species link and net dynamic integration of microbial data · listeria inocua pseudomon as...
TRANSCRIPT
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Centro de Referência em Informação Ambiental, CRIA
speciesLink and SIColNet
dynamic integration of microbial data
Dora Ann Lange Canhos
Centro de Referência em Informação Ambiental, CRIA
1st GBRCN IT-Cluster Workshop
February 14th – 15th 2011 in Braunschweig
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Centro de Referência em Informação Ambiental, CRIA
The Centro de Referência em Informação Ambiental, CRIA
(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,
…
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Centro de Referência em Informação Ambiental, CRIA
μSICol
status
online
cataloguesSIColNet
Agenda
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Centro de Referência em Informação Ambiental, CRIA
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).
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Centro de Referência em Informação Ambiental, CRIA
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
•
•
•
•
•
•
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Centro de Referência em Informação Ambiental, CRIA
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)
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Centro de Referência em Informação Ambiental, CRIA
TAXA
INSTITUTIONS
PEOPLE
DOCUMENTS REFERENCES
PRESERVATION DISTRIBUTION
GENERAL
IDENT
DEPOSITGROWTH
CHARS
PROPS
STOCK
COLLECT
ISOLATION
QCSTOCK MAP
ON-LINE
CATALOG
ADVANCED SEARCH
&
REPORTS
USERSACCESS
CONTROL
GROUPS
CONFIG
USER’S
MANUAL
STRAINS
REPORTS ON
TRACEABILITY
Da
rwin
Co
re2
+ microbial
μSICol • components
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Centro de Referência em Informação Ambiental, CRIA
single user installationsingle user installation
Local Network with a shared serverLocal Network with a shared server
μSICol • installation examples
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Centro de Referência em Informação Ambiental, CRIA
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 ImportanceFiocruz - RJ
CLISTCollection of Listeria
Fiocruz - RJ
CCAMPCollection of Campylobacter
Fiocruz - RJ
CCBHCulture Collection of Hospital Bacteria
Fiocruz - RJ
CENTCollection of Enteropathogenic Bacteria
Fiocruz - RJ
CCFF Culture Collection of Filamentous FungiFiocruz - RJ
CCGB Culture Collection of Bacillus and Related GeneraFiocruz - RJ
CMT Mycological Collection of TrichocomaceaeFiocruz - RJ
ColTryp Collection of Trypanossoma from Wild and Domestic Mammals and VectorsFiocruz - RJ
CBAM Collection of Bacteria from AmazonFiocruz - AM
CFAM Collection of Fungi from AmazonFiocruz - AM
CBMA Bacteria Collection of the Atlantic ForestFiocruz - RJ
CFP Collection of Pathogenic FungiFiocruz - RJ
INCQS Coleção de Microrganismos de Referência do Instituto Nacional de Controle de Qualidade em SaúdeFiocruz - RJ
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Centro de Referência em Informação Ambiental, CRIA
μSICol • strains • list
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Centro de Referência em Informação Ambiental, CRIA
μSICol • strains • general info
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Centro de Referência em Informação Ambiental, CRIA
μSICol • strains • collect info
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Centro de Referência em Informação Ambiental, CRIA
μSICol • strains • deposit info
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Centro de Referência em Informação Ambiental, CRIA
μSICol • strains • characteristics
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Centro de Referência em Informação Ambiental, CRIA
μSICol • strains • internal link to images
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Centro de Referência em Informação Ambiental, CRIA
μSICol • strains • internal link to documents
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Centro de Referência em Informação Ambiental, CRIA
μSICol • strains • quality control tests
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Centro de Referência em Informação Ambiental, CRIA
μSICol • preservation • list
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Centro de Referência em Informação Ambiental, CRIA
μSICol • preservation • details
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Centro de Referência em Informação Ambiental, CRIA
μSICol • preservation • stock map
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Centro de Referência em Informação Ambiental, CRIA
μSICol • strains • stock list
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Centro de Referência em Informação Ambiental, CRIA
μSICol • security
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Centro de Referência em Informação Ambiental, CRIA
μSICol • taxa • data input
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Centro de Referência em Informação Ambiental, CRIA
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
•
•
•
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Centro de Referência em Informação Ambiental, CRIA
μSICol
status
online
cataloguesSIColNet
Agenda
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Centro de Referência em Informação Ambiental, CRIA
ccb
s.fi
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ccbs.fiocruz.br/ccbh
ccbs.fiocruz.br/cent
ccbs.fiocruz.br/ccamp
ccbs.fiocruz.br/clist
Fiocruz sub-collections web sites
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Centro de Referência em Informação Ambiental, CRIA
μSICol catalogues integrated to web sites
CLIOC websiteCLIOC collection catalogue available
μSICol
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Centro de Referência em Informação Ambiental, CRIA
μSICol catalogues integrated to web sites
CMT websiteCMT collection catalogue available
μSICol
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Centro de Referência em Informação Ambiental, CRIA
Unicamp collection web sites
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Centro de Referência em Informação Ambiental, CRIA
μSICol catalogues integrated to web sites
μSICol
CBMAI website
CBMAI collection catalogue available
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Centro de Referência em Informação Ambiental, CRIA
μSICol
status
online
cataloguesSIColNet
agenda
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Centro de Referência em Informação Ambiental, CRIA
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, 11.205 on-line records of bacteria, filamentous
fungi, yeasts and protozoa.
