1. Global Biodiversity Information Facility GLOBAL BIODIVERSITY INFORMATION FACILITY Meredith A. Lane & Donald G. Hobern Information Systems on Biodiversity of Species & Ecosystems 1 December 2003 WWW.GBIF.ORG

2. Global Biodiversity Information Facility This PPT file about GBIF is on the web: l Go to WWW.GBIF.ORGWWW.GBIF.ORG l Click on “What is GBIF” l Click on “Download a PPT about GBIF”

3. Global Biodiversity Information Facility What is GBIF ? GBIF is a megascience facility aimed at l Making the world’s biodiversity data freely and universally available via the Internet l Sharing primary scientific biodiversity data for society, science and a sustainable future

4. Global Biodiversity Information Facility What is GBIF ? In this information age, there are many wishes about what should be on the Internet:

5. Global Biodiversity Information Facility Biodiversity Researchers want: l easy online access to georeferenced specimen data l a complete, global, electronic index to scientific names and thus to the scientific literature and databases l a means to link together data from disparate sources (e.g. DNA, specimen, species observation and ecosystem) to answer complex questions l opportunities for within- and cross-disciplinary collaboration l a means to infuse biodiversity policy and management decisions with real, scientific data

6. Global Biodiversity Information Facility Policy-makers and managers want: l Better prediction of areas most suitable for parks, wildlife reserves, etc. l Rapid identification and information about control of invasive species l Prediction of patterns of spread of new diseases l Ability to understand effects of ecological change on, for example, species distributions

7. Global Biodiversity Information Facility l Current species occurrence data l Correlation of species occurrence with ecological parameters l Potential localities for species believed to be rare l Prediction of change in species occurrences based on environmental change Conservationists want:

8. Global Biodiversity Information Facility D eveloping Countries want: l Access to information associated with a country’s specimens that are housed in foreign institutions l Travel to obtain the data not required l Difficulty of repatriating and expense of housing actual specimens is avoided l Ability to share fully in the common store of humanity’s knowledge about biodiversity l Opportunity for training in the expert development and use of biodiversity information

9. Global Biodiversity Information Facility Why was GBIF established ? l Both biodiversity and biodiversity data are unevenly distributed around the world: Developing World Biodiversity Biodiversity Data Developed World l GBIF was established, in large part, to redress the inequality of data distribution

10. Global Biodiversity Information Facility l To undertake biodiversity informatics activities that must be accomplished on a worldwide basis l To take on tasks not being attempted by other initiatives but which would be of benefit to those initiatives l To make biodiversity databases interoperable among themselves and with molecular, genetic, ecological and other types of databases, thus increasing the value of all of them Why was GBIF established ?

11. Global Biodiversity Information Facility Where is GBIF located ? l Unlike CERN, the megascience instrumentation facility for particle physics that is located in Switzerland, GBIF is a megascience facility that is distributed all over the world, with its many parts connected by the Internet l The small, non-bureaucratic GBIF Secretariat is hosted by the Zoological Museum of the University of Copenhagen, Denmark CERN

12. Global Biodiversity Information Facility GBIF Voting Participants: 24 l Australia l Belgium l Canada l Costa Rica l Denmark l Estonia l Finland l France l Germany l Iceland l Japan l Korea (Republic of) l Mexico l Netherlands l New Zealand l Nicaragua l Portugal l Peru l Slovenia l South Africa l Spain l Sweden l UK l USA

13. Global Biodiversity Information Facility GBIF Associate Participants: 15 countries or economies l Argentina l Austria l Bulgaria l Colombia l Czech Republic l Ghana l India l Madagascar l Morocco l Pakistan l Poland l Slovak Republic l Switzerland l Taiwan l Tanzania

14. Global Biodiversity Information Facility GBIF Associate Participants: 22 International Organizations l ALL Species Foundation l ASEANET l BioNET l BIOSIS l CABI Bioscience l EASIANET l European Commission l Expert Centre for Taxonomic Identification l FreshwaterLife l Inter-American Biodiversity Information Network l Integrated Taxonomic Information System l IUCN l NatureServe l Ocean Biogeographic Information System l SAFRINET Société de Bactériologie Systématique et Vétérinaire l Species 2000 l Taxonomic Databases Working Group l UNESCO Man and the Biosphere Program l UNEP l World Federation for Culture Collections l Wildscreen Trust

15. Global Biodiversity Information Facility What is GBIF ? A distributed facility, comprising a network of Participant nodes that l Share biodiversity data openly and freely l Use common standards for data and metadata l Encourage generation of additional content l Assure that data providers retain control of their own data l Gain access to others’ data by sharing their own

