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GLOBAL BIODIVERSITY

WWW.GBIF.ORG. GLOBAL BIODIVERSITY. INFORMATION FACILITY. GBIF network status, current developments, and plans for 2004. Hannu Saarenmaa, Donald Hobern, Larry Speers, Per Bj ørn & Giorgos Ksouris TDWG 2003 Oieras, 25-26 October 2003. GBIF objective.

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GLOBAL BIODIVERSITY

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  1. WWW.GBIF.ORG GLOBALBIODIVERSITY INFORMATIONFACILITY GBIF network status, current developments, and plans for 2004 Hannu Saarenmaa, Donald Hobern, Larry Speers, Per Bjørn & Giorgos Ksouris TDWG 2003 Oieras, 25-26 October 2003

  2. GBIF objective • GBIF is an international collaborative megascience project • based on a multilateral agreement (MoU) between countries, economies and international organisations, • dedicated to establishing an distributed information infrastructure containing primary biodiversity data, • with initial focus on species- and specimen-level data, • with links to molecular, genetic and ecosystems levels • in order to make the world’s scientific biodiversity information freely and universally available to all.

  3. GBIF needs TDWG • GBIF builds on standards developed and reviewed by the global biodiversity informatics community, i.e., the TDWG. • GBIF is building global information infrastructure for biodiversity. That requires choosing some standards for implementation.

  4. GBIF is a global inte-grator

  5. Resource Resource Resource Metadata Metadata Metadata GBIF DiGIR Architecture User Metadata and name query ( UDDI ) Provider query Index Portal Registry Request Marshaller Metadata Cache Institutions Providers Services Available providers Query Engine Metadata response Accounting Publish availability Metadata and statistics Full data response DiGIR Full data query Synonyms SOAP Name provider Data provider HTTP Provider Services Provider Services other Resource Metadata

  6. UDDI –Universal Description, Discovery and Integration of Web Services Institution Collection Collection businessEntity businessEntity BioCASE digir.php bindingTemplate bindingTemplate InstanceDetails InstanceDetails categoryBag keyedReference keyedReference identifierBag keyedReference keyedReference businessEntity businessService businessService Schemas, protocols, interchange specifications tModels GEO Code Biological taxonomies GBIF Participant IDs Collection, institution codes Thematic network IDs (MaNIS,…)

  7. Technical Models a.k.a. “tModels” White Pages Yellow Pages Green Pages What’s in the Registry? Standards bodies and developers register information about their technical models, including data standards, specifications, taxonomies, etc. Businesses register public information about themselves and the services they offer

  8. GBIF UDDI Registry ProviderRegistrations Services Registrations How does the GBIF UDDI registry work? 6) Scientists, decision- makers, and others use portals to build data sets for analysis and synthesis 1) GBIF Secretariat and other developers create and populate the registry with descriptions of standards (tModels) 5) Specialised portals and search engines can be built to query the registry and the index 2) Museums and other data providers install data provider packages which are automatically registered 4) A global index queries the registry, caches metadata, and creates a unique identifier for each record (and name) 3) GBIF Participant is notified of new provider in their domain, for endorse-ment as a GBIF data provider

  9. Shall we register this new DiGIR provider in GBIF UDDI Registry (http://registry.gbif.net)? Registration is necessary so that users, search engines, and portals can locate your provider. By registering with GBIF you agree that your defined DiGIR-Provider-resources can be queried by applications using the DiGIR protocol, within the limitations that you can set up later and modify as needed. Furthermore, you allow GBIF to publicly serve metadata describing your data. The GBIF Participant Node in your domain will be informed of your registration.