SIColNet uses the same technology developed for speciesLink
global networks
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Centro de Referência em Informação Ambiental, CRIA
DarwinCore2 Microbial extension
data model • DarwinCore2 and extensions
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Centro de Referência em Informação Ambiental, CRIA
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…”
Biodiversity Information Standards (TDWG) is a not for profit scientific andeducational association that is affiliated with the International Union of Biological Sciences.
TAPIR
database
database
database
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Centro de Referência em Informação Ambiental, CRIA
CLIOC
CBMA
ColTryp
CMT
TAPIRLinkTAPIRLink
CCFF CCGB
CENT CCBH CLIST CCAMP
CCBSCCBS
μSICol
INCQSCFP
the pieces put together
Fiocruz - RJ
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Centro de Referência em Informação Ambiental, CRIA
global catalogue distribution maps indicators reports
CLIOC
CBMA
ColTryp
CMT
TAPIRLinkTAPIRLink
CCFF CCGB
CENT CCBH CLIST CCAMP
CCBSCCBS
μSICol
INCQSCFP
Fiocruz - RJ
CBAM
CFAMμSICol
Fiocruz - AM
spLinkerspLinker
CBMAI μSICol Unicamp - SP
datacleaning reports
speciesLink (DarwinCore2)speciesLink (DarwinCore2) SIColNet (DarwinCore2 + microbial)SIColNet (DarwinCore2 + microbial)
the pieces put together
Embrapa Infomicro
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Centro de Referência em Informação Ambiental, CRIA
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Centro de Referência em Informação Ambiental, CRIA
SIColNet • where to search
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Centro de Referência em Informação Ambiental, CRIA
SIColNet • what to search
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Centro de Referência em Informação Ambiental, CRIA
SIColNet • search result summary
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Centro de Referência em Informação Ambiental, CRIA
SIColNet • search result details
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Centro de Referência em Informação Ambiental, CRIA
SIColNet • search result maps
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Centro de Referência em Informação Ambiental, CRIA
SIColNet • other services
information about the collection datacleaning reports
data analysis, indicators reports, georeferencing suggestions
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Centro de Referência em Informação Ambiental, CRIA
Sidnei de Souza
Centro de Referência em Informação Ambiental, CRIA
www.cria.org.br
sicol.cria.org.br
Thank you, obrigado!
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Centro de Referência em Informação Ambiental, CRIA
IBSBF
BGB
BR
CFAF
• Bacillus sporothermodurans Petterson et al., 1996 - contaminante de leite UHTCG
• Trypanosoma cruzi
• Trypanosoma cruziColTryp
• Leishmania major
• Leishmania amazonensisCLIOC
• Aspergillus flavus
• Gliocladium virideCCFF
• Bacillus licheniformis, CCGB1234, Agar media
• Lysinibacillus sphaericusCCGB
• Serratia, Parson1 1876, ATCC 2374, liof
• PseudomonasCBMA
• Cryptococcus neoformans
• Cryptococcus gattiCFP
CBAM
CFAM
• Paecilomyces lilacinus
• Curvularia tuberculataCMT
• Acinetobacter baumannii
• Campylobacter coliCCBS
• Cryptococcus gatti
• Cryptococcus neoformansINCQS
• Bacillus cereus, CBMAI0001, reference
• Escherichia coli, CBMAI8765, referenceCBMAI
splinkersplinker
TA
PIR
TA
PIR
CatalogNumber Genus Species rank Subspecies Depositor
CBMAI0001 Bacillus cereus Luiz André
CCFF0221 Escherichia coli Pedro Paulo
ColTryp9876 Trypanosoma
cruzi Maria Aparecida
IOCL8765 Leishmania major John Doe
CFP8765 Fusarium Mary Ann
CMT6543 Aspergillus flavus Luiggi Pietro
CMT8762 Cryptococcus
gatti Carla Moraes
CFP3421 Cryptococcus
neoformans
CBMAI4321 Serratia sp.
Listeria inocua
Pseudomonas
aeruginosa
Pseudomonas
alcaliphila
Fusarium flavum
Fusarium aquaeductuum
var. medium
Aspergillus niger var. niger
Campylobacter
coli
Serratia marcescens subsp.
sakuensis
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