Presentation given at the MNHM, Paris in December 2011. GIves an overview of the new architecture and new tools available for the community.

1. Antarctic Biodiversity
Networks
New Architecture, New Tools
Bruno Danis
Tuesday 13 December 11

2. Objectives
• get familiar with Antarctic Biodiversity
Networks
• learn about the new architecture, and
functionalities
• get you onboard
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3. On the Menu Today
• Background
• (quick) Technical overview
• Applications
• Functionalities
• Carrots
• Future directions
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4. Background
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5. 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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6. Antarctic Biodiversity
Information Networks
• SCAR Marine Biodiversity Information Network
• Antarctic Biodiversity Information Facility
• Core funding: BELSPO.be
• Also from: SCAR, CAML, AWI, DFG, NWO, AAD
• International Polar Year 2007/08 (IPY)
• Census of Antarctic Marine Life (CAML)
Tuesday 13 December 11

7. Antarctic Biodiversity
Information Networks
• Antarctic Node for OBIS
• Antarctic Node for GBIF
• Data management component for new SCAR PPGs:
ANT-ECO, ANT-ERA
• Biodiversity component of SOOS
• Antarctic Node for GEO-BON
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8. General Philosophy
• Build an electronic ecosystem
• Offer free and open access to data and technology
• Expose all the (biodiversity) data and metadata, in
multiple contexts
• Remain community-driven, and collaborative
• Adopt strong standardization
• Work for science, conservation, management
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9. Tuesday 13 December 11

10. Achievements: dataportals
• Portal up since Oct 2005
• open access
• 935,000 visitors
• 8,400,000 hits
• 60,000,000 dld records
• Citations: 183
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11. Achievements: taxonomy
• The first RAMS
• Board of 60+ editors
• Feeds WoRMS, CoL and EoL
• 17,098 taxa (RAMS)
• Building a dynamic RAS
• 24,248 taxa (RAS)
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12. Achievements: biogeography
• 1,288,441 records
• 198 datasets
• 5,235 taxa
• Feeds OBIS, GBIF
• Downloadable
• WebGIS
• Webservices
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13. Achievements: Progress
Records MarBIN ANTABIF Progress
Metadata 198 7.200 36,4
Occurrence 1.300.000 3.300.000 2,5
Taxonomy 17.000 30.500 1,8
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14. Nuts and Bolts
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15. 100% Open Source
• 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)
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16. Data flow
(your point of view)
Your data DwC-A IPT ANTABIF
standardize upload publish
publish
Data Paper
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17. Data flow
(our point of view)
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18. Applications
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19. Gaps
in
our
knowledge
(spa=al)
Clarke AH, Danis B, Griffiths HJ, DSRII 2011
BENTHOS
PLANKTON
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20. All species
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21. Benthic species
21
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22. Birds and Mammals (nice and fluffy)
Clarke AH, Danis B, Griffiths HJ, DSRII 2011
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23. Nematoda (small and ugly)
Clarke AH, Danis B, Griffiths HJ, DSRII 2011
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24. Echinodermata (in between)
Echinodermata
a b
Clarke AH, Danis B, Griffiths HJ, DSRII 2011
Tuesday 13 December 11

25. Yet another problem
2,8 isopod species described per year
600+ discovered during ANDEEP expeditions
214 years to describe them!
De Broyer C & Danis B, DSRII 2011
Tuesday 13 December 11

26. Biogeographic Atlas
•Re-­‐do
of
a
“classic”:
Hedgepeth
1969
•BASO:
Paper
and
digital
versions
•Predic=ve
maps
(93
env.
parameters
injected...)
•Build
an
interac=ve
plaPorm
•Crossdisciplinary
capacity
building
•Fill
in
gaps
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27. Hedgpeth
1969’s
Folio
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28. Mashing
(and
sharing)
data
layers
Slope
Bathymetry
Chlorophyll
Distance to the continent
Distance to bird colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
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29. Tuesday 13 December 11

30. Functionalities
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31. biodiversity.aq
• organized in subdomains: “.aq” = Antarctica
• www.biodiversity.aq
• data.biodiversity.aq
• ipt.biodiversity.aq
• afg.biodiversity.aq
• scratchpads.biodiversity.aq
• ogc.biodiversity.aq
Tuesday 13 December 11

32. www. biodiversity.aq
• general website
• latest news
• contact
• sponsors
• governance
• RSS feeds: blog, PIC, photostream, slideshare,
Mendeley
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33. www. biodiversity.aq
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34. 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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35. data. biodiversity.aq
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36. ipt. biodiversity.aq
• prepare and clean your data
• publish primary biodiversity data
• publish metadata
• push data and metadata to ANTABIF &
GBIF
• generate and submit a Data Paper
Tuesday 13 December 11

37. ipt. biodiversity.aq
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38. 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 share
Tuesday 13 December 11

39. afg. biodiversity.aq
Tuesday 13 December 11

40. afg. biodiversity.aq
afg.biodiversity.aq
Antarctic Field Guides
Tuesday 13 December 11

41. afg. biodiversity.aq
afg.biodiversity.aq
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42. afg. biodiversity.aq
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43. afg. biodiversity.aq
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44. afg. biodiversity.aq
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45. afg. biodiversity.aq
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46. Carrots
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47. Reward data publishing
Metadata document Data Paper
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48. 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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49. Incentivising Data Discovery
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50. Step-by-Step
• 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
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51. Once paper is accepted
• 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.
Tuesday 13 December 11

52. Important to consider
• 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
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53. NPT
• GBIF - Nodes Portal Toolkit
• To deploy and maintain modular biodiversity data
portals
• Uses GBIF data
• Extensible to accommodate custom needs
• Open Source
• Community developments
Tuesday 13 December 11

54. The
basic
NPT
plaPorm
provides
everything
needed
to
start
a
web
site
Non-­‐technical
staff
can
just
start
adding
content!
Tuesday 13 December 11

55. NPT
Startup
Summary
This
configura=on
is
a
star=ng
point
for
further
development
• Provides
a
customizable
website
/
portal
• Provides
founda=on
for
further
modules
to
be
added
• Displays
GBIF
portal
data
as
data
maps
for
your
country
or
region
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56. 56
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57. 57
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58. 58
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59. 59
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60. 60
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61. 61
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62. Perspectives
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63. Community
• A network of IPTs and NPTs
• Enhanced data flow
• Community involved in data management
• Enhanced interoperability
• Optimization of research efforts/resources
• Integrative, connected science
• Factual, adaptative conservation
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64. Challenges
• Data intensive science
• Data deluge
• Digital divides
• Other data types and integration
• Orphan datasets
• Cultural change
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65. Thanks
www.biodiversity.aq
image
©
NY
Times
Tuesday 13 December 11