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ANTABIF:Architecture and Functionalities Bruno Danis - MARS workshop
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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. »
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Our vision:[ANTARCTIC BIODIVERSITY] Data are open, linked, useful, interoperable and safe.
Copyright: © Christian Morel
Slide stolen from Mark Parsons
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Antarctic Information Networks - scope
Funding: BELSPO, SLOAN, DFG, AWI, SCAR, AAD, NWO David B, Danis B, Griffiths HJThursday 10 May 12
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Antarctic Information Networks - scope
• Born as Census of Antarctic Marine Life as the data, visualization and analysis component
Funding: BELSPO, SLOAN, DFG, AWI, SCAR, AAD, NWO David B, Danis B, Griffiths HJThursday 10 May 12
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Antarctic Information Networks - scope
• Born as Census of Antarctic Marine Life as the data, visualization and analysis component
• Free and open access to biodiversity data
Funding: BELSPO, SLOAN, DFG, AWI, SCAR, AAD, NWO David B, Danis B, Griffiths HJThursday 10 May 12
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Antarctic Information Networks - scope
• 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
Funding: BELSPO, SLOAN, DFG, AWI, SCAR, AAD, NWO David B, Danis B, Griffiths HJThursday 10 May 12
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Antarctic Information Networks - scope
• 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
Funding: BELSPO, SLOAN, DFG, AWI, SCAR, AAD, NWO David B, Danis B, Griffiths HJThursday 10 May 12
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Antarctic Information Networks - scope
• 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
Funding: BELSPO, SLOAN, DFG, AWI, SCAR, AAD, NWO David B, Danis B, Griffiths HJThursday 10 May 12
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Antarctic Information Networks - scope
• 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
• SCAR-MarBIN: Citations : 423, Publications: 58, H-Index: 11
Funding: BELSPO, SLOAN, DFG, AWI, SCAR, AAD, NWO David B, Danis B, Griffiths HJThursday 10 May 12
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Antarctic Information Networks - scope
• 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
• SCAR-MarBIN: Citations : 423, Publications: 58, H-Index: 11
Funding: BELSPO, SLOAN, DFG, AWI, SCAR, AAD, NWO David B, Danis B, Griffiths HJThursday 10 May 12
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Collaboration cloud - who’s in?
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Collaboration cloud - who’s in?
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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
Virtually nothing on Bacteria!!
Taxonomy
De Broyer et al, Register of Antarctic Marine Species 2012
17,098 taxa
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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
Virtually nothing on Bacteria!!
Taxonomy
De Broyer et al, Register of Antarctic Marine Species 2012
17,098 taxa
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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
• Virtually nothing on Bacteria!!Danis et al, Antarctic Biodiversity Information Facility 2012
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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
• Virtually nothing on Bacteria!!Danis et al, Antarctic Biodiversity Information Facility 2012
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Antarctic Information Networks - applications
Danis et al, The SCAR Antarctic Field Guides 2012
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Antarctic Information Networks - applications
• Data-driven Marine Protected Area designation
Danis et al, The SCAR Antarctic Field Guides 2012
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Antarctic Information Networks - applications
• Data-driven Marine Protected Area designation
• Expedition design
Danis et al, The SCAR Antarctic Field Guides 2012
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Antarctic Information Networks - applications
• Data-driven Marine Protected Area designation
• Expedition design
• Biogeographic patterns
Danis et al, The SCAR Antarctic Field Guides 2012
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Antarctic Information Networks - applications
• Data-driven Marine Protected Area designation
• Expedition design
• Biogeographic patterns
• Antarctic Field Guides
Danis et al, The SCAR Antarctic Field Guides 2012
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Antarctic Information Networks - applications
• Data-driven Marine Protected Area designation
• Expedition design
• Biogeographic patterns
• Antarctic Field Guides
• Biogeographic Atlas
Danis et al, The SCAR Antarctic Field Guides 2012
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Antarctic Information Networks - applications
• Data-driven Marine Protected Area designation
• Expedition design
• Biogeographic patterns
• Antarctic Field Guides
• Biogeographic Atlas
• Gap analysisDanis et al, The SCAR Antarctic Field Guides 2012
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Functionalities
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• www.biodiversity.aq
biodiversity.aq
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• www.biodiversity.aq• data.biodiversity.aq
biodiversity.aq
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• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq
biodiversity.aq
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• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq
biodiversity.aq
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• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq
biodiversity.aq
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• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq• share.biodiversity.aq
biodiversity.aq
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• www.biodiversity.aq• data.biodiversity.aq• ipt.biodiversity.aq• afg.biodiversity.aq• atlas.biodiversity.aq• share.biodiversity.aq• mars.biodiversity.aq ?
