speciesLink A System for integrating distributed primary biodiversity data Vanderlei Perez Canhos Centro de Referência em Informação Ambiental, CrIA

Overview CRIA SinBiota and The Species Analyst speciesLink Type of collections involved Number of records Technical features Future plans

CrIA Reference Center on Environmental Information Focus on Biodiversity Informatics Open source software Standards and protocols Systems interoperability Partnerships

mainly United States Location of participant collections: mainly United States several taxa Taxonomic groups: several taxa Z39.50 (migration to DiGIR on process) Protocol: Z39.50 (migration to DiGIR on process) ~ Number of records: ~

Importance of data sharing Paris KU – Natural History Museum 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. speciesLink Distributed Information System for Biological Collections

fish: 3 herbaria: 4 microorganisms: 3 mites: 2 inventories: SinBiota Geographic distribution of the participant collections – phase I São Paulo State Collections

Number of Records availableexisting Herbaria72,000of740,000 Microorganisms1,000of2,700 Mites18,000of22,000 Fish70,000of123,000 Inventories (species) 38,000of38,000 ~200,000of~1,000,000

Microbial Collections CBMAI IBSBF9292,000 Observational Data SinBiota38,109 Botanical Collections ESA73080,000 SP11,280350,000 IAC25,24545,000 SPF21,828133,500 UEC12,860130,000 Zoological Collections ACARISJRP5,3827,000 ACARIESALQ12,39215,000 DSZSJRP (fish) 5,71423,000 LIRP (fish) 4,31430,000 MZUSP (fish) 60,000110,000 Collection Management Software

Support 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 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 Interface

speciesLink site Presentation Layer speciesLink site Presentation Layer DiGIR Portal (Java) DiGIR Portal (Java) Perl Slow or unstable connectivity Fast and stable connectivity Data SOAP client Collection Management System SQL Collection C Data Repository Data SOAP client Collection Management System SQL Collection B Data Repository Postgres PHP Provider SOAP Server SQL Regional Server Data PHP Provider Collection Management System SQL Collection A System’s Architecture

Regional Server Network Design

speciesLink site Presentation Layer speciesLink site Presentation Layer DiGIR Portal (Java) DiGIR Portal (Java) Perl Slow or unstable connectivity Fast and stable connectivity Data SOAP client Collection Management System SQL Collection C Data Repository Data SOAP client Collection Management System SQL Collection B Data Repository Postgres PHP Provider SOAP Server SQL Regional Server Data PHP Provider Collection Management System SQL Collection A System’s Architecture

Data 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 DiGIR Portal (Java) DiGIR Portal (Java) Perl Slow or unstable connectivity Fast and stable connectivity Data SOAP client Collection Management System SQL Collection C Data Repository Data SOAP client Collection Management System SQL Collection B Data Repository Postgres PHP Provider SOAP Server SQL Regional Server Data PHP Provider Collection Management System SQL Collection A System’s Architecture

Regional server Features perl / PostgreSQL combination Can hold data from several collections Interpretation rules can be applied to specific data Postgres Provider PHP SOAP Server (perl) SQL

Query Result (brief)

speciesLink – phase II

>35 collections available

Future plans Mapping tools

Future plans Mapping tools Data cleaning tools

Future plans Mapping tools Data cleaning tools Modelling framework

DiGIR Portal DiGIR Portal Precipitation Vegetation Temperature Environmental layers ACME Bioclim Neural Net GARP specimens BioCASE Portal BioCASE Portal Modelling algoritms Infrastructure for Species Distribution Modelling

Instituto de BotânicaUniversidade Estadual de Campinas Universidade de São Paulo Instituto Agronômico de Campinas Instituto Biológico Universidade Estadual Paulista Acknowledgements (phase I) Escola Superior de Agricultura “Luiz de Queiroz”

Fellowships Visiting researchers –Andrew Townsend Peterson (3 months) –Arthur Chapman (1 year) Pos-doctor –Ingrid Koch Technical training (6 TT fellowships)

Summing 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

Thank you!