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GLOBAL BIODIVERSITY

GLOBAL BIODIVERSITY. INFORMATION FACILITY. The Global Biodiversity Information Facility: An Interoperable Network of Primary Biodiversity Databases Jim Edwards, Campinas, Brazil, 4 March 2004. WWW.GBIF.ORG. What is GBIF ?. A network of Participant nodes that

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GLOBAL BIODIVERSITY

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  1. GLOBALBIODIVERSITY INFORMATIONFACILITY The Global Biodiversity Information Facility: An Interoperable Network of Primary Biodiversity Databases Jim Edwards, Campinas, Brazil, 4 March 2004 WWW.GBIF.ORG

  2. What is GBIF ? • A network of Participant nodes that • Make primary biodiversity data openly and freely available over the Internet • Use common standards for data and metadata • Encourage generation of additional content • Assure that data providers retain control of their own data • Provide access to biodiversity data through a single portal

  3. Why was GBIF established? • Georeferenced biodiversity data of good quality and historical depth resides in the world’s natural history collections and observational databases • These data were being digitised in a haphazard, piecemeal fashion • GBIF was formed to help synergise and pull together species- and specimen-level databases and make them interoperable

  4. Developed World Biodiversity Data Biodiversity Developing World Why was GBIF established? • Both biodiversity and biodiversity data are unevenly distributed around the world: • GBIF is helping to redress the inequality of data distribution

  5. GBIF ... • Was recommended by an OECD working group and endorsed by OECD science ministers • But is independent from the OECD • Is not part of the United Nations • But works closely with many UN bodies • Convention on Biological Diversity • World Conservation Monitoring Centre • Is based on a non-binding Memorandum of Understanding between countries and international organisations

  6. Each Participant in GBIF agrees to: • Share scientific biodiversity data • Develop an Internet node to access those data • In addition, Voting Participants agree to • Make a specific contribution toward GBIF’s activities

  7. GBIF Voting Participants 25 • Netherlands • New Zealand • Nicaragua • Norway (Feb. 2004) • Portugal • Peru • Slovenia • South Africa • Spain • Sweden • UK • USA • Australia • Belgium • Canada • Costa Rica • Denmark • Estonia • Finland • France • Germany • Iceland • Japan • Republic of Korea • Mexico

  8. Argentina Austria Bulgaria Colombia Czech Republic Ghana India Madagascar Morocco Pakistan Papua/New Guinea (Feb 04) Poland Slovak Republic Switzerland Taiwan Tanzania ALL Species Foundation ASEANET BioNET BIOSIS CABI Bioscience EASIANET European Commission Expert Centre for Taxonomic Identification Freshwater Biological Association Inter-American Biodiversity Information Network Integrated Taxonomic Information System IUCN NatureServe Ocean Biogeographic Information System SAFRINET Société de Bactériologie Systématique et Vétérinaire Species 2000 Taxonomic Databases Working Group UNESCO Man and the Biosphere Program UNEP (World Conservation Monitoring Centre) World Federation for Culture Collections Wildscreen Trust GBIF Associate Participants 16 + 24

  9. GBIF’s focus is on primary data • Primary data result from the direct observation of nature, for example • A specimen of an organism • Banding a bird • Primary data can be used and reused to answer many kinds of questions, both scientific and societal • Georeferenced primary data can be analysed in many ways, e.g. • Choosing best sites for conservation areas or future biodiversity collecting efforts • Predicting effects of climate change on biota • Choosing best sites for GMO field trials • Predicting the spread of invasive species

  10. What are GBIF’s primary data ? • Associated notes, recordings, observational databases, etc. • These data must be digitised in order to be shared and fully utilised • Label data on ~ 1.5 - 3.0 billion specimens in natural history collections

  11. Example: The Cactus Moth Cactoblastis cactorum • Study done by Jorge Soberon, CONABIO, Mexico, and collaborators • Cactoblastis devours every single species of prickly-pear (Platyopuntia) cactus that has been examined • In the US and Mexico there are more than 90 species of Platyopuntia, many endangered, that are vital components of arid ecosystems. • In Mexico, Platyopuntia is the 10th most important agricultural product

  12. Cactoblastis cactorum Data points obtained from the NMNH, USA

  13. Climate surface obtained by Floramap (12 layers)

  14. Platyopuntia localities MNHSD, IBUNAM, ENCB, MOBOT, NMNH, UAH

  15. Predicted number of species of Platyopuntia Opuntia lagunae Fotografías de la planta y el fruto de Jon Rebman Fotografía de las flores de George Lindsay http://www.oceanoasis.org/fieldguide/opun-lag-sp.html

  16. Vulnerable areas to Cactoblastis(right climate and right food) Red isolines: High similarity to climate in the original Cactoblastis cactorum sites. Blue regions: Richness of species of Platyopuntia.

