The New GBIF Data Portal Web Services and Tools

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The New GBIF Data Portal Web Services and Tools

• Donald Hobern
• GBIF Deputy Director for Informatics
• October 2006

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Background
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Background and history

• Current GBIF data portal (prototype) released in
  February 2004
• Fixes and enhancements by Secretariat, CRIA
  (Brazil) and CBIT (Australia)
• Mapping services from BeBIF (Belgium) and CBIF
  (Canada), including Google Earth support
• Mirror sites in Germany and Korea
• Function very limited
• Taxonomic navigation using Catalogue of Life data
• Integration of data from DiGIR-Darwin Core and
  BioCASe-ABCD data providers
• Search and download only by single species
• (Almost) no web services

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New portal development

• Team based in Copenhagen throughout 2006
• Three Java developers
• Data portal administrator
• Complete redevelopment of portal
• Improved registration of data resources richer
  metadata
• New, more flexible approach to indexing data
  resources
• Validation of data content performed as part of
  indexing
• User interface redeveloped to address user needs
• User interface components available for embedding
  in other portals
• Web services to support other portals and
  applications
• Platform to support community development of
  tools and extensions
• Three online surveys
• User requirements and expectations (April 2006)
• Data provider requirements and expectations (May
  2006)
• Technical approaches (September 2006)
• Review workshop involving representatives from
  Nodes (14-15/09/2006)
• Launching beta programme (new server being
  installed in Copenhagen)

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Explore Species
Species Page
Quick Search
Home
Explore Countries
Country Page
Explore Occurrences
Explore Datasets
Dataset Page
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Tools Quick Search
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Tools Explore Species/Countries/Datasets and
other taxa/other regions/institutions/networks
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Tools Summary Pages
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Tools Explore Occurrences
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Other matters
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Indexing

• Broader range of supported import formats and
  protocols
• Occurrence data
• Darwin Core (original 1.2, MaNIS, OBIS, new 2.0
  with extensions)
• ABCD (1.20, 2.06)
• Taxonomic data
• Catalogue of Life CD-ROM (moving to dynamic
  checklist when appropriate)
• Nomenclators via tab-delimited lists of LSIDs
  (work under way)
• Data from ECAT projects (models and tools under
  way)
• Other resources
• Discussions under way with other resources
  (GenBank, BOLD, ARKive)
• General support for handling XML and
  tab-delimited formats
• Validation and annotation of data during indexing
• Is country name recognisable?
• Is record georeferenced?
• Are coordinates and country names consistent?
• Is locality consistent with the declared
  geographic scope of the dataset?
• Is date present and interpretable?
• Can scientific name be parsed?
• Is scientific name recognisable?

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Web services

• SOAP and REST (URL-based key-value pair) web
  services ready for test
• Two versions
• Less complete, but more data from current data
  portal http//ws-test.gbif.org/
• More complete, but less data from beta data
  portal http//newportal.gbif.org/
• Search one or all taxonomic resources for taxa
  with a (partial or complete) scientific name
• Basic response
• Taxon Concept Schema response
• SPICE TCS?
• Search for occurrences for a taxon with filters
  for country, bounding box, time period, data
  resource, etc.
• Basic response
• Darwin Core response
• TAPIR and WFS planned
• Services to list provider countries, providers by
  country, and data resources by provider

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Getting involved

• Test site currently at http//newportal.gbif.org/
• Official launch of beta programme in next few
  weeks
• Will include specific requests to review
  different functions as they are made available
• Test web service interfaces
• Contact me for information on how to connect and
  use these
• Early in 2007, we will start testing how to embed
  portions of the interface in other portals
  (national, thematic, etc.)
• Interested to know of any institutions who may be
  able to host a mirror site and perhaps develop
  additional interfaces over the data or additional
  processed fields in the index
• Develop visualisation or analysis tools

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Contact

• Global Biodiversity Information Facility
• Donald Hobern, GBIF Deputy Directory for
  Informatics, dhobern_at_gbif.org
• http//www.gbif.org/ - Communications Portal
• http//www.gbif.net/ - Prototype Data Portal
• http//newportal.gbif.org/portal/ - Test version
  of new Data Portal
• Development team
• Andrea Hahn, Ali Kalufya, Giorgos Ksouris, Dave
  Martin, Tim Robertson, Ciprian Vizitiu (GBIF)
• Damian Barnier (CBIT)
• None of this would be possible without the work
  of
• TDWG subgroups in developing relevant standards
  and protocols
• All participant organisations within the GBIF
  network in sharing data