GBIF registry (GBRDS), at European Nodes meeting in Alicante, Spain (10 March 2010)
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GBIF registry (GBRDS), at European Nodes meeting in Alicante, Spain (10 March 2010)

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Regional NODES meeting of Europe 2010. Presentation of the Global Biodiversity Resources Discovery System (GBRDS, under development) for the NODES. How do we the NODES want the GBRDS to look like. ...

Regional NODES meeting of Europe 2010. Presentation of the Global Biodiversity Resources Discovery System (GBRDS, under development) for the NODES. How do we the NODES want the GBRDS to look like. What do we the NODES wish/need the GBRDS to be.

http://www.gbif.org/
http://gbrds.gbif.org/
http://code.google.com/p/gbif-registry/

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  • PPT: Nick King and Vishwas Chavan, Albuquerque, 2-7 Aug. 2009
  • Image source: University of Ottawa, Distributed Computing Research Group: http://www.genie.uottawa.ca/research/rsrch_site.php?lang=e&id=90 (Google Images).
  • PPT: Nick King and Vishwas Chavan, Albuquerque, 2-7 Aug. 2009
  • PPT: Nick King and Vishwas Chavan, Albuquerque, 2-7 Aug. 2009
  • PPT: VishwasChavan, GBRDS Workshop Copenhagen 17-18 September 2009
  • PPT: VishwasChavan, GBRDS Workshop Copenhagen 17-18 September 2009
  • PPT: SamyGaiji, GBRDS Workshop Copenhagen 17-18 September 2009
  • PPT: SamyGaiji, GBRDS Workshop Copenhagen 17-18 September 2009
  • PPT: Tim Robertson, GBRDS Workshop Copenhagen 17-18 September 2009
  • PPT: VishwasChavan, GBRDS Workshop Copenhagen 17-18 September 2009
  • PPT: Tim Robertson, GBRDS Workshop Copenhagen 17-18 September 2009
  • PPT: SamyGaiji, GBRDS Workshop Copenhagen 17-18 September 2009
  • PPT: Tim Robertson, GBRDS Workshop Copenhagen 17-18 September 2009
  • PPT: Tim Robertson, GBRDS Workshop Copenhagen 17-18 September 2009
  • PPT: Tim Robertson, GBRDS Workshop Copenhagen 17-18 September 2009
  • PPT: Vishwas Chavan,Helsinki, 13 August 2009

GBIF registry (GBRDS), at European Nodes meeting in Alicante, Spain (10 March 2010) GBIF registry (GBRDS), at European Nodes meeting in Alicante, Spain (10 March 2010) Presentation Transcript

