Antabif on mars

ANTABIF:Architecture and Functionalities Bruno Danis - MARS workshop

Thursday 10 May 12

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. »

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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


• 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

• SCAR-MarBIN: Citations : 423, Publications: 58, H-Index: 11


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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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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• Data-driven Marine Protected Area designation


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• Expedition design


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• Biogeographic patterns


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• Antarctic Field Guides


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• Biogeographic Atlas


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• Biogeographic Atlas

• Gap analysisDanis et al, The SCAR Antarctic Field Guides 2012

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Functionalities

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biodiversity.aq

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http://www.antabif.be


• www.biodiversity.aq

biodiversity.aq

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http://www.biodiversity.aq




• 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-Resources-

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www. biodiversity.aq-shared repository-

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www. biodiversity.aq-Mendeley-

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www. biodiversity.aq-Pictures-

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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

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


FLEXIBLE

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Data portal recipe


FLEXIBLEINTEROPERABLE

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Data portal recipe


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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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

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r: 0.

514

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afg. biodiversity.aq• Identification aid• Publication/sharing platform for

customized Field Guides• High quality (useful) pictures• Expert Descriptions• Built dynamically from various sources• Generate a pdf for your taxa/area of

interest, and shareThursday 10 May 12

afg. biodiversity.aq

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atlas. biodiversity.aq

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• Biogeographic Atlas of the Southern Ocean


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• Redo of Hedgepeth 1969 Folio


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• Predictive approach


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• Predictive approach

• Static and dynamic versions


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• Dynamic approach to a Biogeographic Atlas


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• Collaborative project: 70+ specialists involved


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• interdisciplinary: taxonomy, oceanography, ecology, phylogeography, modelization, data management, GIS, conservationists


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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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Perspectives for MARS

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Community

• Get the Community involved in data management

• Enhance interoperability• Optimize research efforts/resources• Towards integrative, connected science

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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@biodiversityaq

image © NY Times

Thanks and questions?

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http://www.polarcommons.org

Antabif on mars

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