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Biodiversity & Drupal

burkeker@gate.sinica.edu.tw




July 10th, 2010
image: http://web1.nsc.gov.tw/ct.aspx?xItem=7991&ctNode=40&mp=1
•                   ...
    •
    •
    •
    •
    •       (DNA)
    • ...
•


                    cc by-nd Nick Kurzenko, Greg Rouse, and the U. S. Fish and Wildlife Service
•                       (NHM)

                                                                           •
                                                                           •
                                                                           •

    Lepidoptera                       British Fleas


                     Chalcid Wasps                    Martian Meteorites
                                                                           •
                                                                           •
                                                                           •
                                                                           •
                                                                           •
                                                                           •
Spanish Sandflies                     Solanaceae
                                                                           •
                    Loch Ness Worms                     Bumble bees
                                                                           a slide from V.Smith
Joomla   WordPress




Plone     Drupal


                     a slide from V.Smith
http://www.idealware.org/comparing_os_cms/
                                       a slide from V.Smith
http://scratchpads.eu   a multisite implementation of Drupal




                                                    a slide from V.Smith
a slide from V.Smith
BiotaTaiwanica - a pilot Drupal project
•
•             LifeDesks
           ScratchPads


•
    http://psybugs.biota.biodiv.tw
specimens          node



                                                                         image
                       collecting events           node
              tags
                                                                         citation
latin names

       keywords                   image metadata          node
                                                                     collecting event
  vernaculars

          categories
                                                                        specimen

                                 literatures           node
                                                                       description




                         diagnostic descriptions       node
•
Content Types                                  (system components)   Workflows                   Products

 Taxonomic Information (Name data)              Taxonomic               Validation Service /     Darwin Core Checklist Archive
                                                Backbone               File Archiving Service     (DwC-A)
   IUCN red list
   ISSG invasive species          attributes
   CBD indicators                                                        Species Profiling        Species Profiles (TDWG)
                                                                             Service             Plazi TaxonX
 Species description
 Multimedia / digital objects - derived         Data Store                                       Modeling Results
 LIterature                                                             Modeling/Statistical
                                                                             Service             e.g. diagrams, numerical matrics
                                                        query                                    Connections to R
 Species occurrence: polygons
 Species occurrence: points                              producer
 Environmental spatial features                                          Mapping Service         WMS, WFS
 - Habitats                                     GIS-Ready
 - Ecosystems                                   Data Store
 - Climate                                                             Metadata Packaging        CASSIA, EML, FGDC-BDP,
 - Geographic                                                               Service              ISO-19115 or other metadata
 Other types of spatial data                                                                     formats

 Metadata                                       Metadata                   Other service
                                                                            workflows             Other results
 Annotation layers                              Catalogue
LifeDesks Classification modules (EOL)                                                                          Taxonomy module (Drupal core)
 - utilize Drupal taxonomy                                                                                      - defines vocabulary
 - provide editable name flags                                                                                   - classification is one vocabulary
 - easy drag & drop edit interface                                                                              - allows multiple tagging
 - export in Darwin Core & other formats                                                                        - ability to relate between terms



Modules for attributing name entries
- maybe one more biological flag needed




LifeDesks Taxon Page modules (EOL)
 - create content type: Taxon Page
 - map to Species Profile Model
 - customizable headers and chapters
 - connect to EOL as a content partner
                                                         Content Types                                  (system components)              Workflows                     Products

                                                          Taxonomic Information (Name data)              Taxonomic                            Validation Service /     Darwin Core Checklist Archive
                                                                                                         Backbone                            File Archiving Service     (DwC-A)
Image module (community)
and others designed to handle                               IUCN red list
various media types                                         ISSG invasive species          attributes
                                                            CBD indicators                                                                     Species Profiling        Species Profiles (TDWG)
                                                                                                                                                   Service             Plazi TaxonX
                                                          Species description
                                                          Multimedia / digital objects - derived         Data Store                                                    Modeling Results                   Modules for connecting to
Biblio module (community)                                 LIterature                                                                          Modeling/Statistical
                                                                                                                                                   Service             e.g. diagrams, numerical matrics   statistical solutions
- provides forms for managing citations                                                                                                                                Connections to R
- BibTex import/export                                    Species occurrence: polygons                           query
- redirect to Google Scholar                              Species occurrence: points                              producer
                                                          Environmental spatial features                                                       Mapping Service         WMS, WFS                           WFS module
                                                          - Habitats                                     GIS-Ready                                                                                        - export geodata as WFS
                                                          - Ecosystems                                   Data Store
                                                          - Climate                                                                          Metadata Packaging        CASSIA, EML, FGDC-BDP,
Darwin Core module (ScratchPads)
                                                          - Geographic                                                                            Service              ISO-19115 or other metadata
- combined with Location module and Gmap module
                                                          Other types of spatial data                                                                                  formats
- handle specimen and observation data
                                                          Metadata                                       Metadata                                   Other service
                                                                                                                                                     workflows          Other results
                                                          Annotation layers                              Catalogue