  • European GBIF Nodes Meeting 2010, March 10th-12th Alicante, Spain
    Dag Endresen, Nordiv Genetic Resources Center, NordGen
    GBRDS
    Global Biodiversity Resources Discovery System
  • What is the Global Biodiversity Information Facility?
    GBIF enables free and open access to biodiversity data online.
    An international government-initiated and funded initiative focused on making biodiversity data available to all and anyone, for scientific research, conservation and sustainable development. 
    GBIF’s Data Portal provides this infrastructure.
    GBIF site :: http://www.gbif.org/index.php?id=269
  • GBIF from prototype to full operation
    Global informatics research infrastructure:
    • Global participation, a global network of partners
    • Enabling publishing of biodiversity data
    • Promoting development of data exchange standards
    • Building an informatics architecture
    • Capacity building
    • Catalysing development of analytical tools
    • Data provider
    • Data aggregator
  • GBRDS :: Linking resources
    Who? (Institutions, Collections, Networks, ...)
    What? (Data sets, Services, Persistent Identifiers...)
    Where? (Locations, Service access points, ...)
    When? (Temporal scope)
    How? (Formats, protocols, ...)
    As a distributed service
  • Available APIs (so far)
    Question: Do we (the NODES) miss an important API here, or are these good to go?
    Visit GBRDS at Google Code: http://code.google.com/p/gbif-registry/w/list
  • At the core, a Discovery System
    DiscoverySystem
    ServicePublishers
    Others…
    Registering
    Discovering
    DataPublishers
    Consumers
    Searching
    Retrieving
    Slide by Vishwas Chavan, GBRDS workshop September 2009
  • GBIF GBRDS
    http://gbrds.gbif.org
    Slide prepared by GBIF (SamyGaiji)
  • USE CASES & mock-up examples
    The same primary biodiversity data can be analyzed differently for different uses
    Discussion: Do we the NODES, have other important use cases?
    Discussion: Do we the NODES have other requirements for the GBRDS user interface?
  • Uses cases primary biodiversity data
    What can you do with georeferenced biodiversity data?
    • Predict effects of climate change
    • Analyse and predict spread of pests and diseases of humans, crops, livestock, wildlife, etc.
    • Predict best places to set up new protected areas
    • Analyse invasive species and predict invasion pathways
    • Provide policymaker-relevant data of all kinds
    • Be a resource for biodiversity science communities
    The same primarybiodiversity data canbeanalyzeddifferently for differentuses.
    http://code.google.com/p/gbif-registry/wiki/UseCases
    Modified from slide by Vishwas Chavan, GBRDS workshop September 2009
  • Moving towards…global integration
    ?
    Migratory Spp.
    ThreatenedSpp.; Red List Spp.
    Invasives, cropwild relatives, medicinals,
    etc.
    Slide by Vishwas Chavan, GBRDS workshop September 2009
  • Mock-upexamples
    Global Biodiversity Resources Discovery System
    empowering discovery of biodiversity data
    microhyla ornata western ghats 1980
    Discover
    779 resources in six categories discovered, with 428 accessible, 351 resources records
    1-5 of 351, <<Next>>
    Database of Frogs of Southern India..........(more)
    AmphibiaWeb...................................................(more)
    Fauna of India Database..................................(more)
    Microhyla of the World....................................(more)
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    Names (82)
    Primary Biodiversity Data (200)
    Resources (351)
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    ............................................
    Multimedia (12)
    Maps (28)
    Literature (106)
    About GBRDS
    Bug Report
    @ 2009, GBIF
    Slide by Vishwas Chavan, GBRDS workshop September 2009
  • Mock-upexamples
    Database of Frogs of Southern India: South Asian Centre for Biodiversity Monitoring, Kathmandu, Nepal
    CDROM, published November 2006, ISBN-001-898-0788, sacbm@sacbm.org . <<Click here for complete metadata record>>
    AmphibiaWeb: http://www.amphibiaweb.org/ Access point live as on 20th June 2009
    <<Click here for complete metadata record>>
    Fauna of India Database: National Centre for Biodiversity Informatics, New Delhi, India
    In-house database, accessible through bi-lateral arrangement, fid@ncbi.org.in <<Click here for complete metadata record>>
    Microhyla of the World: Smithsonian Institution, Washington DC, USA
    257 specimen records: 1700 – 2001: http://www.si.edu/amphibia/microhyla/ Access point live as on 12th Jan 2009
    <<Click here for complete metadata record>>
    Amphibian Collection of Raffles Museum: Raffles Museum, Singapore
    7004 specimens, non-digital: curator@raffles.sg. <<Click here for complete metadata record>>
    Global Biodiversity Resources Discovery System
    empowering discovery of biodiversity data
    779 resources in six categories discovered, with 428 accessible, 351 resources records
    Resources
    Names
    PrimaryBiodiversity Data
    Multimedia
    Maps
    Literature