biodiversity.aq
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• general website• latest news• contact• sponsors• governance• ressources
www. biodiversity.aq
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www. biodiversity.aq-shared repository-
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data. biodiversity.aq• find primary biodiversity data• visualize occurrence data on map• view taxonomic data• download data• view metrics• send feedback• access technical documentation
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Data portal recipe• 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), EMLThursday 10 May 12
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Data portal recipe
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Data portal recipe
GEO ORIENTED
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Data portal recipe
GEO ORIENTEDOPEN SOURCE
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Data portal recipe
GEO ORIENTEDOPEN SOURCE
FLEXIBLE
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Data portal recipe
GEO ORIENTEDOPEN SOURCE
FLEXIBLEINTEROPERABLE
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Data portal recipe
GEO ORIENTEDOPEN SOURCE
FLEXIBLEINTEROPERABLE
EXPANDABLE
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data. biodiversity.aq
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ipt. biodiversity.aq• Integrated Publishing Toolkit
• standardize and clean your data• manage your primary biodiversity data
• manage your associated metadata• choose your collaborators• generate and submit a Data Paper
• push data and metadata to Information Systems
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ipt. biodiversity.aq
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ipt. biodiversity.aq
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ipt. biodiversity.aq
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ipt. biodiversity.aq
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ipt. biodiversity.aq
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Data PaperMetadata document
Reward data publishing
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The Data Paper• A scholarly journal publication whose primary purpose is to
describe a dataset or group of datasets, rather than to report a research investigation.
• Benefits of the Data Paper
–Scholarly credit to Data Publishers
–Describe the data in structured human readable form
–Bring the existence of the data to the attention of the scholarly community
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Incentivising Data Discovery
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• Complete metadata of a dataset using metadata editor in IPT 2.0.2
• Generate ‘Data Paper’ manuscript (menu: Manage Resource – RTF Download)
• Submit the manuscript for possible publication in one of the PenSoft publication (ZooKeys, PhytoKeys, BioRisks, NeoBiota, Biodiversity Data Journal, Nature Conservation).
• Revision (if any) is carried out using metadata editor in IPT 2.0.2 and manuscript re-submitted to PenSoft Open Journal System
Step-by-Step
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• Digital Object Identifier is assigned to the Data Paper
• Paper is published in (a) print format, (b) PDF format, (c) semantically enhanced HTML, and (d) XML is archived in PubMedCentral
• DOI of the Data Paper is linked with the Persistent Identifier of the metadata document in the GBIF Registry
• Data Paper is indexed by Web of Knowledge (ISI), PubMedCentral, Scopus, Zoological Record, Google Scholar, CAB Abstracts, Directory of Open Access Journal (DOAJ), EBSCO.
Once paper is accepted
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• Metadata is complete in all the respect• All the claims are adequately substantiated• Data described in ‘Data Paper’ is freely
available at the time of submission of the manuscript
Important to consider
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This is realAntarctic 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
ct F
acto
r: 0.
514
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This is realAntarctic 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.
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This is realAntarctic 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.
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acto
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atlas. biodiversity.aq
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• Biogeographic Atlas of the Southern Ocean
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• Biogeographic Atlas of the Southern Ocean
• Redo of Hedgepeth 1969 Folio
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• Biogeographic Atlas of the Southern Ocean
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• Biogeographic Atlas of the Southern Ocean
• Redo of Hedgepeth 1969 Folio
• Predictive approach
• Static and dynamic versions
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• Dynamic approach to a Biogeographic Atlas
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• Dynamic approach to a Biogeographic Atlas
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• Dynamic approach to a Biogeographic Atlas
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• interdisciplinary: taxonomy, oceanography, ecology, phylogeography, modelization, data management, GIS, conservationists
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• Dynamic approach to a Biogeographic Atlas
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• interdisciplinary: taxonomy, oceanography, ecology, phylogeography, modelization, data management, GIS, conservationists
• Modelization workshop coming up
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Available data layers SlopeBathymetryChlorophyllDistance to the continentDistance to bird coloniesDistance to iceDistance to shelfDistance to canyonFloor temperature+ ANTABIF Occurrence records
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Available data layers SlopeBathymetryChlorophyllDistance to the continentDistance to bird coloniesDistance to iceDistance to shelfDistance to canyonFloor temperature+ ANTABIF Occurrence records
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Perspectives for MARS
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Community
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through Open Access
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Challenges
• Data deluge• Digital divides• Missing data types• Orphan datasets• Cultural change
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ANTABIF on MARS
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ANTABIF on MARS• Architectural plasticity
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ANTABIF on MARS• Architectural plasticity• DarwinCore + MiXS extension
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ANTABIF on MARS• Architectural plasticity• DarwinCore + MiXS extension• GBIF IPT/HIT
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ANTABIF on MARS• Architectural plasticity• DarwinCore + MiXS extension• GBIF IPT/HIT• Interoperability
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ANTABIF on MARS• Architectural plasticity• DarwinCore + MiXS extension• GBIF IPT/HIT• Interoperability• ElasticSearch
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ANTABIF on MARS• Architectural plasticity• DarwinCore + MiXS extension• GBIF IPT/HIT• Interoperability• ElasticSearch• Strong community
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ANTABIF on MARS• Architectural plasticity• DarwinCore + MiXS extension• GBIF IPT/HIT• Interoperability• ElasticSearch• Strong community• Incentives and valorization
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