1. ANTABIF:
Antarctic Biodiversity Information
Facility Workshop 2012
Antarctic Biodiversity Information

2. Background

3. 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. »

4. Our vision:
Antarctic biodiversity data are
open, linked, useful, interoperable and safe.
open, linked, useful, interoperable and safe.2011
Parsons et al.

5. ANTABIF - background
• Born during the IPY 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
QuickTime™ en een
• Science, conservation and -decompressor
zijn vereist om deze afbeelding weer te geven.
management
• Networked community
developments
David B, Danis B, Griffiths HJ

6. Collaboration cloud - who’s in?

7. Taxonomy
17,098 taxa
The first dynamic Register of Antarctic Marine Species
Taxonomic backboneBoard of 64 editorsFeeds World
Register of Marine Species, Catalogue of Life and
Encyclopedia of Life

8. 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

9. Projects and
Products

10. afg. biodiversity.aq
• Identification aid
• High quality (useful) pictures
• Expert Descriptions
• Built on-the-fly from various
sources
• Generates a pdf for taxa/area of
interest

11. afg. biodiversity.aq

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afg.biodiversity.aq
Antarctic Field Guides

15. afg. biodiversity.aq
afg.biodiversity.aq

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19. afg. biodiversity.aq

20. atlas.biodiversity.aq
• Biogeographic Atlas of the Southern Ocean
• Redo of Hedgepeth 1969 Folio
• Predictive approach
• Static and dynamic versions
• Modelization loops are ready

21. atlas.biodiversity.aq
• Dynamic approach to a Biogeographic Atlas
• Collaborative project: 90+ specialists involved
• interdisciplinary: taxonomy, oceanography,
ecology, phylogeography, modelization, data
management, GIS, conservationists
• Modelization loops are ready (R-scripts with GUI)
• Results also valuable for SO-MPA designation

22. Slope
94 Interpolated data Bathymetry
Chlorophyll
layers Distance to the
continent
Distance to bird
colonies
Distance to ice
Distance to shelf
Distance to canyon
Floor temperature
...
+
ANTABIF Occurrence
records

23. R-functions GUI for
BRT and GDM

25. Architectural
design

26. biodiversity.aq
• www.biodiversity.aq MODULAR ARCHITECTURE
• data.biodiversity.aq Data discovery
Data products
• ipt.biodiversity.aq Data visualization
270
270
270
270
• afg.biodiversity.aq
270
270
• atlas.biodiversity.aq
• mars.biodiversity.aq
ANTABIF

27. ww
w.biodiversity.aq
• general website
• latest news
• contact
• sponsors
• governance
• resources
• projects

28. ww
w.biodiversity.aq
-resources-
redo these slides with new
redo these slides with new
structure of webportal (projects vs
structure of webportal (projects vs
resources)
resources)

29. ww
w.biodiversity.aq
-mendeley-

30. ww
w.biodiversity.aq
-pictures-

31. ww
w.biodiversity.aq
-projects-

32. share.biodiversity.aq
-shared repository-

33. data.biodiversity.aq
• data discovery interface
• visualize occurrence data on map
• view taxonomic data
• download data
• view metrics
• send feedback
• access technical documentation

34. Under the hood
• Language: RubyFramework:
SPATIALLY EXPLICIT
Rails(ActiveRecord) and YUI (smart) Search
OPEN SOURCE
engine: Full text (ElasticSearch-
Lucene)Database/GIS server/SpatialDB:
FLEXIBLE
PostGresql/Geoserver/PostGIS Mapping client:
INTEROPERABLE
OpenLayers Web services: RESTish (all
resources)Protocols/Standards: DIF, DwC,
EXPANDABLE
DwC-A, Tapir…etcGBIF tools : HIT, IPTHosting:
MULTI-STANDARDS
BeBIF (ULB/VUB joint IT Center)Metadata
systems: GCMD API (DIF), EML

35. data.
biodiversity.aq

44. Data publication
tools

45. ipt.biodiversity.aq
• Integrated Publishing Toolkit
• standardize and clean your data
• manage primary biodiversity data
• manage associated metadata
• choose collaborators
• generate and submit a Data Paper
• push data and metadata to Information
Systems

46. ipt. biodiversity.aq

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50. ipt. biodiversity.aq

51. Reward data
publishing
Metadata document Data Paper

52. Impact Factor: 0.514
Proof of concept

53. Communication
tools

54. Communication
• ANTABIF Blog
• Other blogs
• Facebook page
• Twitter accounts
• Mendeley library
• Various community sites

55. Upcoming events

56. Upcoming events
• CCAMLR workshop
• GBIF Governing Board
• APECS BeNeLux symposium
• OBIS Managers meeting
• ATCM 2013

57. Cooperation and
integration

58. Cooperation and
Integration
• GBIF
• OBIS
• SOOS
• SCADM
• New PPGs
• GEOSS
• New Environmental Portal

59. Microbial Antarctic
Resource System

60. mars.biodiversity.a
q
• Microbial Antarctic Resource System
• The organisms are small… but their environmental
impacts are critical to many Antarctic ecosystems
• They are the dominant and most diverse form of
life in the oceans and in the various microbial
habitats on the continent
• Access to their diversity is becoming cost-
effective and increasing exponentially

61. mars.biodiversity.a
q
• Integrate Antarctic microbial DNA sequence data in
ANTABIF
• Phased approach:
Step 0: data description and discovery
Step 1: microbial sequence and habitat metadata
Step 2: sequence data
Step 3: batch sequence data processing
Step 4: customized sequence data processing

62. mars.biodiversity.a
q
• Potential applications:
Is there a biogeography of Antarctic
microbes?
Document Antarctic bioprospecting activities
Assess bioindicating value of microbial
diversity as early warning system of
ecosystems shifts

63. Perspectives

64. Challenges
• Data deluge
• Huge gaps in the data
• Missing data types
• Orphan datasets
• True integration of complex data

65. Highlights
• new architecture deployed
• new data publication tools
• flexible design: ready for integration in many
contexts
• exciting data products being developed
• mARS paving the way to complex
genomics data processing
• so much to do... so little time

66. Thanks and questions?
@biodiversityaq
image © NY Times