16. Global Biodiversity Information Facility GBIF’s focus is on primary data l Primary data result from the direct observation of nature, for example l collecting event l Christmas bird count l Primary data can be used to answer many kinds of questions, both scientific and societal l Primary data can be analyzed in various ways, e.g. l biodiversity modelling l biogeography l conservation area siting

17. Global Biodiversity Information Facility What are GBIF’s primary data ? l Associated notes, recordings, observational databases, etc. l These data must be digitised in order to be shared and fully utilised l Label data on ~ 1.5 billion specimens in natural history collections

18. Global Biodiversity Information Facility GBIF Vision for Uses of Biodiversity Data Edu- cation Conser- vation General Public Industry Research Regu- lation Sustainable Development ….. l Primary data available for all sorts of users l Reuse of data, avoidance of duplication of effort l Interoperability with other kinds of data (genetic, molecular, geographic, etc.) l Alleviation of gaps in knowledge Primary data

19. Global Biodiversity Information Facility GBIF’s focus is on primary data l Primary data, because they are difficult or too time-consuming to access, are at present not often used in natural resource policy or management decisions l Primary data that are available digitally can significantly improve decision-making and research CONABIO’s map of 700,000 plant specimen records drawn from 25 institutions

20. Global Biodiversity Information Facility GBIF’s area of data responsibility l The types of data that GBIF will provide are unique; there is no duplication of any existing effort. l The return on the investments made in the other areas will be enhanced by the data and interoperability provided by GBIF.

21. Global Biodiversity Information Facility GBIF contribution to interoperability Example: Until now, it has not been possible to combine data from GenBank with specimen and ecological data from other sources without painstaking work by a person. With GBIF’s components in place, data can be drawn directly from different sources with a single query. Compiled specimen, genetic, and ecological information

22. Global Biodiversity Information Facility biodiversity informatics True bioinformatics … “bioinformatics” ecoinformatics genomics proteomics

23. Global Biodiversity Information Facility But it isn’t an easy task... which is why GBIF is a megascience activity

24. Global Biodiversity Information Facility What does GBIF do ? l GBIF has a set of tasks that is distinct from that of any other organization. l In order to promote the sharing and use of scientific biodiversity data by everyone, it currently focuses on four areas of activity:

25. Global Biodiversity Information Facility Outreach and Capacity Building To reach out to all countries and to bridge biodiversity information technology “digital divides” through training and capacity building, to ensure that people in every country have open access to and can efficiently use biodiversity information. OCB

26. Global Biodiversity Information Facility Digitisation of Natural History Collections To facilitate the expansion of biodiversity knowledge and the sustainable use of biodiversity resources by making legacy and newly acquired primary species occurrence data dynamically accessible DIGIT

27. Global Biodiversity Information Facility Electronic Catalogue of Names of Known Organisms To facilitate the exploration and rapid expansion of biodiversity knowledge, and to enable interoperability among specimen, genetic and ecological databases… ECAT

28. Global Biodiversity Information Facility Data Access and Database Interoperability To facilitate the full use of biodiversity and other databases by establishing an information architecture that enables interoperability and facilitates data-mining DADI

29. Global Biodiversity Information Facility GBIF deals with 1 biodiversity data Family: Pyralidae Order: Lepidoptera Class: Insecta Genus: Ostrinia Hübner, 1825 Vernacular (FR): Pyrale du maïs Vernacular (ES): Piral del maíz Vernacular (DE): Maiszünsler Vernacular (EN): European Corn-borer Collection:DGH Lepidoptera Record id:DGHEUR_003217 Country:France Coordinates:03.047˚E 48.730˚N Date:28 June 2003 Collector:Donald Hobern Specimen & Observation Data DIGIT + DADI Taxonomic Names ECAT + DADI Species: Ostrinia nubilalis (Hübner, 1796) Synonym: Pyralis nubilalis Hübner, 1796 o Foodplant: Zea mais L. 1753 Ecological Interactions Locus:AAL35331 Definition:acyl-CoA Z/E11 desaturase 1 mvpyattadg hpekdecfed... Sequence Data Average Rainfall Location: 48.82°N 2.29°E Jan Feb Mar Apr... 182.3 120.6 158.1 204.9... Abiotic Data Diagnosis: Wingspan 26-30mm; sexually dimorphic;male: forewings ochreous to dark brown; female: forewings pale yellow; … Taxonomic Descriptions Pheromones of Ostrinia http://www.nysaes.cornell.edu/fst/faculty/a cree/pheronet/phlist/ostrinia.html Digital Literature and Web Resources

30. Global Biodiversity Information Facility How can GBIF data be made to interoperate? GBIF Show records of Erinaceus europaeus 6 records 35 records 17 records 0 records 81 records: 1.Museum AParis 2.Museum ANice 3.Museum AParis 4.Museum A Avignon 5.Museum A Avignon 6.Museum A Marseille 7.Observer X Norwich 8.Observer X Norwich 9.Observer X Southampton...

