Transcript GLOBAL BIODIVERSITY

GLOBAL
BIODIVERSITY
INFORMATION
FACILITY
GBIF - From Prototype
towards
Full Operation
Éamonn Ó Tuama, Vishwas Chavan, Markus
Döring, Samy Gaiji, David Remsen,
Tim Robertson
GBIF Secretariat
What does GBIF do?
- emphasises participation and working through partners
- mobilises biodiversity data
- promotes standards to enable interoperability
- builds an informatics architecture
- promotes capacity building
- catalyses development of analytical tools
data provider
/ aggregator
GBIF Themes & Work Areas
Nodes, Training, Communications, Outreach
Participation
GBIF
Secretariat
Informatics
IDA1, DIGIT, ECAT, IIP2
1Inventory,
Discovery, Access
2Informatics Infrastructure and Data Portal
GBIF Informatics Thematic Area
Area
Focus
IDA 1
Standards, metadata, interoperability
DIGIT
Mobilisation of primary biodiversity data
ECAT
Global Names Architecture
IIP 2
Integrated data publishing tools, GBIF
portal, web services, decentralisation
1 Inventory,
Discovery, Access
2 Informatics
Infrastructure and Portal
GBIF Task Groups
- New modus operandi
- Replacement for standing Science Sub Committees
- Time limited, defined task with report as outcome
- Draw on broader community of experts
- Examples:
- Observational Data Task Group
- Multimedia Resources Task Group
Vishwas Chavan
Proof of Concept Demonstrated
- First five-year phase: 2002-2006
- A global network is feasible
- Barriers: social rather than technical
- Key requirement: well designed informatics architecture
- Key requirement: enabled, committed Participants
- All benefit from contributing to “common good”
http:/data.gbif.org
http://data.gbif.org/countries/datasharing
Rich Internet Application
GBIF Web Services
occurrence record data
http://data.gbif.org/ws/rest/occurrence
taxon data
occurrence density data
http://data.gbif.org/ws/rest/taxon
http://data.gbif.org/ws/rest/density
Software applications that
run over the internet and
use a standardised message
passing system to handle
request and response,
usually based on XML.
GBIF's web services are
based on the REST
architecture style.
GBIF
Web
Services
http://data.gbif.org/ws/rest/resource
http://data.gbif.org/ws/rest/provider
dataset metadata
data provider metadata
http://data.gbif.org/ws/rest/network
data network metadata
The Geospatial Web - OGC
Coastlines, Boundaries,
Remote sensing imagery
data
Web Map
Service
1
Web Services
Occurrences,
Names
Meteorological,
Oceanographic
data
data
Web Feature
Service
Web Coverage
Service
Prototype OGC web services
developed by GBIF:
national and thematic portals
• Web Map Service
• Web Feature Service
(TDWG GML2 application schema)
1Open
Geospatial Consortium
2Geography
Markup Language
Species Response to Climate Change
The range of the common roadside skipper (Amblyscirtes vialis) will move
about 300 km northwards by 2050 under the most conservative IPCC climate
change scenario (B1)
Ref: Predicting the impact of climate change on biodiversity – a GEOSS scenario. Nativi et al. In “The Full Picture,
A publication for the GEO Ministerial Summit, ‘Earth Observation for Sustainable Growth and Development’
Cape Town, 30 November 2007”
Number of Occurrence Records Indexed
A scalable, distributed network of Participants
Challenge
- Meeting requirements of Participants in terms
of growth, scalability, capacity, visibility
Poster
Strategy
- Developing a full suite of IT infrastructure,
architecture, services and tools
Key components
- GBRDS, IPT, GNA, Harvesting Indexing Toolkit, Nodes
Portal Toolkit
Key Informatics Components
- Global Biodiversity Resources Discovery System (GBRDS)
- Integrated Publishing Toolkit (IPT)
- Global Names Architecture (GNA)
- Harvesting Indexing Tool
- Node Portal Toolkit
Global Biodiversity Resources
Discovery System
(GBRDS)
Poster
Integrated Publishing Toolkit
(IPT)
IPT: publishing data to the world
- Easy hosting and sharing of data
- Focus on specific data types for richer environment
- Data cache based on embedded or external database
- Link to existing relational DBs; import text files; assign
GUIDs; detect changes for incremental harvesting
- Each data type has core entity; one-to-many relation to
extension tables
Interface for mapping
from local database
schema to Darwin Core
Interface for
events logging
IPT: multiple interfaces to data
- Publishes data to web; statistics and maps via Google Chart
API; fulltext search via Lucene
- Serves compressed archive of tab delimited files
- Incremental harvesting via OAI PMH
- TAPIR for Darwin Core and ABCD
- REST web services delivering XML and JSON records
- TCS for taxonomic checklists (also tab delimited archives)
- GeoServer for OGC Web Map and Web Feature services
- RSS feed announcing new or modified resources
Interfaces to Data
Poster
Demo
Markus Döring
“The key to modern biological
information are the scientific names of
organisms, and the electronic catalogue
of the names that GBIF is building is
fundamental to searching within and
among the types of data indicated.”