    microhyla ornata western ghats 1980
    Discover
    Digital, Offline
    Resources (351): 1-5 of 351
    : Next : Previous : Last :
    Digital, Free, Online
    Digital,
    Restricted Access
    Digital, Free, Online
    About GBRDS
    Bug Report
    @ 2009, GBIF
    Non- Digital
    Slide by Vishwas Chavan, GBRDS workshop September 2009
  • Online demo (pre-alpha)
  • Online demo (pre-alpha)
  • GBRDS? What’s that?
    eBiosphere resolution recommendation:
    “Complete durable global registries of biodiversity informatics resources”
    Slide by SamyGaiji, GBRDS workshop September 2009
  • Is this the GBRDS?
    The GBRDS is 1) a Registry of resources and services and 2) a set of discovery services interacting with existing infrastructure such as GBIF to facilitate the discovery of biodiversity information. The most important component, the Registry would facilitate the inventory of information resources by creating a single annotated index of publishers, institutions, networks, collections (datasets), schema repository and services. The envisaged GBRDS is not conceived to be designed as simply a collection of centralized indexes but much more as an integrated ‘Yellow Pages’ reference of all biodiversity information resources, reconciling all distributed resources and providing a meaningful way to discover them in a distributed manner.
    Slide by SamyGaiji, GBRDS workshop September 2009
  • Registry: The past…
    Universal Description Discovery and Integration (UDDI)
    “…XML-based registry for businesses worldwide to list themselves on the Internet …”
    NB! Capitaliseonresources (investments) till date, re-useprevious solutions.
    Modified from slide by Tim Robertson, GBRDS workshop September 2009
  • Technical specifications
    • Re-use of registry for your own purposes, and thematic networks (model sub networks)
    • Identification of duplicate datasets / records
    • Scalable, up-time (24/7/365)
    • How to build relations between resources (Perhaps FaceBook style: “Institution X requests to be associated with you. Would you like to accept this association?”)
    • Central curation, or distributed community curation?
    • Allow the tagging of resources (human, machine)
    • Discussion: Any additional specifications to add from the NODES?
    Source: slides by Tim Robertson, GBRDS workshop September 2009
  • GBRDS Planning:Someissuesto consider
  • GBIF Network: The real scenario
    Challenge #1:
    Model the true nature of the network makeup.
    • A graph and not a tree
    • Multiple entity types
    • Institutions, networks, collections, GBIF Nodes
    • Many relationship types
    Slide by Tim Robertson, GBRDS workshop September 2009
  • GBRDS scalability/portability to other communities/locations will be critical!
    Slide by SamyGaiji, GBRDS workshop September 2009
  • Where metadata fits in ...
    NB! Remember import / compatibility with other metadata catalogues / systems
    Modified from slide by Éamonn Ó Tuama, GBRDS workshop September 2009
  • GBRDS : Persistent Identifiers
    The Persistent Identifier is a digital name tag
    Also called Global Unique Identifiers (GUID)
    Life Science Identifiers (LSID) is one example
    Digital Object Identifier (doi) is another example
    The Persistent Identifier concept introduces a straightforward approach to naming and identifying data resources stored in multiple, distributed data stores.
    Persistent Identifiers provides a naming standard to supportinteroperability.
    Discussion: Are Persistent Identifiers an important task for the GBRDS? (From NODES view-point)
  • LSID-GUID Task Group: summary
    Effective identification of data objects is essential for linking the world’s biodiversity data. If GBIF is to enable the exchange of biodiversity data it must promote identifier adoption through:
    • education, training, outreach
    • leadership
    • practical services
    Recommendation 10:
    GBIF should provide services to support identifier resolution, redirection, metadata hosting, and caching.
    Source: slides by Éamonn Ó Tuama, GBRDS workshop September 2009
  • GBRDS : Provider monitoring
    Endpoint monitoring http://bioguid.info/status/ (Rod Page)
    Modified from slide by Tim Robertson, GBRDS workshop September 2009
  • GBRDS : Provider monitoring
    Date Last Updated: 2010-03-08 08:15:01+0000
    Endpoint monitoringhttp://bigdig.ecoforge.net/ (David Vieglais, Kansas University, 2006)
  • GBRDS : Provider monitoring
    Endpoint monitoring http://chm.grinfo.net/ (Bioversity, Dag Endresen, March 2006)
  • REMEMBER : the small data providers
    • Long tail or Dark Data is economically and ecologically very critical
    • Most of existing and future data would be hold by Small Data Publishers
    • The early focus of GBIF was the low hanging fruits – the LARGE datasets
    • Further expansion of the GBIF data network should struggle to include the small datasets
    • Source: Curating the Dark Data in the Long tail of science by P. Bryan Heidorn (Google Tech Talk, August 28, 2008, http://www.youtube.com/watch?v=mgN74bR57i0
    Source: slides by Vishwas Chavan, GBRDS workshop September 2009
  • Thanks for listening