open access to biodiversity data: the specieslink experience dora ann lange canhos dora@cria.org.br

Open access to biodiversity data: the speciesLink experience

Dora Ann Lange Canhos

dora@cria.org.br

How to promote data sharing?

• Cultural barriers (internet, informatics, …)• Technical limitations (interoperability, archiving, …)• Legal impediments (biosafety, access to

biodiversity, …)

It doesn’t only depend on the “will” to share data....

• Must be organized: data models, standards, protocols...

• Must be feasible (“doable”)• Must be planned: adequate resources, expertise,

infrastructure

Working with data providers

routine should not be disrupted they must have full control over their data participation must be easy they must be acknowledged they must also benefit from sharing their data

COL 1

COL 2

COL 3

COL 4

COL 5

program

search

interface

Win2000Brahms

LinuxMySQL

Win98Access

Win98Biota

FreeeBSDPostgreSQL

??

??

?

speciesLink data providers: biological collections

Challenges

Integrate data from different taxonomic groups distributed in different collections

Regardless of where the collections are located what software the collections uses the Internet connectivity available the expertise available

Without changing the routine Maintaining full control of data by the collection Not expensive (open source and free software) Integrated with other networks

(local and international)

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

Collection’s database

Map

ping

dat

a fie

lds

Dar

win

Cor

e da

ta

mod

el

Database available on-line

Filter for sensitive data

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

Mirror 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 using a regular expression

Other Applications …

data cleaning collection profiles indicators ecological niche modeling

Data cleaning

species name georeferencing

Collection profile ...

Indicators

592,185 (83,28%)

18,727 (2.63%)

Ecological niche modeling

See demonstration of openModeller with Tim Sutton, Renato De Giovanni,

The speciesLink networkThe speciesLink network

descriptivedata

nomenclature taxonomy

modeling

Data quality

maps

primary data

educationresearch

Decision making

Biological collection

Building data infrastructure

is necessarily a collaborative effort

http://splink.cria.org.brdora@cria.org.br

ObrigadaObrigada