- GBIF Strategic Plan p.17
Fundamental as a “taxonomic backbone”
Information about Names
Semantic and syntactic information that is focus of ECAT and its sources
Syntactic
Semantic
As namestrings
(data managers)
• Literal representation in data
• Orthographic grouping
• homography
As nomenclature (names
tied to nomenclatural acts)
(primary nomenclators +
satellite contributors)
• Absolute scope of nomenclature
• Identification & scope of homonymy
• Correct orthography of names
• Nomenclatural synonymy
Taxonomy
(aggregators, GSDs, floras,
faunas, thematic
checklists)
• Correct name of taxon sensu source
• Disambiguation of homonyms
• Taxonomic synonymy
• Circumscription
• Taxonomic classification
Global Names Architecture
- Mobilise, index and cross reference nomenclatural and
taxonomic resources
- Common registration system (GBRDS)
- Standard exchange formats and GUIDs
- Assign GUIDS to normalised and stable nomenclature
- Map nomenclatural components of taxon concepts
- Reconcile names usages within data objects
Enhanced discovery and access methods by which
objects can be linked to taxon concepts
Integrate taxonomic, nomenclatural resources with indexes of biodiversity content
Poster
David Remsen
Harvesting Indexing Toolkit
Key Features
- Use of existing TDWG protocols
- Scheduling of data source harvesting
Use to facilitate
fast development
of data portals
- Web based console to view progress and errors
- Cached copy of complete “raw” data held on disk
- Synchronising with UDDI registries
- Fully internationalised web application
- Role based security model
- Simple codebase, easy to extend (Java)
Could this be a tool
to Certify provider
installations?
Harvesting Indexing Toolkit
Early development screenshot
[Protocol selection]
Harvesting Indexing Toolkit
Early development screenshot
[Datasource creation]
Harvesting Indexing Toolkit
Early development screenshot
[Internationalised web based log console]
demo
Tim Robertson
Node Portal Toolkit
Goal
To provide a simple-to-use, simple-to-extend ‘core
features’-only portal toolkit as the basis for development
of customised portals tailored to particular needs.
Will leverage functionality already developed for the
Integrated Publishing Toolkit and Harvsting/Indexing Toolkit.
GBIF and TDWG
- GBIF: representing needs of broader biodiversity community
- TDWG standards process
- Supported by GBIF task groups
- Involving the wider community
- GBIF Informatics Advisory Group
How to contact GBIF:
Web site:
www.gbif.org
Data portal: data.gbif.org
GBIF Secretariat
Universitetsparken 15
DK-2100 Copenhagen Ø
Denmark
E-mail: [email protected]
Phone: +45 3532 1470
Fax:
+45 3532 1480
GBIF Secretariat building, supported by a grant from
the Aage V. Jensens Fonde