  17. What does GBIF do ? • GBIF has a set of tasks that is distinct from that of any other organization. • In order to promote the sharing and use of scientific biodiversity data by everyone, it focuses on four areas of activity: • Digitisation of Natural History Collections (DIGIT) • Electronic Catalog of Names of Known Organisms (ECAT) • Data Access and Database Interoperability (DADI) • Outreach and Capacity Building (OCB)

  18. GBIF contribution to interoperability 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

  19. Prototype of GBIF data portal now open for use and comment • www.gbif.net • Currently contains >12 million specimen and observational records, • Provided by more than 34 data record providers and about 20 names providers • Can search on scientific names (including synonyms), see record information, plot maps, get lists of taxa by country, etc. • Portal still in prototype stage • Expect to add many more records and to improve search methodologies throughout 2004 • Please provide comments to help us improve it!!

  20. GBIF’s contributions to interoperability • Work with Taxonomic Databases Working Group (TDWG) to establish standards for data and interoperability • E.g., Darwin Core, DiGIR, GIS standards • Work with Catalogue of Life and others to finish Electronic Catalogue of the world’s scientific names by 2010 • Including consensus taxonomy, synonyms, common names • Will be an authority file for use by all

  21. GBIF’s support for biodiversity informatics • Database components of several activities of the Convention on Biological Diversity • Clearing House Mechanism, Global Taxonomy Initiative, Global Strategy for Plant Conservation • Seed-money grants for digitisation and for developing components of the Electronic Catalogue • GBIF-UNESCO Chairs in Biodiversity Informatics • Begin 2005 with 4 chairs in developing countries, 2 in developed • White papers on IPR, digitisation technologies, etc. • Training courses • Ebbe Nielsen Prize

  22. Contact details Jim Edwards jedwards@gbif.org www.gbif.org GBIF Secretariat Universitetsparken 15 Copenhagen 2100 DENMARK New GBIF Secretariat headquarters, supported by grant from Aage V. Jensens Fonde

  23. GBIF Voting Participants 25 • Netherlands • New Zealand • Nicaragua • Norway • Portugal • Peru • Slovenia • South Africa • Spain • Sweden • UK • USA • Australia • Belgium • Canada • Costa Rica • Denmark • Estonia • Finland • France • Germany • Iceland • Japan • Republic of Korea • Mexico

  24. Argentina Austria Bulgaria Colombia Czech Republic Ghana India Madagascar Morocco Pakistan Poland Slovak Republic Switzerland Taiwan Tanzania ALL Species Foundation ASEANET BioNET BIOSIS CABI Bioscience EASIANET European Commission Expert Centre for Taxonomic Identification Freshwater Biological Association Inter-American Biodiversity Information Network Integrated Taxonomic Information System IUCN NatureServe Ocean Biogeographic Information System SAFRINET Société de Bactériologie Systématique et Vétérinaire Species 2000 Taxonomic Databases Working Group UNESCO Man and the Biosphere Program UNEP (World Conservation Monitoring Centre) World Federation for Culture Collections Wildscreen Trust GBIF Associate Participants 15 + 24

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

  26. What is GBIF? • A distributed facility, comprising an ever- growing network of Participant nodes that • Share biodiversity data openly and freely • Use common standards for data and metadata • Encourage generation of additional content • Assure that data providers retain control of data

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

  28. Why was GBIF established ? • To undertake biodiversity informatics activities that must be accomplished on a worldwide basis in order to make the Internet into a highly valuable, dynamic library of biological information • To take on tasks not being attempted by other initiatives but which would be of benefit to those initiatives (e.g. CHM, GTI, others) • 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