31. Global Biodiversity Information Facility GBIF Information Architecture GBIF Data Nodes Specimen Data Links to other data Specimen Data Name Lists Specimen Data Observation Data Specimen Data Catalogue of Life Biodiversity Data Access Portal Biodiversity Data Index Taxo- nomic Name Service (ECAT) Metadata User Requests Query

32. Global Biodiversity Information Facility Users and applications need data structured according to standards 2003-06-08 DGH DGH Lepidoptera DGHEUR_0002976 Dichomeris marginella (Fabricius, 1781) O Animalia Lepidoptera Gelechiidae Dichomeris marginella (Fabricius, 1781) Donald Hobern 2003 06 08 Europe Denmark Gentofte Amt Merianvej, Hellerup 12.538 55.737 100 1 1 in Skinner trap June 2003 S M T W T F S 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 Observation record formatted using the Darwin Core

33. Global Biodiversity Information Facility Web services enable the aggregation of structured data HeterogeneousDatabases Web Services Standardised Structured Data User … … …

34. Global Biodiversity Information Facility Data Providers Specimens: Flowering Plants of Africa Specimens: Proteaceae of the World Taxon Names: Proteaceae of the World Museum A Specimens: Mammals of North Europe Taxon Names: Mammals of the World Further Links: Mammals Museum C Specimens: Bacteria Cultures Taxon Names: Bacteria Further Links: Bacteria University D Observations: Birds of Central America Observations: Butterflies of Belize Observations: Erinaceus of Europe Observer Network B GBIF Network GBIF Data Providers install web services

35. Global Biodiversity Information Facility GBIF Info Architecture also relies on a registry of Data Providers Data NodeType of dataTaxonRegion# Records Museum ASpecimen/ObservationFlowering PlantsAfrica327000 Specimen/ObservationProteaceaeWorld23000 Taxonomic NamesProteaceaeWorld1500 Observer Network BSpecimen/ObservationBirdsCentral America68500 Specimen/ObservationErinaceusEurope & Asia4200 Name ListBirdsBelize587 Museum CSpecimen/ObservationMammalsNorth Europe1800 Taxonomic NamesMammalsWorld8000 General ResourcesMammalsWorld600 University DSpecimen/ObservationBacteriaWorld1200 Taxonomic NamesBacteriaWorld5000 General ResourcesBacteriaWorld400

36. Global Biodiversity Information Facility Why share data through GBIF? l The value of data is in its use l Data that potential users are not aware of or cannot access is of little or no value l Currently, a significant proportion biodiversity data is under- utilised because potential users are not aware of its existence or cannot access it l Synergistic effects in combining data: 1+1 > 2 l Exposing information leads to improved quality l Feedback and data cleansing l Increased awareness of and utilisation of existing species level biodiversity data highlights the importance of natural history collections and observational data l This in turn increases the recognition of the importance of the associated work and will in the longer term increase funding opportunities

37. Global Biodiversity Information Facility GBIF monitors & reports data usage Show specimen records for Upupa epops Data Usage Reports 81 records: 1.Museum AParis 2.Museum ANice 3.Museum AParis... Show bird specimen records from Nice 126 records: 1.Museum AUpupa epops 2.Museum AApus apus 3.Museum AAthene noctua... Data Usage Logs GBIF Usage: Museum A 16 August 2003 Search: Upupa epops 5 records returned 18 Augúst 2003 Search: Birds from Nice 16 records returned GBIF Usage: Observer B 16 August 2003 Search: Upupa epops 2 records returned GBIF Portal

38. Global Biodiversity Information Facility GBIF Participant Nodes can offer tailored information Show specimen records for Erinaceus europaeus from Russia 58 GBIF records: 1. Museum AW Siberia 2. Museum ABoksary 3. Museum AVasuganje 4. Museum AAvignon 5. Museum AAvignon 6. Museum ANakhodka 7. Observer BNorwich 8. Observer BNorwich 9. Observer BSouthampton... 58. Museum CToulouse 26 records: 1. Museum AW Siberia 2. Museum ABoksary 3. Museum AVasuganje 4. Museum ANovosibirsk 5. Museum ASargatka 6. Museum ANakhodka 23. Observer BKedrovaya 29. Observer BShkotovdkyi... 58. Museum CNovosibirsk Show photo & occurrence of Обыкновенный еж GBIF Portal GBIF Russia Geographic Services

39. Global Biodiversity Information Facility WWW.GBIF.ORG