1 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia GBIF and Ocean Biodiversity Building the data web with OBIS Éamonn Ó Tuama GBIF Secretariat, Universitetsparken 15 DK-2100 Copenhagen Ø Denmark

2 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia Outline Role of GBIF in biodiversity informatics Universal Biodiversity Data Bus GBIF web services & geospatial web GBIF and OBIS – working together The GBIF architecture Outstanding issues

3 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia Image source: The species is the fundamental unit of biodiversity

4 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø GBIF has five main programmes of work Outreach and capacity building (OCB) 4 Themes Informatics Content Participation Campaigns Digitisation of natural history collections (DIGIT) Building regional and local infrastructure (NODES) Electronic catalogue of names of known organisms (ECAT) Data access and database interoperability (DADI)

5 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia

6 Core data types on GBIF network Taxon names Taxon occurrence information specimen records from natural history collections observational records Fields used in indexing records Mandatory Scientific name Institutional code Collection code Catalogue number Highly desirable Geospatial location Collection date Higher taxon info Date last modified

7 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia datasets metadata name providers datasets metadata data providers registry institutions providers services index metadata data cache logging data portal query engine request handling web services Components of GBIF Architecture

8 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia index repatriated datasets web services data portal ( country, regional, thematic, global ) index metadata data cache logging names service global catalogue country catalogues datasets GBIF REST, OGC WMS, OGC WFS, OGC WCS Building a more distributed architecture

9 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia Service registry Data standards Transport standards & protocols client data client service data client data UBDB Universal Biodiversity Data Bus A common set of standards for publishing, discovering and accessing biodiversity data over the internet service

10 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia

11 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia

12 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia

13 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia Web Services Software applications that run over the internet and use some kind of standardised message passing system to handle request and response, usually based on XML.

14 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia GBIF Data Portal Web Services occurrence record data occurrence density data dataset metadata data provider metadata data network metadata taxon data

15 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia GBIF Occurrence Web Service ? Main actions: Get, List, Count Parameter list: key-value pairs scientificname=Ensis+ensis&format=darwin-1.2

16 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia

17 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia GBIF Occurrence Web Service scientificname taxonconceptkey dataproviderkey datasourcekey resourcenetworkkey basisofrecord minlatitude maxlatitude minlongitude maxlongitude cellid georeferencedonly hostisocountrycode originisocountrycode startdate enddate modifiedsince startindex maxresults format icon mode stylesheet Parameter list: keys

18 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia (TDWG GML 1 application schema) Open Geospatial Consortium (OGC) Web Services Web Map Service Web Feature Service Web Coverage Service 1 Geography Markup Language

19 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia integrating national and thematic portals Coastlines, Marine areas, Remote sensing imagery Occurrences, Names Meteorological, Oceanographic data Web Map Service Web Feature Service Web Coverage Service The Geospatial Web Beyond the UBDB

20 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia Use of GBIF mediated Data LifeMapper ( GBIF Mapa ( GEOSS demonstration project ( BioGeoSDI workshop (

21 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia Outstanding Issues Mobilising data Data quality Record duplication Richer metadata – a profile for biodiversity data (MMI, EML, ISO 19139)

22 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia Data Quality Incorrect taxonomic identifications Use of incorrect / outdated taxonomic authorities Lack of measure of precision for geographic coordinates good metadata (identification procedures; dubious datasets); feedback mechanisms Solutions Use of online taxonomic catalogues, e.g. ECAT Use of Darwin Core spatial extension; BioGeomancer tools Issues

23 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia Event Log for Datasets - Name parsing - Geospatial issues

24 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia Life Science Identifiers (LSIDs) 1. LSID Designator 2. Authority Identifier 3. Namespace Identifier 4. Object Identifier 5. Revision Identifier An LSID is a Uniform Resource Name with 5 parts urn:lsid: : : :[version] urn:lsid:ncbi.nlm.nig.gov:GenBank:T48601:2 Globally Unique Identifiers (GUIDs)

25 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia Example LSIDs PubMed article: urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org: pubmed: GenBank sequence: urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org: genbank: ubio NameBank: urn:lsid:ubio.org:namebank:

26 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia LSID Resolvers

27 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia GBIF and OBIS - working together GBIF visualisation/mapping services Another portal for OBIS data Data quality checking GBIF portal customisation (language; datasets, thematic) GBIF nodes infrastructure (management, spread load, training, software, GB14 meeting) GBIF REST web services (occurrence, taxon, density, provider, resource, network) GEOSS OGC web services (web map service, web feature service) GEOSS

28 GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia Thank you