Gbrds Sg


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Gbrds Sg

  1. 1. GLOBAL BIODIVERSITY INFORMATION FACILITY Samy Gaiji GBIF Head of Informatics GBRDS Stakeholders Planning Workshop 17-18 September 2009 GBIF Informatics Work Program: How we plan to address the challenge
  2. 2. Key issues <ul><li>What’s the overall GBIF infrastructure strategy? </li></ul><ul><li>What’s the role of the GBRDS? </li></ul><ul><li>What are the key challenges? </li></ul><ul><li>How are we addressing them? </li></ul><ul><ul><li>Short-term (today) </li></ul></ul><ul><ul><li>Medium and long-term (>2010) </li></ul></ul>
  3. 3. GBRDS? What’s that?
  4. 4. GBRDS? What’s that? eBiosphere resolution recommendation: “ Complete durable global registries of biodiversity informatics resources”
  5. 5. This is GBIF mandate… <ul><li>Priorities: </li></ul><ul><li>mobilising biodiversity data, </li></ul><ul><li>developing protocols and standards </li></ul><ul><li>building a global informatics architecture </li></ul><ul><li>promoting capacity building, and </li></ul><ul><li>catalysing development of scientific analytical tools for improved decision-making </li></ul>-to facilitate free and open access to biodiversity data worldwide, via the Internet, to underpin scientific research, conservation and sustainable development.
  6. 6. GBIF Infrastructure (2008) Universal Description, Discovery and Integration (UDDI) A UDDI business registration consists of three components: - White Pages — address, contact, and known identifiers; - Yellow Pages — industrial categorizations based on standard taxonomies; - Green Pages — technical information about services exposed by the business.
  7. 7. Resolving the codes! While the UDDI addresses the challenges of mapping the network publishers, it doesn’t address more complex issues such as facilitating the understanding, conservation, and utilisation of institutions and collections up to individual record identification. Within the DarwinCore schema the two fundamental concepts (InstitutionCode and CollectionCode), are supposed to refer to a “standard” code identifier that uniquely identifies the institution and collection. The DarwinCore schema clearly states that no global registry exists for assigning institutional (and collection) codes and that publishers should use a code that is a &quot;standard&quot; in the various disciplines.
  8. 8. Understanding our network!
  9. 9. BCI: An average ‘success’ In 2008, aware of this growing challenge GBIF initiated together with other partner institutions, a parallel feasibility project called ‘Biodiversity Collections Index’ (BCI) with the aim to facilitate the understanding, conservation and utilisation of global biodiversity resources by creating a single global annotated index of biodiversity collections based on existing authoritative references . The BCI feasibility Project intended to do this by collaborating with the organisations and individuals, who curate these collections). The BCI was not intended to duplicate these authoritative references but mostly to reconcile these through a central reference point.
  10. 10. 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.
  11. 11. 2009-2010 Work Programme Diagram developed in 2008 as part of the GBIF 2009-2010 Work Programme.
  12. 12. 2009-2010 Work Programme
  13. 13. 2009-2010 Work Programme
  14. 14. 2009-2010 Work Programme Essential services for the user community Core components required for 2009
  15. 15. 2009-2010 Work Programme Exponential growth in requirements
  16. 16. 2009-2010 Work Programme GBRDS scalability/portability to other communities/locations will be critical !