Location module
 - manage locality and coordinate

                                                                          CCK + Views
                                                                          - create content type
                                                                          - include custom fields
                                                                          - provide forms for entering data
Gmap module                                                               - publish as XML using Views modules
- provide Google Map layer




Nice Map module
- provide Google Map layer




                                                                                                                                                                                                          Profile
Modules for handling geospatial data                                                                                                                                                                      - settings of a functioning site
- may need to combine with other geospatical solutions                                                                                                                                                    - used of quickly setup of a new site
Biodiversity is life
Biodiversity is our life
Drupal




         20

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[DCTPE2010] Biodiversity & Drupal

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  • 4. ... • • • • • (DNA) • ... • cc by-nd Nick Kurzenko, Greg Rouse, and the U. S. Fish and Wildlife Service
  • 5. (NHM) • • • Lepidoptera British Fleas Chalcid Wasps Martian Meteorites • • • • • • Spanish Sandflies Solanaceae • Loch Ness Worms Bumble bees a slide from V.Smith
  • 6. Joomla WordPress Plone Drupal a slide from V.Smith
  • 8. http://scratchpads.eu a multisite implementation of Drupal a slide from V.Smith
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  • 17. BiotaTaiwanica - a pilot Drupal project • • LifeDesks ScratchPads • http://psybugs.biota.biodiv.tw
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  • 19. specimens node image collecting events node tags citation latin names keywords image metadata node collecting event vernaculars categories specimen literatures node description diagnostic descriptions node
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  • 28. Content Types (system components) Workflows Products Taxonomic Information (Name data) Taxonomic Validation Service / Darwin Core Checklist Archive Backbone File Archiving Service (DwC-A) IUCN red list ISSG invasive species attributes CBD indicators Species Profiling Species Profiles (TDWG) Service Plazi TaxonX Species description Multimedia / digital objects - derived Data Store Modeling Results LIterature Modeling/Statistical Service e.g. diagrams, numerical matrics query Connections to R Species occurrence: polygons Species occurrence: points producer Environmental spatial features Mapping Service WMS, WFS - Habitats GIS-Ready - Ecosystems Data Store - Climate Metadata Packaging CASSIA, EML, FGDC-BDP, - Geographic Service ISO-19115 or other metadata Other types of spatial data formats Metadata Metadata Other service workflows Other results Annotation layers Catalogue
  • 29. LifeDesks Classification modules (EOL) Taxonomy module (Drupal core) - utilize Drupal taxonomy - defines vocabulary - provide editable name flags - classification is one vocabulary - easy drag & drop edit interface - allows multiple tagging - export in Darwin Core & other formats - ability to relate between terms Modules for attributing name entries - maybe one more biological flag needed LifeDesks Taxon Page modules (EOL) - create content type: Taxon Page - map to Species Profile Model - customizable headers and chapters - connect to EOL as a content partner Content Types (system components) Workflows Products Taxonomic Information (Name data) Taxonomic Validation Service / Darwin Core Checklist Archive Backbone File Archiving Service (DwC-A) Image module (community) and others designed to handle IUCN red list various media types ISSG invasive species attributes CBD indicators Species Profiling Species Profiles (TDWG) Service Plazi TaxonX Species description Multimedia / digital objects - derived Data Store Modeling Results Modules for connecting to Biblio module (community) LIterature Modeling/Statistical Service e.g. diagrams, numerical matrics statistical solutions - provides forms for managing citations Connections to R - BibTex import/export Species occurrence: polygons query - redirect to Google Scholar Species occurrence: points producer Environmental spatial features Mapping Service WMS, WFS WFS module - Habitats GIS-Ready - export geodata as WFS - Ecosystems Data Store - Climate Metadata Packaging CASSIA, EML, FGDC-BDP, Darwin Core module (ScratchPads) - Geographic Service ISO-19115 or other metadata - combined with Location module and Gmap module Other types of spatial data formats - handle specimen and observation data Metadata Metadata Other service workflows Other results Annotation layers Catalogue Location module - manage locality and coordinate CCK + Views - create content type - include custom fields - provide forms for entering data Gmap module - publish as XML using Views modules - provide Google Map layer Nice Map module - provide Google Map layer Profile Modules for handling geospatial data - settings of a functioning site - may need to combine with other geospatical solutions - used of quickly setup of a new site
  • 31. Drupal 20