  10. Supported by helpdesk@gbif.org Turn-key package Based on PHP and DiGIR project code Available now for Linux and Windows Registration with GBIF UDDI registry

  11. Data Repository Tool • Enable data custodians to manage and publish their own data • Make available a simple data warehouse tool for those who want to host datasets for the community • Upload and manage datasets in document format such as spreadsheet and XML • Parses the data into embedded MySQL database that becomes available to the public as a DiGIR resource • Revoke release (data is deleted from database)

  12. What is my institution code and collection code? • The most common question at helpdesk and training now. • Why should each record have a globally unique ID? • To trace downloaded data back to the original source • Support data usage accounting services • To allow for updates/corrections • To create a URL to view the data • How: LSID/URN with 4+ elements • Format network:institution:collection:key • Example gbif:helsinki.fi:Lepi-SPS:44622 • Issues • Global lists of institution and collection codes for UDDI? • Work with Index Herbariorum & others to standardise codes and related information exchange

  13. GBIF node responsibilities GBIF Registry, Index, and Portal • Coordination • Network • Registry • Standards • Tools • Consolidated Data • Network • Registry • Standards • Tools • Identify Data Nodes • Endorse and quality assure data nodes • National Language Interfaces Data Node Participant Node Portal • Metadata • Data • Encourage participation • Manage registration of Data Nodes

  14. Participants are currently working on their network topologies GBIFIndex GBIFPortal GBIFRegistry Decentralised Centralised Participant Portal B Participant Portal C Participant Portal A Data Warehouse Data Warehouse

  15. GBIF network status • NODES committee set its goal to have a DiGIR network up and running by end of 2003 • Seven regional workshops and training events • Two DiGIR provider implementations available • GBIF UDDI registry is up and running • Think of it as The One Global Marketplace of biodiversity data and services • Register your data now • Global index Q4/2003 • Portal to browse and search data Q4/2003, toolkit Q1/2004 • helpdesk@gbif.org

  16. GBIF Development Status Presentation by Donald Hobern GBIF Program Officer for Data Access and Database Interoperability

  17. GBIF Aggregated Data Portal HTML (Forms) Interface Service Metadata Index Data Biodiversity Data Name Data User Feedback Biodiversity Access Framework (XML Services) Presentation Service Session Manager Registry Manager Search Engine Taxonomic Name Service Index Manager Data Connection Framework Service Metadata Access and Feedback Data Geographic Service Data Biodiversity Data Name Data

  18. Key Standards and Elements • XML data exchange based on Providers, Services and Biodiversity Data Records • UDDI registry for technical (access) metadata • Descriptive metadata retrieved through service interfaces • Specimen/observation exchange using DiGIR-Darwin Core or BioCASE-ABCD • Taxonomic name data from Catalogue of Life (annual checklist for first release, moving to service-based approach as possible) • Java (and JSP) components being developed centrally for GBIF Portal • Current portal development using Tomcat, Xerces, Log4J, MySQL • Components to be packaged for reuse as appropriate

  19. Legend GBIF Secretariat activities GBIF Participant activities Implementation Plan for GBIF Network 2003 2004 January August September October November December February Software Packages for Data Providers available Training Courses in use of Software Packages GBIF Participants establish Data Nodes Registration tools tested GBIF Participants register Data Nodes Registry of Data Nodes established Data Indexing tools tested GBIF Portal offers access to Biodiversity Data Usage Reporting tools tested GBIF Portal reports data usage to Data Nodes

  20. DADI Work Programme 2004 • Support development of DiGIR/BioCASE tools (seeking to merge protocols) • Encourage inclusion of native DiGIR/BioCASE support in key collection/observation databasing packages • Investigate special requirements for observational data sets • Work with TDWG Taxonomic Names Subgroup on standards for exchange of taxonomic name data • Work to integrate nomenclators into names architecture • Development of metadata standard and tools • Work with TDWG Spatial Data Subgroup to plan (and start developing) GIS infrastructure for biodiversity data • Investigate long-term integration of ecological and genetic data levels • Investigate long-term integration of Structured Descriptive Data • Investigate long-term models for Digital Biodiversity Literature

  21. DIGIT and ECAT in the GBIF work programmes 2003 and 2004Presentation by Larry Speers

  22. DIGIT- Goals • To facilitate access to data associated with the specimens in the world’s natural history collections • To identify efficient and cost effective ways to organize and accelerate the specimen digitization process • To facilitate the sharing of specimen data with users in the developing world • To facilitate the advancement of biodiversity science through improved access to primary species occurrence data

  23. DIGIT 2003 Work Program Purpose:Use a request for proposals (RFP) to award seed money to partially fund different categories of digitisation projects, including some new projects and some projects aimed at improving existing databases and bringing them on-line. Time Period: Up to 18 months from date of award

