicol CMT CFP INCQS CCFF CCGB CLIOC Embrapa

37 the pieces put together CBAM μsicol CFAM CBMAI μsicol Unicamp - SP Fiocruz - AM CENT CCBH CLIST CCAMP CCBS ColTryp CBMA μsicol CMT CFP INCQS CCFF CCGB CLIOC Embrapa Infomicro TAPIRLink specieslink (DarwinCore2) Fiocruz - RJ splinker SIColNet (DarwinCore2 + microbial) global catalogue distribution maps indicators reports datacleaning reports

39 SIColNet where to search

40 SIColNet what to search

41 SIColNet search result summary

42 SIColNet search result details

43 SIColNet search result maps

44 SIColNet other services information about the collection datacleaning reports data analysis, indicators reports, georeferencing suggestions

45 Thank you, obrigado! Sidnei de Souza sicol.cria.org.br

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