Download - Bruno Progress Report
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SCAR-MarBIN.beProgress Report - workshop 09
Held at the British Antarctic Survey, hosted by Katrin Linse & Huw Griffiths
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Background
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SCAR-MarBIN
• Funding: Belgian science Policy office
• International Polar Year 2007/08
• Census of Antarctic Marine Life
• Ocean Biogeographic Information System
• Global Biodiversity Information Network
• Encyclopedia of Life
Marine Biodiversity Information Network
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• Build a network
• Offer free and open access to data and technology
• Expose all the (biodiversity) data and metadata
• Remain community-driven
• Adopt strong standardization
• Work for science, conservation, management
Philosophy
Riddle, M. Australian Antarctic Division
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What sort of data?
• Primary Biodiversity data
• Taxonomy and Systematics
• Occurence/abundance data
• Genetic data
• DwC
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Present situation
• BAD NEWS:
• BELSPO Funding Ended
• No developper
• GOOD NEWS:
• International contributions
• New project to keep MarBIN alive
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Results
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Tangible results
• The first RAMS
• Board of 60 editors
• Feeds WoRMS, CoL and EoL
• 16,224 taxa
• 9,253 species
• 8,211 valid species
• 10,605 checked taxa (65%)
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Tangible results
all taxa
all species
valid species
0 3.750 7.500 11.250 15.000
Acanthocephala Annelida Arthropoda Brachiopoda Bryozoa Cephalorhyncha Chaetognatha Chordata Cnidaria Ctenophora Echinodermata Echiura Hemichordata Mesozoa Mollusca Myxozoa Nematoda Nemertina Platyhelminthes Porifera Rotifera Sipuncula Tardigrada
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Tangible results
all taxa
all species
valid species
0 500 1.000 1.500 2.000
Biliphyta ViridaeplantaeProtoctista StramenopilaMonera Chromista
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Tangible results
1,031,732 records138 datasets
over 5,200 taxaDownloadable
WebGISWebservices OGC
+RESTish
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Synthesizing knowledge
• RAMS: information on 16,000 taxa
• ANTOBIS: 1,000,000+ records
• Polar Macroscope Synthesis team
• Injection into conservation processes
• New insights in biogeography
• New insights in ecological processes
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Meetings attended
• e-Biosphere 09
• OBIS MC 09
• GBIF GB 09
• WCMC 09
• Diversitas 09
• SCAR-OSC 09
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Funding• BELSPO: down, funding new project
• SCAR: 5 kUSD per year
• CAML: 20 kUSD one shot (for 2009-10)
• AAD: 6k AUD (two years)
• German Science Foundation: 5 kEUR (two years)
• Dutch Science Foundation: 5 kUSD (one year)
• AWI: 7 kEUR (two years)
• ArcOD: 3 kUSD one shot
• TOTAL Foundation: 260 kEUR one shot
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Applications
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Identifying gaps
Griffiths HJ, British Antarctic Survey
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AllSpecies
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Identifying gaps
Over 50% of samples taken in waters shallower than 400m
Similar trend for recorded benthic species
Most of the Southern Ocean is abyssal
Griffiths HJ, Clarke A, Danis B, submitted
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Identifying gaps
2,8 isopod species are descibed every year
600+ were discovered during ANDEEP
We will need 214 years to describe them!
De Broyer C & Danis B, submitted
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Webportal V2.0
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SCAR-MarBIN V2
•Main goals
• Better, faster, simpler
• Improve usability
• Improve interoperability
• Improve dissemination and visibility
• Extend functionalities
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Systems comparisonV1 V2
Languages PHP4 (procedural part OOish) Java, Groovy (100% OO)
Design patterns - MVC-ORM-AOP-IoC…
Framework - (100% homebrew) Grails (Spring, Hibernate), YUI
Template engine - SiteMesh
Search engine SQL-based Full text (SOLR-lucene)
DB SQL server SQL server - PostGresql
GIS server mapserver Geoserver
Spatial DB - PostGIS
Mapping client chameleon openLayers
Web services SOAP (RAMS) RESTish (all resources)
OS Windows server FreeBSD
Open source Partly 100% (minus legacy DB)
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I know you love stats
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Portal useage
0
3.000
6.000
sept
-05
déc-
05
mar
s-06
juin
-06
sept
-06
déc-
06
mar
s-07
juin
-07
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-07
déc-
07
mar
s-08
juin
-08
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déc-
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mar
s-09
juin
-09
sept
-09
Unique visitors
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Portal useage
0
10.000
20.000
sept
-05
déc-
05
mar
s-06
juin
-06
sept
-06
déc-
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mar
s-07
juin
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déc-
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s-08
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juin
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bandwidth
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Portal useage