  17. 17. Long-term vision G lobal B iodiversity R esources D iscovery S ystem
  18. 18. Long-term vision data information knowledge action Increasing refinement & utility of data the real world observations <ul><li>Decision making </li></ul><ul><ul><li>conservation </li></ul></ul><ul><ul><li>restoration biology </li></ul></ul><ul><ul><li>resource mgmt </li></ul></ul><ul><ul><li>utili z ation </li></ul></ul><ul><li>Policy & strategy </li></ul><ul><ul><li>government </li></ul></ul><ul><ul><li>corporate </li></ul></ul><ul><ul><li>individual </li></ul></ul>Increasing support
  19. 19. Long-term vision (from the bioinformatics community)
  20. 20. GLOBAL BIODIVERSITY INFORMATION FACILITY Samy Gaiji GBIF Head of Informatics GBRDS Stakeholders Planning Workshop 17-18 September 2009 GBRDS Registry: BCI
  21. 25. GLOBAL BIODIVERSITY INFORMATION FACILITY Samy Gaiji GBIF Head of Informatics GBRDS Stakeholders Planning Workshop 17-18 September 2009 GBRDS Registry: How we are addressing the challenge
  22. 26. Activities <ul><li>Support the development of the GBIF Global Biodiversity Resources Discovery System (GBRDS) registry. This includes: </li></ul><ul><ul><li>The development of a proper user management business logic </li></ul></ul><ul><ul><li>The development of flexible database backend </li></ul></ul><ul><ul><li>The development of a Web user interface </li></ul></ul><ul><ul><li>The development of a Web services API </li></ul></ul><ul><li>The user management business logic covers: </li></ul><ul><ul><li>The management of roles (e.g. Administrator, Editor and Guest) </li></ul></ul><ul><ul><li>The support for GBIF node managers to edit the relevant section of the GBRDS </li></ul></ul><ul><ul><li>The notification to ‘people’ about the status of registration (e.g. Pending, Approved, Rejected) </li></ul></ul><ul><li>  </li></ul>
  23. 27. Activities <ul><li>The database backend willsupport the storage and management of: </li></ul><ul><ul><li>Institutions </li></ul></ul><ul><ul><li>Collections </li></ul></ul><ul><ul><li>Aggregators </li></ul></ul><ul><ul><li>Relations between these entities </li></ul></ul><ul><ul><li>Registration of services (e.g. WMS, WFS, GBIF supported protocols such as TAPIR, GBIF supported tools such as the IPT) </li></ul></ul><ul><ul><li>Registration of extensions </li></ul></ul><ul><ul><li>Registration of thesaurus </li></ul></ul><ul><ul><li>Registration of schema (as repository) </li></ul></ul><ul><ul><li>Registration of services binding similar to the UDDI </li></ul></ul>
  24. 28. Activities <ul><li>The Web site of the GRBRDS Registry covers: </li></ul><ul><ul><li>Basic CRUD of back-end entities </li></ul></ul><ul><ul><li>Represent the GBIF business rules for email notifications </li></ul></ul><ul><ul><li>Ability to search based on a set of use cases provided by GBIFS (e.g. querying which node managers have not answered requests for endorsement) </li></ul></ul><ul><ul><li>Allow the registration of organization (and their relevant collections) as well as the management of resources. </li></ul></ul><ul><li>The API Webs services covers: </li></ul><ul><ul><li>Basic CRUD of back-end entities </li></ul></ul><ul><ul><li>Allow registration of IPT instances (based on codes already developed by GBIFS) </li></ul></ul><ul><ul><li>Registration of RSS, WMS, WFS etc… (based on codes developed previously by GBIFS) </li></ul></ul>
  25. 29. Activities (Phase 08/10 2009) Additional requirements:   - Dynamic agent types: Introduce dynamic agent types (Admin can add/remove new Agent Types). Agents will be listed and grouped by type instead of showing IPT, HIT etc in specific tabs.   - Recently viewed: Instead of the existing breadcrumb navigation there will be a navigation list with the recently viewed resources / agents to quickly jump to a recently viewed entity.   - Tag browser: A new navigation menu entry will be created linking to a page that shows all available namespaces (with counts of distinct tags) and all tags with their namespaces.  
  26. 30. Activities (Phase 08/10 2009) Additional requirements:   - Email notification: Email notifications for certain data manipulations are required to inform the responsible persons about manipulation of data within their domain. - IPT linkage: The registry v1 REST web-services as used by the IPT have to be supported (in addition to the new rest web-services).   - Extension browser: Add web pages for browsing Darwin core extensions and vocabularies.
  27. 31. Activities (Phase 08/10 2009) Additional requirements:   - Linking via UUID: UUIDs should be used everywhere including the URLs (local ID should not be exposed on the user interface)   - CSS fixes: Address some styling/CSS issues to meet GBIF corporate branding.   - Terminology: Address some terminology/language coherency on the user interface.