1. Global Biodiversity Information Facility GLOBAL BIODIVERSITY INFORMATION FACILITY Hannu Saarenmaa, Donald Hobern, Larry Speers, Per Bjørn & Giorgos Ksouris TDWG 2003 Oieras, 25-26 October 2003 WWW.GBIF.ORG GBIF network status, current developments, and plans for 2004

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

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

4. Global Biodiversity Information Facility GBIF is a global inte- grator

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

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

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

8. Global Biodiversity Information Facility How does the GBIF UDDI registry work? GBIF UDDI Registry Services Registrations Provider Registrations 1) GBIF Secretariat and other developers create and populate the registry with descriptions of standards (tModels) 2) Museums and other data providers install data provider packages which are automatically registered 6) Scientists, decision- makers, and others use portals to build data sets for analysis and synthesis 5) Specialised portals and search engines can be built to query the registry and the index 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. Global Biodiversity Information Facility Shall we register this new DiGIR provider in GBIF UDDI Registry (http://registry.gbif.net)?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. Global Biodiversity Information Facility

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

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

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

15. Global Biodiversity Information Facility GBIF node responsibilities GBIF Registry, Index, and Portal Data Node Participant Node Portal 1.Network 2.Registry 3.Standards 4.Tools 1.Encourage participation 2.Manage registration of Data Nodes 1.Coordination 2.Network 3.Registry 4.Standards 5.Tools 6.Consolidated Data 1.Metadata 2.Data 1.Identify Data Nodes 2.Endorse and quality assure data nodes 3.National Language Interfaces

16. Global Biodiversity Information Facility Participants are currently working on their network topologies Decentralised Centralised Participant Portal A Participant Portal C Data Warehouse Participant Portal B Data Warehouse GBIF Portal GBIF Registry GBIF Index

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

18. Global Biodiversity Information Facility GBIF Development Status Presentation by Donald Hobern GBIF Program Officer for Data Access and Database Interoperability

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

20. Global Biodiversity Information Facility 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

21. Global Biodiversity Information Facility Implementation Plan for GBIF Network OctoberNovemberDecember January February 20032004 SeptemberAugust Registry of Data Nodes established 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 Data Indexing tools tested GBIF Portal offers access to Biodiversity Data Usage Reporting tools tested GBIF Portal reports data usage to Data Nodes GBIF Secretariat activities GBIF Participant activities Legend

22. Global Biodiversity Information Facility 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

23. Global Biodiversity Information Facility DIGIT and ECAT in the GBIF work programmes 2003 and 2004 Presentation by Larry Speers

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

25. Global Biodiversity Information Facility 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

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

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

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

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

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

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

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

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

34. Global Biodiversity Information Facility 1.An assessment of the efficiency of the digitization processes including data quality issues 2.Updating ‘Best Practices Handbook’ 3.A ‘Request for Proposals’ for seed money to partially support the liberation of existing data sets, new digitization initiatives and exploring new innovative approaches to digitization 4.An update of the digitization software review 5.An update of the Natural History Collections digitization assessment DIGIT 2004 Work Program – Proposed Activities

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

36. Global Biodiversity Information Facility Guidelines l GBIF’s global perspective gives it a unique role. l As a general principle, GBIF should support projects that contribute to the development of a global biodiversity information infrastructure. l 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.