130712 antabif workshop

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

Antarctic Field Guidesafg.biodiversity.aqafg. biodiversity.aq

afg.biodiversity.aqafg. biodiversity.aq

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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)

www.biodiversity.aq-mendeley-

www.biodiversity.aq-pictures-

www.biodiversity.aq-projects-

share.biodiversity.aq -shared repository-

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. biodiversity.aq

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

ipt. biodiversity.aq

ipt. biodiversity.aq

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ipt. biodiversity.aq

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Data PaperMetadata document

Reward data publishing

Proof of concept

Impact

Fact

or:

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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

Thanks and questions?