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GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 1
GBIF and Ocean Biodiversity
Building the data web with OBIS
Éamonn Ó Tuama
GBIF Secretariat,
Universitetsparken 15
DK-2100 Copenhagen Ø
Denmark
email: [email protected]
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 2
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
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 3
Image source: http://news.nationalgeographic.com/news/2006/03/0309_060309_yeti_crab.html
The species is the fundamental unit of biodiversity
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 4
GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ØGBIF 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)
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 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
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 7
datasets metadata
name providers
datasets metadata
data providers
registry
institutionsprovidersservices
index
metadata data cache
logging
data portal
queryengine
request handling web services
Components of GBIF Architecture
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 8
indexrepatriateddatasets
web services
data portal (country, regional, thematic, global)
indexmetadata data cache
logging
names service
global catalogue
country catalogues
datasets
GBIF REST,OGC WMS,OGC WFS,OGC WCS
Building a more distributed architecture
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 9
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
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 10
http:/data.gbif.org
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
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.
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 14
GBIFData Portal
Web Services
occurrence record datahttp://data.gbif.org/ws/rest/occurrence
occurrence density datahttp://data.gbif.org/ws/rest/density
dataset metadatahttp://data.gbif.org/ws/rest/resource
data provider metadatahttp://data.gbif.org/ws/rest/provider
data network metadatahttp://data.gbif.org/ws/rest/network
http://data.gbif.org/ws/rest/taxon taxon data
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 15
GBIF Occurrence Web Service
http://data.gbif.org/ws/rest/occurrence/<action>?<parameter_list>
Main actions: Get, List, Count
Parameter list: key-value pairs
http://data.gbif.org/ws/rest/occurrence/list?
scientificname=Ensis+ensis&format=darwin-1.2
http://data.gbif.org/ws/rest/occurrence/get/801914
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 16
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 17
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
http://data.gbif.org/ws/rest/occurrence
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 18
(TDWG GML1 application schema)
Open Geospatial Consortium (OGC) Web Services
Web Map Service
Web Feature Service
Web Coverage Service1Geography Markup Language
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 19
integrating national and thematic portals
Coastlines,Marine areas,Remote sensing imagery
Occurrences,Names
Meteorological,Oceanographic
data data data
Web MapService
Web FeatureService
Web CoverageService
The Geospatial Web
Beyond the UBDB
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 20
Use of GBIF mediated Data
LifeMapper (www.lifemapper.org)
GBIF Mapa (http://gbifmapa.austmus.gov.au/mapa/)
GEOSS demonstration project (http://www.tdwg.org/proceedings/article/view/241)
BioGeoSDI workshop(http://www.tdwg.org/proceedings/article/view/203)
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 21
Outstanding Issues
Mobilising data
Data quality
Record duplication
Richer metadata – a profile for biodiversity data (MMI, EML, ISO 19139)
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 22
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
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 23
Event Log for Datasets
- Name parsing
- Geospatial issues
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 24
Life Science Identifiers (LSIDs)
1. LSID Designator2. Authority Identifier3. Namespace Identifier4. Object Identifier5. Revision Identifier
An LSID is a Uniform Resource Name with 5 parts
urn:lsid:<authority>:<namespace>:<ObjectID>:[version]
urn:lsid:ncbi.nlm.nig.gov:GenBank:T48601:2
Globally Unique Identifiers (GUIDs)
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 25
Example LSIDs
PubMed article: urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:pubmed:12441807
GenBank sequence: urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:genbank:30350027
ubio NameBank: urn:lsid:ubio.org:namebank:2501662
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 26
LSID Resolvershttp://lsids.sourceforge.net/
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 27
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
GBIF and Ocean Biodiversity, OBI'07 Conference, Oct 2-4, 2007, Dartmouth, Nova Scotia 28
Thank you