  24. DIGIT 2003 Work Program Results • 139 Pre-proposals received • Full Proposals requested from 39 Pre-proposal applicants • 2 decided not to submit • 1 submitted late and not included in the final review • 36 Full Proposals Reviewed • A total of $1,628,770 (US) requested • Proposals included projects for imaging of type specimens, digitising specimen labels, improving data quality, digitisation tool development

  25. DIGIT Proposal Review Criteria • Proposals were evaluated for scientific excellence. • In addition, they were evaluated on how well they supported the GBIF philosophy: • Potential for the earliest possible access to large data sets • Potential for networking and building increased 'Natural History Collections Community' collaboration • Potential for testing and documenting digitisation 'Best Practices' • Emphasis on data-sharing with countries of origin • Potential for international collaboration • Potential for leveraging additional long term funding to support the specimen digitisation process • Components for training and capacity building

  26. DIGIT 2003 Work Program Results • Review committee recommendation • If funds available, fund 33 of the 36 proposals • Funding was available to fund the top 17 of the 33 recommended proposals: • Taxonomic coverage of top 17 proposals • 1 tool development project • 5 vascular plant collection digitisation projects • 5 zoological collection digitisation projects • 4 projects involving digitisation of both zoological and botanical collections • 1 project each in mycology and bryophyte collections digitisation • Abstracts of funded projects are available on GBIF Website (www.gbif.org)

  27. DIGIT 2003 Work Program Results • DIGIT seed money grants will leverage approximately $2.8 million (US) in investment in Natural History Collections digitisation activities • DIGIT seed money awards should, by the end of 2004: • Make more than 1 million new specimen records available for internet access • Make more than 70,000 records of type specimens including images available for internet access • Geo-reference, quality check and make available 800,000 existing specimen records

  28. ECAT Proposal Review Criteria • Proposals were evaluated for scientific excellence. • In addition, they were evaluated on how well they supported the GBIF philosophy: • Likelihood to produce results within a limited timeframe, and potential for the earliest possible access to large data sets • Feasibility • Cost-effectiveness -- low cost per name • Collaboration among institutions and/or organisations • Potential for networking and building collaborative networks of taxon specialists, with potential for training and capacity-building • Linkage with existing projects (including projects with a DIGIT aspect)

  29. ECAT RFP Results • 67 Pre-proposals • Requested Full-Proposals from 32 applicants • 32 Full-Proposals Reviewed • A total of $1,375,095 (US) requested • Proposals included digitising of printed catalogues, GSD development at various stages, checklist writing, and programming of “wrappers”

  30. ECAT RFP Results • Review Committee recommendation • If funds available fund 28 of the 32 proposals • Funding was available to fund the top 12 of the 28 recommended proposals: • Taxonomic coverage of top 12 proposals • 2 vascular plant GSD projects • 2 projects developing nomenclators for animals and fungi • 6 projects building GSDs of insect groups, e.g. Weevils, Flies • 1 regional mollusc GSD • 1 to develop tool for producing “wrappers” • Abstracts of funded projects available on GBIF website

  31. ECAT RFP Results • ECAT seed money grants will leverage approximately $7.25 million (US) investments in nomenclators, GSDs and networking activities • ECAT seed money awards should by the end of 2004 result in • Addition of 701,000 names to existing GSDs and nomenlators • Addition of 366,850 species to existing and newly emerging GSDs • - all available through GBIF Network • - very conservative estimate

  32. DIGIT - ECAT 2004 - Request for Proposals • Call for proposals will be announced on GBIF web site in late 2003 • Process and criteria currently being developed with input from DIGIT and ECAT Science Sub-Committees • Expect to fund approximately 9 projects for DIGIT and 6 projects for ECAT • Maximum award $50K US • Process and criteria expected to be similar to 2003 seed money RFP

  33. Guidelines • GBIF’s global perspective gives it a unique role. • As a general principle, GBIF should support projects that contribute to the development of a global biodiversity information infrastructure. • In particular, it should fund the development of datasets, networks or tools needed for the global effort but are difficult for local or regional funding agencies to support.

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