ANTABIF: Antarctic Biodiversity Information Facility Workshop 2012
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ANTABIF:Antarctic Biodiversity Information
Facility Workshop 2012
Background
Antarctic Treaty
« In order to promote international cooperation in scientific investigation in Antarctica, […],
Scientific observations and results from Antarctica shall be exchanged and made freely available. »
Our vision:Antarctic biodiversity data are open, linked, useful, interoperable and safe.
Parsons et al. 2011
QuickTime™ en een-decompressor
zijn vereist om deze afbeelding weer te geven.
ANTABIF - background
•Born during the IPY as Census of Antarctic Marine Life as the data, visualization and analysis component
•Free and open access to biodiversity data
•SCAR-MarBIN and ANTABIF projects
•Science, conservation and management
•Networked community developments
•Scientific impact: Citations : 423, Publications: 58, H-Index: 11
David B, Danis B, Griffiths HJ
Collaboration cloud - who’s in?
The first dynamic Register of Antarctic Marine Species
Taxonomic backboneBoard of 64 editorsFeeds World Register of Marine Species, Catalogue of Life and Encyclopedia of Life
Taxonomy17,098 taxa
Biogeography
•Single access to 900 datasets
•2.5 million records
•Data back to 1900 (Pygoscelis adeliae)
•Spatial data on over 5000 taxa
•Downloadable
•Interoperable
•Free and open
Projects and Products
afg. biodiversity.aq
• Identification aid
• High quality (useful) pictures
• Expert Descriptions
• Built on-the-fly from various sources
• Generates a pdf for taxa/area of interest
afg. biodiversity.aq
afg. biodiversity.aq
afg. biodiversity.aq
afg. biodiversity.aq
afg. biodiversity.aq
afg. biodiversity.aq
afg. biodiversity.aq
•Biogeographic Atlas of the Southern Ocean
•Redo of Hedgepeth 1969 Folio
•Predictive approach
•Static and dynamic versions
•Modelization loops are ready
atlas.biodiversity.aq
•Dynamic approach to a Biogeographic Atlas
•Collaborative project: 90+ specialists involved
•interdisciplinary: taxonomy, oceanography, ecology, phylogeography, modelization, data management, GIS, conservationists
•Modelization loops are ready (R-scripts with GUI)
•Results also valuable for SO-MPA designation
atlas.biodiversity.aq
94 Interpolated data layers
SlopeBathymetryChlorophyllDistance to the continentDistance to bird coloniesDistance to iceDistance to shelfDistance to canyonFloor temperature...+ ANTABIF Occurrence records
R-functions GUI for BRT and GDM
Architectural design
• www.biodiversity.aq
• data.biodiversity.aq
• ipt.biodiversity.aq
• afg.biodiversity.aq
• atlas.biodiversity.aq
• mars.biodiversity.aq
biodiversity.aq
Data discovery
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ANTABIF
MODULAR ARCHITECTURE
Data visualization
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Data products2
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• general website
• latest news
• contact
• sponsors
• governance
• resources
• projects
www.biodiversity.aq
www.biodiversity.aq-resources-
redo these slides with new structure of webportal (projects vs resources)
redo these slides with new structure of webportal (projects vs resources)
data.biodiversity.aq
• data discovery interface
• visualize occurrence data on map
• view taxonomic data
• download data
• view metrics
• send feedback
• access technical documentation
Under the hood
• Language: RubyFramework: Rails(ActiveRecord) and YUI (smart) Search engine: Full text (ElasticSearch-Lucene)Database/GIS server/SpatialDB: PostGresql/Geoserver/PostGIS Mapping client: OpenLayers Web services: RESTish (all resources)Protocols/Standards: DIF, DwC, DwC-A, Tapir…etcGBIF tools : HIT, IPTHosting: BeBIF (ULB/VUB joint IT Center)Metadata systems: GCMD API (DIF), EML
SPATIALLY EXPLICITOPEN SOURCE
FLEXIBLEINTEROPERABLE
EXPANDABLEMULTI-STANDARDS
Data publication tools
ipt.biodiversity.aq• Integrated Publishing Toolkit
• standardize and clean your data
• manage primary biodiversity data
• manage associated metadata
• choose collaborators
• generate and submit a Data Paper
• push data and metadata to Information Systems
Data PaperMetadata document
Reward data publishing
Communication tools
Communication• ANTABIF Blog
• Other blogs
• Facebook page
• Twitter accounts
• Mendeley library
• Various community sites
Upcoming events
Upcoming events
• CCAMLR workshop
• GBIF Governing Board
• APECS BeNeLux symposium
• OBIS Managers meeting
• ATCM 2013
Cooperation and integration
Cooperation and Integration
• GBIF
• OBIS
• SOOS
• SCADM
• New PPGs
• GEOSS
• New Environmental Portal
Microbial Antarctic Resource System
•Microbial Antarctic Resource System
•The organisms are small… but their environmental impacts are critical to many Antarctic ecosystems
•They are the dominant and most diverse form of life in the oceans and in the various microbial habitats on the continent
•Access to their diversity is becoming cost-effective and increasing exponentially
mars.biodiversity.aq
• Integrate Antarctic microbial DNA sequence data in ANTABIF
• Phased approach:
Step 0: data description and discovery
Step 1: microbial sequence and habitat metadata
Step 2: sequence data
Step 3: batch sequence data processing
Step 4: customized sequence data processing
mars.biodiversity.aq
•Potential applications:
Is there a biogeography of Antarctic microbes?
Document Antarctic bioprospecting activities
Assess bioindicating value of microbial diversity as early warning system of ecosystems shifts
mars.biodiversity.aq
Perspectives
Challenges
• Data deluge
• Huge gaps in the data
• Missing data types
• Orphan datasets
• True integration of complex data
Highlights• new architecture deployed
• new data publication tools
• flexible design: ready for integration in many contexts
• exciting data products being developed
• mARS paving the way to complex genomics data processing
• so much to do... so little time
@biodiversityaq
image © NY Times
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