Antarctic Biodiversity                          Networks                         New Architecture, New Tools              ...
Objectives                   • get familiar with Antarctic Biodiversity                         Networks                  ...
On the Menu Today                   • Background                   • (quick) Technical overview                   • Applic...
BackgroundTuesday 13 December 11
Antarctic Treaty                         « In order to promote international                         cooperation in scient...
Antarctic Biodiversity                  Information Networks     •      SCAR Marine Biodiversity Information Network     •...
Antarctic Biodiversity                  Information Networks    • Antarctic Node for OBIS    • Antarctic Node for GBIF    ...
General Philosophy    • Build an electronic ecosystem    • Offer free and open access to data and technology    • Expose a...
Tuesday 13 December 11
Achievements: dataportals •      Portal up since Oct 2005 •      open access •      935,000 visitors •      8,400,000 hits...
Achievements: taxonomy  •      The first RAMS  •      Board of 60+ editors  •      Feeds WoRMS, CoL and EoL  •      17,098 ...
Achievements: biogeography  •      1,288,441 records  •      198 datasets  •      5,235 taxa  •      Feeds OBIS, GBIF  •  ...
Achievements: Progress                         Records    MarBIN      ANTABIF     Progress                         Metadat...
Nuts and BoltsTuesday 13 December 11
100% Open Source    •       Language: Ruby    •       Framework: Rails(ActiveRecord) and YUI    •       (smart) Search eng...
Data flow                                        (your point of view)  Your data                            DwC-A          ...
Data flow                         (our point of view)Tuesday 13 December 11
ApplicationsTuesday 13 December 11
Gaps	  in	  our	  knowledge	  (spa=al)                                                        Clarke AH, Danis B, Griffiths...
All speciesTuesday 13 December 11
Benthic species                         21Tuesday 13 December 11
Birds and Mammals (nice and fluffy)                                     Clarke AH, Danis B, Griffiths HJ, DSRII 2011Tuesday ...
Nematoda (small and ugly)                                            Clarke AH, Danis B, Griffiths HJ, DSRII 2011Tuesday 13...
Echinodermata (in between)                            Echinodermata                                  a                    ...
Yet another problem                  2,8 isopod species described per year                  600+ discovered during ANDEEP ...
Biogeographic Atlas      •Re-­‐do	  of	  a	  “classic”:	  Hedgepeth	  1969      •BASO:	  Paper	  and	  digital	  versions ...
Hedgpeth	  1969’s	  FolioTuesday 13 December 11
Mashing	  (and	  sharing)	  data	  layers                                              Slope                              ...
Tuesday 13 December 11
FunctionalitiesTuesday 13 December 11
biodiversity.aq         • organized in subdomains: “.aq” = Antarctica         • www.biodiversity.aq         • data.biodive...
www. biodiversity.aq         • general website         • latest news         • contact         • sponsors         • govern...
www. biodiversity.aqTuesday 13 December 11
data. biodiversity.aq                   • find primary biodiversity data                   • visualize occurrence data on m...
data. biodiversity.aqTuesday 13 December 11
ipt. biodiversity.aq                   • prepare and clean your data                   • publish primary biodiversity data...
ipt. biodiversity.aqTuesday 13 December 11
afg. biodiversity.aq                   • Identification aid                   • Publication/sharing platform for customized...
afg. biodiversity.aqTuesday 13 December 11
afg. biodiversity.aq                             afg.biodiversity.aq                     Antarctic Field GuidesTuesday 13 ...
afg. biodiversity.aq                                afg.biodiversity.aqTuesday 13 December 11
afg. biodiversity.aqTuesday 13 December 11
afg. biodiversity.aqTuesday 13 December 11
afg. biodiversity.aqTuesday 13 December 11
afg. biodiversity.aqTuesday 13 December 11
CarrotsTuesday 13 December 11
Reward data publishing                         Metadata document   Data PaperTuesday 13 December 11
The Data Paper        • A scholarly journal publication whose primary purpose is to          describe a dataset or group o...
Incentivising Data DiscoveryTuesday 13 December 11
Step-by-Step       • Complete metadata of a dataset using metadata editor in IPT         2.0.2       • Generate ‘Data Pape...
Once paper is accepted       • Digital Object Identifier is assigned to the Data Paper       • Paper is published in (a) pr...
Important to consider       • Metadata is complete in all the respect       • All the claims are adequately substantiated ...
NPT       • GBIF - Nodes Portal Toolkit       • To deploy and maintain modular biodiversity data              portals     ...
The	  basic	  NPT	  plaPorm	  provides	  everything	  needed	  to	                              start	  a	  web	  site	   ...
NPT	  Startup	  Summary       This	  configura=on	  is	  a	  star=ng	  point	  for	  further	         development       • P...
56Tuesday 13 December 11
57Tuesday 13 December 11
58Tuesday 13 December 11
59Tuesday 13 December 11
60Tuesday 13 December 11
61Tuesday 13 December 11
PerspectivesTuesday 13 December 11
Community                   • A network of IPTs and NPTs                   • Enhanced data flow                   • Communi...
Challenges                   • Data intensive science                   • Data deluge                   • Digital divides ...
Thanks                         www.biodiversity.aq                              image	  ©	  NY	  Times	  Tuesday 13 Decemb...
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Antarctic Biodiversity Networks: new architecture, new tools

