speciesLink
A System for integrating distributed primary biodiversity data
Vanderlei Perez Canhos
Centro de Referência em Informação Ambiental, CrIA
OverviewOverview
• CRIA
• SinBiota and The Species Analyst
• speciesLink
• Type of collections involved
• Number of records
• Technical features
• Future plans
CrIAReference Center on Environmental Informationhttp://www.cria.org.br
Focus on Biodiversity
Informatics
• Open source software
• Standards and protocols
• Systems interoperability
• Partnerships
http://speciesanalyst.net/
Location of participant collections: mainly United Statesmainly United States
Taxonomic groups: several taxaseveral taxa
Protocol: Z39.50 (migration to DiGIR on process)Z39.50 (migration to DiGIR on process)
Number of records: ~ 50.000.000~ 50.000.000
Importance of data sharingImportance of data sharing
Paris
KU – Natural HistoryMuseum
British Museum
Field Museum
The main goal of
speciesLink was to
build a distributed
system integrating
several biological
collections and
making their primary
data available on the
Internet.
speciesLinkDistributed Information System for Biological Collections
http://splink.cria.org.br
fish: 3
herbaria: 4 microorganisms: 3
mites: 2
inventories: SinBiota
Geographic distribution of the participant collections – phase I
São Paulo State CollectionsSão Paulo State Collections
Number of RecordsNumber of Records
available existing
Herbaria 72,000 of 740,000
Microorganisms 1,000 of 2,700
Mites 18,000 of 22,000
Fish 70,000 of 123,000
Inventories (species)
38,000 of 38,000
~200,000 of ~1,000,000
Microbial CollectionsMicrobial Collections
CBMAI 110 700
IBSBF 929 2,000
Observational DataObservational Data
SinBiota 38,109 38,109
Botanical CollectionsBotanical Collections
ESA 730 80,000
SP 11,280 350,000
IAC 25,245 45,000
SPF 21,828 133,500
UEC 12,860 130,000
Zoological CollectionsZoological Collections
ACARISJRP 5,382 7,000
ACARIESALQ 12,392 15,000
DSZSJRP(fish)
5,714 23,000
LIRP(fish)
4,314 30,000
MZUSP
(fish)
60,000 110,000
Collection Management SoftwareCollection Management Software
Support to collectionsSupport to collections
• Providing basic equipment and network infrastructure
• Helping to choose a management system, when needed
• Helping to train and to import data, when needed
Protocol and Content SchemaProtocol and Content Schema
• DiGIR protocol (Distributed Generic Information Retrieval)
Potential to be globally accepted
• DiGIR software (Java Portal & PHP Provider)
Collaborative development
• DarwinCore v.2
Covers the basic content elements (taxonomic
identification, location and date of collecting event)
Simple Search Simple Search InterfaceInterface
speciesLink site
Presentation Layer
speciesLink site
Presentation Layer
DiGIRPortal(Java)
DiGIRPortal(Java)
PerlPerl
Slow or unstable connectivity
Fast and stable connectivity
DataSOAP client
CollectionManagement
System
SQL
Collection C
DataRepository
DataSOAP client
CollectionManagement
System
SQL
Collection B
DataRepository
PostgresPHP
Provider
SOAP Server
SQL
Regional Server
DataPHP
Provider
Collection Management
System
SQL
Collection A
System’s System’s ArchitectureArchitecture
RegionalServer
RegionalServer
RegionalServer
RegionalServer
Network DesignNetwork Design
speciesLink site
Presentation Layer
speciesLink site
Presentation Layer
DiGIRPortal(Java)
DiGIRPortal(Java)
PerlPerl
Slow or unstable connectivity
Fast and stable connectivity
DataSOAP client
CollectionManagement
System
SQL
Collection C
DataRepository
DataSOAP client
CollectionManagement
System
SQL
Collection B
DataRepository
PostgresPHP
Provider
SOAP Server
SQL
Regional Server
DataPHP
Provider
Collection Management
System
SQL
Collection A
System’s System’s ArchitectureArchitecture
Data Migration ClientData Migration Client
• Platform independent (java)
• Connects to any database accessible via JDBC(simple text files are also supported)
• Complete control over data
• Low traffic
• Possibility to filter sensitive data using a regular expression
speciesLink site
Presentation Layer
speciesLink site
Presentation Layer
DiGIRPortal(Java)
DiGIRPortal(Java)
PerlPerl
Slow or unstable connectivity
Fast and stable connectivity
DataSOAP client
CollectionManagement
System
SQL
Collection C
DataRepository
DataSOAP client
CollectionManagement
System
SQL
Collection B
DataRepository
PostgresPHP
Provider
SOAP Server
SQL
Regional Server
DataPHP
Provider
Collection Management
System
SQL
Collection A
System’s System’s ArchitectureArchitecture
Regional serverRegional server
Features
• perl / PostgreSQL combination
• Can hold data from several collections
• Interpretation rules can be applied to specific data
PostgresProvider
PHP
SOAP Server(perl)
SQL
Query Result (brief)Query Result (brief)
speciesLink – phase IIspeciesLink – phase II
>35 collections available>35 collections available
Future plansFuture plans
• Mapping tools
Future plansFuture plans
• Mapping tools
• Data cleaning tools
Future plansFuture plans
• Mapping tools
• Data cleaning tools
• Modelling framework
DiGIRPortal
DiGIRPortal Precipitation
Vegetation
Temperature
Environmental layers
ACME
BioclimNeural
Net GARP
specimens
BioCASEPortal
BioCASEPortal
Modelling algoritms
Infrastructure for Species Distribution ModellingInfrastructure for Species Distribution Modelling
Instituto de Botânica Universidade Estadual de Campinas
Universidade de São Paulo
Instituto Agronômico de Campinas
Instituto Biológico
Universidade Estadual Paulista
Acknowledgements (phase I)Acknowledgements (phase I)
Escola Superior de Agricultura “Luiz de
Queiroz”
FellowshipsFellowships
• Visiting researchers
– Andrew Townsend Peterson (3 months)– Arthur Chapman (1 year)
• Pos-doctor
– Ingrid Koch
• Technical training (6 TT fellowships)
Summing upSumming up
• Achieved proof of concept
• Data is already available
• Low cost for connecting new collections
• Triggered off a movement within the collections to improve the quality of data and to increase the amount of available information
• Adoption of standards and protocols
• International partnerships: DiGIR, modelling framework
• Interoperability with similar initiatives