open access to biodiversity data: the specieslink experience dora ann lange canhos [email protected]
TRANSCRIPT
Open access to biodiversity data: the speciesLink experience
Dora Ann Lange Canhos
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