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

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Antarctic Biodiversity Networks: new architecture, new tools

  1. 1. Antarctic Biodiversity Networks New Architecture, New Tools Bruno DanisTuesday 13 December 11
  2. 2. Objectives • get familiar with Antarctic Biodiversity Networks • learn about the new architecture, and functionalities • get you onboardTuesday 13 December 11
  3. 3. On the Menu Today • Background • (quick) Technical overview • Applications • Functionalities • Carrots • Future directionsTuesday 13 December 11
  4. 4. BackgroundTuesday 13 December 11
  5. 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. »Tuesday 13 December 11
  6. 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. 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-BONTuesday 13 December 11
  8. 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, managementTuesday 13 December 11
  9. 9. Tuesday 13 December 11
  10. 10. Achievements: dataportals • Portal up since Oct 2005 • open access • 935,000 visitors • 8,400,000 hits • 60,000,000 dld records • Citations: 183Tuesday 13 December 11
  11. 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)Tuesday 13 December 11
  12. 12. Achievements: biogeography • 1,288,441 records • 198 datasets • 5,235 taxa • Feeds OBIS, GBIF • Downloadable • WebGIS • WebservicesTuesday 13 December 11
  13. 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 1,8Tuesday 13 December 11
  14. 14. Nuts and BoltsTuesday 13 December 11
  15. 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)Tuesday 13 December 11
  16. 16. Data flow (your point of view) Your data DwC-A IPT ANTABIF standardize upload publish publish Data PaperTuesday 13 December 11
  17. 17. Data flow (our point of view)Tuesday 13 December 11
  18. 18. ApplicationsTuesday 13 December 11
  19. 19. Gaps  in  our  knowledge  (spa=al) Clarke AH, Danis B, Griffiths HJ, DSRII 2011 BENTHOS PLANKTONTuesday 13 December 11
  20. 20. All speciesTuesday 13 December 11
  21. 21. Benthic species 21Tuesday 13 December 11
  22. 22. Birds and Mammals (nice and fluffy) Clarke AH, Danis B, Griffiths HJ, DSRII 2011Tuesday 13 December 11
  23. 23. Nematoda (small and ugly) Clarke AH, Danis B, Griffiths HJ, DSRII 2011Tuesday 13 December 11
  24. 24. Echinodermata (in between) Echinodermata a b Clarke AH, Danis B, Griffiths HJ, DSRII 2011Tuesday 13 December 11
  25. 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 2011Tuesday 13 December 11
  26. 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  gapsTuesday 13 December 11
  27. 27. Hedgpeth  1969’s  FolioTuesday 13 December 11
  28. 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 ...Tuesday 13 December 11
  29. 29. Tuesday 13 December 11
  30. 30. FunctionalitiesTuesday 13 December 11
  31. 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.aqTuesday 13 December 11
  32. 32. www. biodiversity.aq • general website • latest news • contact • sponsors • governance • RSS feeds: blog, PIC, photostream, slideshare, MendeleyTuesday 13 December 11
  33. 33. www. biodiversity.aqTuesday 13 December 11
  34. 34. data. biodiversity.aq • find primary biodiversity data • visualize occurrence data on map • view taxonomic data • download data • view metrics • send feedback • access technical documentationTuesday 13 December 11
  35. 35. data. biodiversity.aqTuesday 13 December 11
  36. 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 PaperTuesday 13 December 11
  37. 37. ipt. biodiversity.aqTuesday 13 December 11
  38. 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 shareTuesday 13 December 11
  39. 39. afg. biodiversity.aqTuesday 13 December 11
  40. 40. afg. biodiversity.aq afg.biodiversity.aq Antarctic Field GuidesTuesday 13 December 11
  41. 41. afg. biodiversity.aq afg.biodiversity.aqTuesday 13 December 11
  42. 42. afg. biodiversity.aqTuesday 13 December 11
  43. 43. afg. biodiversity.aqTuesday 13 December 11
  44. 44. afg. biodiversity.aqTuesday 13 December 11
  45. 45. afg. biodiversity.aqTuesday 13 December 11
  46. 46. CarrotsTuesday 13 December 11
  47. 47. Reward data publishing Metadata document Data PaperTuesday 13 December 11
  48. 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 communityTuesday 13 December 11
  49. 49. Incentivising Data DiscoveryTuesday 13 December 11
  50. 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 SystemTuesday 13 December 11
  51. 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. 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 manuscriptTuesday 13 December 11
  53. 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 developmentsTuesday 13 December 11
  54. 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. 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  regionTuesday 13 December 11
  56. 56. 56Tuesday 13 December 11
  57. 57. 57Tuesday 13 December 11
  58. 58. 58Tuesday 13 December 11
  59. 59. 59Tuesday 13 December 11
  60. 60. 60Tuesday 13 December 11
  61. 61. 61Tuesday 13 December 11
  62. 62. PerspectivesTuesday 13 December 11
  63. 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 conservationTuesday 13 December 11
  64. 64. Challenges • Data intensive science • Data deluge • Digital divides • Other data types and integration • Orphan datasets • Cultural changeTuesday 13 December 11
  65. 65. Thanks www.biodiversity.aq image  ©  NY  Times  Tuesday 13 December 11

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