ANTABIF at the BELSPO-SOA event

ANTABIF:Antarctic Biodiversity Information Facility

Bruno Danis - SOA-BELSPO event

http://creativecommons.org/licenses/by/2.0/




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.

Antarctic Information Networks - scope

David B, Danis B, Griffiths HJ


• Born 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







• Networked community developments

• Scientific impact: Citations : 423, Publications: 58, H-Index: 11


Collaboration cloud - who’s in?

The first dynamic Register of Antarctic Marine Species

Taxonomic backbone

Board of 64 editors

Feeds 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

Antarctic Information Networks - applications


• Data-driven Marine Protected Area designation



• Expedition design




• Biogeographic patterns





• Antarctic Field Guides






• Biogeographic Atlas







• Gap analysis







• Gap analysis

• more...

Functionalities

biodiversity.aq

http://www.antabif.be


http://data.biodiversity.aq










• www.biodiversity.aq

biodiversity.aq

http://www.biodiversity.aq














• www.biodiversity.aq• data.biodiversity.aq

biodiversity.aq















• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq

biodiversity.aq















• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq

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• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq

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• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq• mars.biodiversity.aq

biodiversity.aq
















biodiversity.aqPromote)the)communityEdriven)

development)of)NPT)•  GBIF)promotes)training)and)use)of)NPT)

ANTABIF

MODULAR ARCHITECTURE
















biodiversity.aqNodes)Investment)in)new)func@onality)

•  Nodes)extend)the)plaGorm)with)new)modules)

A)module)I)need)A)module)we)all)need)

Data discovery

Promote)the)communityEdriven)development)of)NPT)

•  GBIF)promotes)training)and)use)of)NPT)

ANTABIF

MODULAR ARCHITECTURE



















Data discovery



ANTABIF

MODULAR ARCHITECTURENodes)Investment)in)new)func@onality)



Data visualization



















Data discovery



ANTABIF

MODULAR ARCHITECTURENodes)Investment)in)new)func@onality)



Data visualization

NPT)can)be)extended)by)crea@ng)and)installing)Modules)

Data products















• 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)



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: Ruby

• Framework: 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…etc

• GBIF tools : HIT, IPT

• Hosting: BeBIF (ULB/VUB joint IT Center)

• Metadata systems: GCMD API (DIF), EML

Under the hood

Under the hood

SPATIALLY EXPLICIT

Under the hood

SPATIALLY EXPLICITOPEN SOURCE

Under the hood


FLEXIBLE

Under the hood


FLEXIBLEINTEROPERABLE

Under the hood



EXPANDABLE

Under the hood



EXPANDABLEMULTI-STANDARDS

data. biodiversity.aq






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

http://ipt.biodiversity.aq





ipt. biodiversity.aq






Data PaperMetadata document

Reward data publishing

Proof of conceptAntarctic Star!sh (Echinodermata: asteroidea) from the ANDEEP3 expedition 73

Antarctic Starfish (Echinodermata, Asteroidea) from the ANDEEP3 expedition

Bruno Danis1, Michel Jangoux2, Jennifer Wilmes2

1 ANTABIF, 29, rue Vautier, 1000, Brussels, Belgium 2 Université Libre de Bruxelles, 50, av FD Roosevelt, 1050, Brussels, Belgium

Corresponding author: Bruno Danis ([email protected])

Academic editor: Vishwas Chavan | Received 13 March 2012 | Accepted 18 April 2012 | Published 23 April 2012

Citation: Danis B, Jangoux M, Wilmes J (2012) Antarctic Star"sh (Echinodermata: asteroidea) from the ANDEEP3 expedition. ZooKeys 185: 73–78. doi: 10.3897/zookeys.185.3078

Abstract#is dataset includes information on sea stars collected during the ANDEEP3 expedition, which took place in 2005. #e expedition focused on deep-sea stations in the Powell Basin and Weddell Sea.

Sea stars were collected using an Agassiz trawl (3m, mesh-size 500µm), deployed in 16 stations during the ANTXXII/3 (ANDEEP3, PS72) expedition of the RV Polarstern. Sampling depth ranged from 1047 to 4931m. Trawling distance ranged from 731 to 3841m. #e sampling area ranges from -41°S to -71°S (latitude) and from 0 to -65°W (longitude). A complete list of stations is available from the PANGAEA data system (http://www.pangaea.de/PHP/CruiseReports.php?b=Polarstern), including a cruise report (http://epic-reports.awi.de/3694/1/PE_72.pdf ).

#e dataset includes 50 records, with individual counts ranging from 1-10, reaching a total of 132 specimens.

#e andeep3-Asteroidea is a unique dataset as it covers an under-explored region of the Southern Ocean, and that very little information was available regarding Antarctic deep-sea star"sh. Before this study, most of the information available focused on star"sh from shallower depths than 1000m. #is dataset allowed to make unique observations, such as the fact that some species were only present at very high depths (Hymenaster crucifer, Hymenaster pellucidus, Hymenaster praecoquis, Psilaster charcoti, Freyella attenuata, Freyastera tuberculata, Styrachaster chuni and Vemaster sudatlanticus were all found below -3770m), while others displayed remarkable eurybathy, with very high depths amplitudes (Bathybiaster loripes (4842m), Lysasterias adeliae (4832m), Lophaster stellans (4752m), Cheiraster planeta (4708m), Er-emicaster crassus (4626m), Lophaster gaini (4560m) and Ctenodiscus australis (4489m)).

Even if the number of records is relatively small, the data bring many new insights on the taxonomic, bathymetric and geographic distributions of Southern star"sh, covering a very large sampling zone. #e dataset also brings to light six species, newly reported in the Southern Ocean.

#e quality of the data was controlled very thoroughly, by means of on-board Polarstern GPS sys-tems, checking of identi"cation by a renowned specialist (Prof. Michel Jangoux, Université Libre de Brux-

ZooKeys 185: 73–78 (2012)

doi: 10.3897/zookeys.185.3078

www.zookeys.org

Copyright Bruno Danis et al. This is an open access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

DAtA PAPEr

Launched to accelerate biodiversity research

A peer-reviewed open-access journal

Impa

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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

atlas.biodiversity.aq

• Biogeographic Atlas of the Southern Ocean



• Redo of Hedgepeth 1969 Folio




• Predictive approach





• Static and dynamic versions





• Static and dynamic versions

• Modelization loops are ready


94 Interpolated data layersSlopeBathymetryChlorophyllDistance to the continentDistance to bird coloniesDistance to iceDistance to shelfDistance to canyonFloor temperature...+ ANTABIF Occurrence records

R-functions GUI for BRT

mars.biodiversity.aq

• 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




• 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


• 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 3: batch sequence data processing

Step 4: customized sequence data processing


• Potential applications:



Is there a biogeography of Antarctic microbes?




Document Antarctic bioprospecting activities




Document Antarctic bioprospecting activities

Assess bioindicating value of microbial diversity as early warning system of ecosystems shifts


Challenges

Challenges

• Data deluge

Challenges

• Data deluge• Huge gaps in the data

Challenges

• Data deluge• Huge gaps in the data• Missing data types

Challenges

• Data deluge• Huge gaps in the data• Missing data types• Orphan datasets

Challenges

• Data deluge• Huge gaps in the data• Missing data types• Orphan datasets• True integration of complex data

ANTABIF at the BELSPO-SOA event

Technology

Transcript of ANTABIF at the BELSPO-SOA event