130712 antabif workshop


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  • data can be open , while not being linked data can be linked , while not being open data which is both open and linked is increasingly viable the Semantic Web can only function with data which is both open and linked --paul walk's weblog safe from hackers, from obsolescence, from undocumented change, from loss, from the ravages of time
  • An overview of our various projects and products. Offering Antarctic biodiversity data in various context depending on the users requirements.
  • 130712 antabif workshop

    1. 1. ANTABIF:Antarctic Biodiversity Information Facility Workshop 2012Antarctic Biodiversity Information
    2. 2. Background
    3. 3. Antarctic Treaty« In order to promote internationalcooperation in scientific investigation inAntarctica, […],Scientific observations and results fromAntarctica shall be exchanged andmade freely available. »
    4. 4. Our vision:Antarctic biodiversity data areopen, linked, useful, interoperable and safe.open, linked, useful, interoperable and safe.2011 Parsons et al.
    5. 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. 6. Collaboration cloud - who’s in?
    7. 7. Taxonomy 17,098 taxaThe first dynamic Register of Antarctic Marine SpeciesTaxonomic backboneBoard of 64 editorsFeeds WorldRegister of Marine Species, Catalogue of Life andEncyclopedia of Life
    8. 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. 9. Projects and Products
    10. 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. 11. afg. biodiversity.aq
    12. 12. afg. biodiversity.aq
    13. 13. afg. biodiversity.aq
    14. 14. afg. biodiversity.aq afg.biodiversity.aq Antarctic Field Guides
    15. 15. afg. biodiversity.aq afg.biodiversity.aq
    16. 16. afg. biodiversity.aq
    17. 17. afg. biodiversity.aq
    18. 18. afg. biodiversity.aq
    19. 19. afg. biodiversity.aq
    20. 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. 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. 22. Slope94 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. 23. R-functions GUI for BRT and GDM
    24. 24. Architectural design
    25. 25. 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
    26. 26. ww w.biodiversity.aq• general website• latest news• contact• sponsors• governance• resources• projects
    27. 27. www.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)
    28. 28. www.biodiversity.aq -mendeley-
    29. 29. www.biodiversity.aq -pictures-
    30. 30. www.biodiversity.aq -projects-
    31. 31. share.biodiversity.aq -shared repository-
    32. 32. data.biodiversity.aq• data discovery interface• visualize occurrence data on map• view taxonomic data• download data• view metrics• send feedback• access technical documentation
    33. 33. 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
    34. 34. data.biodiversity.aq
    35. 35. Data publication tools
    36. 36. 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
    37. 37. ipt. biodiversity.aq
    38. 38. ipt. biodiversity.aq
    39. 39. ipt. biodiversity.aq
    40. 40. ipt. biodiversity.aq
    41. 41. ipt. biodiversity.aq
    42. 42. Reward data publishingMetadata document Data Paper
    43. 43. Impact Factor: 0.514 Proof of concept
    44. 44. Communication tools
    45. 45. Communication• ANTABIF Blog• Other blogs• Facebook page• Twitter accounts• Mendeley library• Various community sites
    46. 46. Upcoming events
    47. 47. Upcoming events• CCAMLR workshop• GBIF Governing Board• APECS BeNeLux symposium• OBIS Managers meeting• ATCM 2013
    48. 48. Cooperation and integration
    49. 49. Cooperation and Integration• GBIF• OBIS• SOOS• SCADM• New PPGs• GEOSS• New Environmental Portal
    50. 50. Microbial AntarcticResource System
    51. 51. 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
    52. 52. 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
    53. 53. 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
    54. 54. Perspectives
    55. 55. Challenges• Data deluge• Huge gaps in the data• Missing data types• Orphan datasets• True integration of complex data
    56. 56. 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
    57. 57. Thanks and questions? @biodiversityaq image © NY Times