speciesLinkThe Brazilian experience on setting up a network

Renato De Giovannirenato@cria.org.br

Centro de Referência em Informação Ambiental, CrIA

CrIAReference Center on Environmental Informationhttp://www.cria.org.br

CrIA is a not-for-

profit, non-

governmental

organization that

aims to contribute

towards a more

sustainable use of

Brazil’s biodiversity

through the

dissemination of

high quality

information.

Overview of the Overview of the speciesspeciesLinkLink projectproject

• Objective

• Type of collections involved

• Number of records

• Budget

• Technical features

• Future plans

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

The speciesLink

project is being

funded by Fapesp

(São Paulo state

agency) since

October, 2001.

fish: 3

herbaria: 4 microorganisms: 3

mites: 2

inventories: SinBiota

Geographic distribution of the participating collections

São Paulo State CollectionsSão Paulo State Collections

Number of Records from 12 collectionsNumber of Records from 12 collections

available existing

Herbaria 72,000 of 740,000

Microorganisms 1,000 of 2,700

Mites 18,000 of 22,000

Fish 10,000 of 163,000

Inventories (species)

38,000 of 38,000

139,000 of ~1,000,000

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

Project CostProject Cost (2 years)(2 years)

Budget speciesLink

46%

50%

4%

Equipment & Supplies Personnel Others

Budget speciesLink

46%

50%

4%

Equipment & Supplies Personnel Others

~US$ 600K~US$ 600K

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 System 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 by using regular expressions

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 System ArchitectureArchitecture

Regional serverRegional server

• 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)

Future plansFuture plans

• Mapping tool

Future plansFuture plans

• Mapping tool

• Data cleaning tools

Future plansFuture plans

• Mapping tool

• Data cleaning tools

• Modeling framework

and…

>30 collections available>30 collections available

Summing upSumming up

• Achieved proof of concept

• Data is already available (human and machine interfaces)

• Triggered off a movement within the collections to improve the quality of data and to increase the amount of available information

• Most interesting part of the game: interoperability

Thank you!Thank you!

http://splink.cria.org.br

renato@cria.org.br

Obrigado!Obrigado!

Any questions?Perguntas?