1 gbif and ocean biodiversity, obi'07 conference, oct 2-4, 2007, dartmouth, nova scotia gbif...

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]


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


Image source: http://news.nationalgeographic.com/news/2006/03/0309_060309_yeti_crab.html

The species is the fundamental unit of biodiversity


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)


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


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


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


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


http:/data.gbif.org


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.


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 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 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


(TDWG GML1 application schema)

Open Geospatial Consortium (OGC) Web Services

Web Map Service

Web Feature Service

Web Coverage Service1Geography Markup Language


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


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)


Outstanding Issues

Mobilising data

Data quality

Record duplication

Richer metadata – a profile for biodiversity data (MMI, EML, ISO 19139)


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


Event Log for Datasets

- Name parsing

- Geospatial issues


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)


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


LSID Resolvershttp://lsids.sourceforge.net/


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


Thank you

1 gbif and ocean biodiversity, obi'07 conference, oct 2-4, 2007, dartmouth, nova scotia gbif...

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