bruno progress report
DESCRIPTION
Presentation given by Bruno Danis (SCAR-MarBIN) on the progress made during year 2009.TRANSCRIPT
SCAR-MarBIN.beProgress Report - workshop 09
Held at the British Antarctic Survey, hosted by Katrin Linse & Huw Griffiths
Background
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
• 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
What sort of data?
• Primary Biodiversity data
• Taxonomy and Systematics
• Occurence/abundance data
• Genetic data
• DwC
Present situation
• BAD NEWS:
• BELSPO Funding Ended
• No developper
• GOOD NEWS:
• International contributions
• New project to keep MarBIN alive
Results
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%)
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
Tangible results
all taxa
all species
valid species
0 500 1.000 1.500 2.000
Biliphyta ViridaeplantaeProtoctista StramenopilaMonera Chromista
Tangible results
1,031,732 records138 datasets
over 5,200 taxaDownloadable
WebGISWebservices OGC
+RESTish
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
Meetings attended
• e-Biosphere 09
• OBIS MC 09
• GBIF GB 09
• WCMC 09
• Diversitas 09
• SCAR-OSC 09
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
Applications
Identifying gaps
Griffiths HJ, British Antarctic Survey
AllSpecies
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
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
Webportal V2.0
SCAR-MarBIN V2
•Main goals
• Better, faster, simpler
• Improve usability
• Improve interoperability
• Improve dissemination and visibility
• Extend functionalities
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)
I know you love stats
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
sept
-07
déc-
07
mar
s-08
juin
-08
sept
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déc-
08
mar
s-09
juin
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sept
-09
Unique visitors
Portal useage
0
10.000
20.000
sept
-05
déc-
05
mar
s-06
juin
-06
sept
-06
déc-
06
mar
s-07
juin
-07
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07
mar
s-08
juin
-08
sept
-08
déc-
08
mar
s-09
juin
-09
sept
-09
bandwidth
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-
07
mar
s-08
juin
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sept
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déc-
08
mar
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juin
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sept
-09
bandwidth
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
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)
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)
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
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
In the pipeline
Projects
• TOTAL Foundation: minigrants and cybertaxonomy
• AFG
• Barcoding
• PMS
• ABBED
• ARCOD
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).
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).
Upcoming technologies
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
Thanks!!
2008 ToDos
• see review