  29. True bioinformatics … “bioinformatics” ecoinformatics genomics proteomics biodiversity informatics

  30. GBIF contribution to interoperability 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

  31. Show records of Erinaceus europaeus Data Interoperability... Observational Dataset 6 records 35 records Museum A 17 records • 81 records: • Museum A Paris • Museum A Nice • Museum A Paris • Museum A Avignon • Museum A Avignon • Museum A Marseille • Observer X Norwich • Observer X Norwich • Observer X Southampton • . . . Museum B GBIF Culture collection 0 records

  32. o Class: Insecta Taxonomic Names ECAT + DADI Ecological Interactions Sequence Data Order: Lepidoptera Foodplant: Zea mais L. 1753 Locus: AAL35331Definition: acyl-CoA Z/E11 desaturase 1 mvpyattadg hpekdecfed... Family: Pyralidae Synonym: Pyralis nubilalis Hübner, 1796 Genus: Ostrinia Hübner, 1825 Species: Ostrinia nubilalis (Hübner, 1796) Taxonomic Descriptions Diagnosis: Wingspan 26-30mm; sexually dimorphic;male: forewings ochreous to dark brown; female: forewings pale yellow; … Vernacular (EN): European Corn-borer Vernacular (DE): Maiszünsler Vernacular (ES): Piral del maíz Vernacular (FR): Pyrale du maïs Digital Literature and Web Resources Pheromones of Ostrinia http://www.nysaes.cornell.edu/fst/faculty/acree/pheronet/phlist/ostrinia.html Collection: DGH Lepidoptera Record id: DGHEUR_003217 Country: France Coordinates: 03.047˚E 48.730˚N Date: 28 June 2003 Collector: Donald Hobern Abiotic Data Specimen & Observation Data DIGIT + DADI Average Rainfall Location: 48.82°N 2.29°E Jan Feb Mar Apr ... 182.3 120.6 158.1 204.9 ... GBIF deals with 1 biodiversity data

  33. GBIF works cooperatively: • Recently signed Memo of Cooperation with the Catalogue of Life partnership • Also work with the Taxonomic Databases Working Group of CODATA on data standards…

  34. 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 Users and applications need data structured according to standards <?xml version="1.0" encoding="UTF-8"?> <response> <record> <darwin:DateLastModified>2003-06-08</darwin:DateLastModified> <darwin:InstitutionCode>DGH</darwin:InstitutionCode> <darwin:CollectionCode>DGH Lepidoptera</darwin:CollectionCode> <darwin:CatalogNumber>DGHEUR_0002976</darwin:CatalogNumber> <darwin:ScientificName>Dichomeris marginella (Fabricius, 1781)</darwin:ScientificName> <darwin:BasisOfRecord>O</darwin:BasisOfRecord> <darwin:Kingdom>Animalia</darwin:Kingdom> <darwin:Order>Lepidoptera</darwin:Order> <darwin:Family>Gelechiidae</darwin:Family> <darwin:Genus>Dichomeris</darwin:Genus> <darwin:Species>marginella</darwin:Species> <darwin:ScientificNameAuthor>(Fabricius, 1781)</darwin:ScientificNameAuthor> <darwin:IdentifiedBy>Donald Hobern</darwin:IdentifiedBy> <darwin:Collector>Donald Hobern</darwin:Collector> <darwin:YearCollected>2003</darwin:YearCollected> <darwin:MonthCollected>06</darwin:MonthCollected> <darwin:DayCollected>08</darwin:DayCollected> <darwin:ContinentOcean>Europe</darwin:ContinentOcean> <darwin:Country>Denmark</darwin:Country> <darwin:County>Gentofte Amt</darwin:County> <darwin:Locality>Merianvej, Hellerup</darwin:Locality> <darwin:Longitude>12.538</darwin:Longitude> <darwin:Latitude>55.737</darwin:Latitude> <darwin:CoordinatePrecision>100</darwin:CoordinatePrecision> <darwin:IndividualCount>1</darwin:IndividualCount> <darwin:Notes>1 in Skinner trap</darwin:Notes> </record> </response> Observation record formatted using the Darwin Core

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

  36. <request> <response> <record> … <response> <record> … <request> <response> <record> … <request> Web services enable the aggregation of structured data Web Services Data indexing & registry are part of these Heterogeneous Databases Standardised Structured Data

  37. But it isn’t an easy task... which is why GBIF is a megascience activity... and why training in biodiversity informatics is needed

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