0
2.000
4.000
sept
-05
déc-
05
mar
s-06
juin
-06
sept
-06
déc-
06
mar
s-07
juin
-07
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déc-
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bandwidth
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2007 connections origin (hits)
0%0%0%1%0%1%1%1%1%1%1%1%1%2%2%2%
8%
2%3%2%4%
8%11%
16%
30%
UnknownBelgiumNetworkCommercialGermanyPolandItalySpainUnknownFranceBrazilUnited KingdomCanadaAustraliaRussian FederationUSA EducationalNon-Profit OrganizationsNetherlandsJapanArgentinaMoldovaChilePortugalGreeceUkraine
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0%0%0%0%0%0%0%0%1%1%1%1%3%1%1%1%1%2%2%2%
4%
7%
8%
20%
41%
UnknownCommercialBelgiumNetworkFrancePolandGermanyUnited KingdomRussian FederationCanadaBrazilSpainUnknownUSA EducationalItalyAustraliaNetherlandsJapanSingaporeLatviaChileArgentinaNew ZealandNon-Profit OrganizationsChina
2008 connections origin (hits)
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0%0%0%0%0%0%0%0%1%1%0%1%1%1%1%2%1%2%2%2%5%
7%
5%
21%
45%
UnknownCommercialUnited KingdomNetworkBelgiumGermanyPolandBrazilRussian FederationItalySpainCanadaUSA EducationalFranceSingaporeAustraliaArgentinaBahamasJapanIsraelUkraineNew ZealandDenmarkNetherlandsChina
2009 connections origin (hits)
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Distribution data providersdatasets records % of datamass
Argentina 2 374 0,036249724
Australia 29 740243 71,747605
Belgium 8 10804 1,047171165
France 2 4293 0,416096428
Germany 2 7598 0,736431554
International 3 71236 6,904506209
Italy 2 683 0,066199362
Japan 1 19 0,001841564
New-Zealand 1 47865 4,639286171
Norway 2 69 0,006687783
Poland 1 87 0,008432422
Russia 1 2504 0,242698685
Spain 1 25 0,00242311
Ukraine 1 592 0,057379242
United Kingdom 5 48797 4,729619707
USA 11 96543 9,357371876
TOTAL 72 1114108 100
16 countries providing data
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Metadata providersmetadata records %metadata
Australia 36 26,08695652Belgium 14 10,14492754Poland 13 9,420289855BoL 12 8,695652174
United Kingdom 11 7,971014493International 9 6,52173913
USA 9 6,52173913Germany 7 5,072463768France 6 4,347826087
Argentina 3 2,173913043Spain 3 2,173913043Brazil 2 1,449275362Italy 2 1,449275362
Norway 2 1,449275362Russia 2 1,449275362Austria 1 0,724637681
Denmark 1 0,724637681Ireland 1 0,724637681Japan 1 0,724637681
Netherlands 1 0,724637681New Zealand 1 0,724637681
Ukraine 1 0,724637681TOTAL 138
22 countries providing metadata
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In the pipeline
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Projects
• TOTAL Foundation: minigrants and cybertaxonomy
• AFG
• Barcoding
• PMS
• ABBED
• ARCOD
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Total minigrants: Inventory of the Southern Ocean biodiversity
• A database of living Antarctic benthic Foraminifera (Protista) for SCAR-MarBIN RAMS (Prof. A.J. Gooday, National Oceanography Centre, Southampton, UK). (in progress).
• Databasing Antarctica marine Bioconstructors: Adding Large Sessile Habitat-forming Animals to SCAR-MarBIN (Dr H. Griffiths, British Antarctic Survey, Cambridge. UK). (in progress).
• SCAR-MarBIN database of Ostracoda Myocopida and Podocopida (Dr S. Brandao, Zoologisches Museum, Universitat Hamburg, Germany). (in prep.).
• Cumacea (Crustacea: Peracarida) of the Southern Ocean (Dr U. Muhlenhardt-Siegel, Biozentrum Grindel und Zoologisches Museum, Universitat Hamburg, Germany). (done).
• Synopsis of the Amphipoda Hyperiidea of the Southern Ocean, with distribution and ecological data (Dr W. Zeidler, South Australian Museum, Adelaide, Australia). (done).
• Building a biogeographic baseline of obligate Antarctic benthic brooders: isopods for the Southern Ocean Mollusc database (SOMBASE) and SCAR-MarBIN (Dr S. Kaiser, Zoologisches Museum, Universitat Hamburg, Germany). (in progress).
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Total minigrants: Inventory of the Southern Ocean biodiversity
• Biogeographic distribution of the Antarctic and Sub-Antarctic brachiopods (living forms) (Dr C. Emig, Marseille, France). (in progress).
• Systematics and distribution of echinoids collected during Australian cruises in East Antarctica (Dr T. Saucede, Universite de Bourgogne, Dijon, France). (in progress).
• Biodiversity of Antarctic and Sub-Antarctic Crinoids (Dr M. Eleaume, Musee National d’Histoire Naturelle, Paris, France). (in prep.).
• Biogeographic database of Antarctic and sub-Antarctic Polychaetes (Dr A. Glover, Natural History Museum, London, UK). (in prep.).
• Contribution to the SCAR-MarBIN Molluscs database (Dr M. Schrodl, Zoologisches Staatsammlung Munchen, Germany). (in prep.).
• Various general contributions to the SCAR-MarBIN RAMS and ANTOBIS (Henri Robert, Laboratory of Carcinology, Institut Royal des Sciences Naturelles de Belgique, BELGIUM.: Output: occurrence and taxonomic data (various groups), contributions to literature database, to expeditions database, to biogeographic synthesis).
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Upcoming technologies
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ANTABIF
• New project: Antarctic Biodiversity Information Facility
• Funding: BELSPO (two years)
• Objective: build (fast) a new portal giving access on all available information on Antarctic biodiversity
• www.biodiversity.aq
• Close collaboration with AAD/EBA/SCADM
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Thanks!!
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2008 ToDos
• see review