Architecture and Tools for Biodiversity Data Exchange

1
Architecture and Tools for Biodiversity Data
Exchange

• Donald Hobern
• GBIF Program Officer for Data Access and
  Database Interoperability
• dhobern_at_gbif.org
• http//www.gbif.org/ - http//www.gbif.net/
• December 2004

2
Primary biodiversity data
Class Insecta
Taxonomic Names
Sequence Data
Order Lepidoptera
Synonym Pyralis nubilalis Hübner, 1796
Locus AAL35331Definition acyl-CoA Z/E11
desaturase 1 mvpyattadg hpekdecfed...
Family Pyralidae
Genus Ostrinia Hübner, 1825
Taxonomic Descriptions
Species Ostrinia nubilalis (Hübner, 1796)
Diagnosis Wingspan 26-30mm sexually
dimorphicmale 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
Family Gramineae
Pheromones of Ostrinia http//www.nysaes.cornell.e
du/fst/faculty/acree/pheronet/phlist/ostrinia.html
Foodplant Zea mais L. 1753
Ecological Interactions
Collection DGH Lepidoptera Record
id DGHEUR_003217 Country France Coordinates 03.
047E 48.730N Date 28 June 2003 Collector Donal
d Hobern
Specimens and Observations
Abiotic Data
Average Rainfall Location 48.82N 2.29E Jan
Feb Mar Apr ... 182.3 120.6 158.1 204.9
...
3
Standardised structured data
lt?xml version"1.0" encoding"UTF-8"?gt ltresponsegt
ltrecordgt ltdarwinDateLastModifiedgt2003-06-08lt/d
arwinDateLastModifiedgt ltdarwinInstitutionCodegt
DGHlt/darwinInstitutionCodegt ltdarwinCollectionC
odegtDGH Lepidopteralt/darwinCollectionCodegt ltdar
winCatalogNumbergtDGHEUR_0002976lt/darwinCatalogNu
mbergt ltdarwinScientificNamegtDichomeris
marginella (Fabricius, 1781)lt/darwinScientificNam
egt ltdarwinBasisOfRecordgtOlt/darwinBasisOfRecord
gt ltdarwinKingdomgtAnimalialt/darwinKingdomgt ltd
arwinOrdergtLepidopteralt/darwinOrdergt ltdarwinF
amilygtGelechiidaelt/darwinFamilygt ltdarwinGenusgt
Dichomerislt/darwinGenusgt ltdarwinSpeciesgtmargin
ellalt/darwinSpeciesgt ltdarwinScientificNameAuth
orgt(Fabricius, 1781)lt/darwinScientificNameAuthorgt
ltdarwinIdentifiedBygtDonald Hobernlt/darwinIden
tifiedBygt ltdarwinCollectorgtDonald
Hobernlt/darwinCollectorgt ltdarwinYearCollectedgt
2003lt/darwinYearCollectedgt ltdarwinMonthCollect
edgt06lt/darwinMonthCollectedgt ltdarwinDayCollect
edgt08lt/darwinDayCollectedgt ltdarwinContinentOce
angtEuropelt/darwinContinentOceangt ltdarwinCountr
ygtDenmarklt/darwinCountrygt ltdarwinCountygtKøbenh
avns Amtlt/darwinCountygt ltdarwinLocalitygtMerian
vej, Helleruplt/darwinLocalitygt ltdarwinLongitud
egt12.538lt/darwinLongitudegt ltdarwinLatitudegt55.
737lt/darwinLatitudegt ltdarwinCoordinatePrecisio
ngt100lt/darwinCoordinatePrecisiongt ltdarwinIndiv
idualCountgt1lt/darwinIndividualCountgt ltdarwinNo
tesgt1 in Skinner traplt/darwinNotesgt lt/recordgt lt/
responsegt
Observation record formatted using the Darwin Core
4
Central GBIF registry of data nodes
5
DiGIR Protocol
lt?xml version"1.0" encoding"UTF-8"?gt ltrequest
xmlns"http//digir.net/schema/protocol/2003/1.0"
xmlnsxsd"http//www.w3.org/2001/X
MLSchema" xmlnsdarwin"http//digi
r.net/schema/conceptual/darwin/2003/1.0"gt
ltheadergt ltversiongt1.0.0lt/versiongt
ltsendTimegt2004-07-20T095600-0500lt/sendTimegt
ltsourcegt127.0.0.1lt/sourcegt ltdestination
resource"HDS"gthttp//any.net/digir/DiGIR.phplt/des
tinationgt lttypegtsearchlt/typegt lt/headergt
ltsearchgt ltfiltergt ltandgt
ltequalsgt ltdarwinCollectorgtThomas,
J.lt/darwinCollectorgt lt/equalsgt
ltequalsgt ltdarwinGenusgtRubuslt/darwinGen
usgt lt/equalsgt lt/andgt lt/filtergt
ltrecords limit"3" start"0"gt
ltstructuregt ltxsdelement name"record
minOccurs"0 maxOccurs"unbounded"gt
ltxsdcomplexTypegt ltxsdsequencegt
ltxsdelement ref"darwinInstitutionCode"
/gt ltxsdelement ref"darwinCollecti
onCode"/gt ltxsdelement
ref"darwinCatalogNumber"/gt
ltxsdelement ref"darwinScientificName"/gt
ltxsdelement ref"darwinLatitude"/gt
ltxsdelement ref"darwinLongitude"/gt
lt/xsdsequencegt
lt/xsdcomplexTypegt lt/xsdelementgt
lt/structuregt lt/recordsgt
ltcountgttruelt/countgt lt/searchgt lt/requestgt
lt?xml version"1.0" encoding"utf-8" ?gt ltresponse
xmlns"http//digir.net/schema/protocol/2003/1.0"gt
ltheadergt ltversiongtRevision 1.96
lt/versiongt ltsendTimegt2004-07-20T095603-0500
lt/sendTimegt ltsource resource"HDS"gthttp//any.
net/digir/DiGIR.phplt/sourcegt
ltdestinationgt127.0.0.1lt/destinationgt
lttypegtsearchlt/typegt lt/headergt ltcontent
xmlnsdarwin"http//digir.net/schema/conceptual/d
arwin/2003/1.0"gt ltrecordgt
ltdarwinInstitutionCodegtINSlt/darwinInstitutionCod
egt ltdarwinCollectionCodegtCOLlt/darwinCollec
tionCodegt ltdarwinCatalogNumbergt27694lt/darwi
nCatalogNumbergt ltdarwinScientificNamegtRubu
s brasiliensislt/darwinScientificNamegt
ltdarwinLatitudegt-23.6625lt/darwinLatitudegt
ltdarwinLongitudegt-46.7738lt/darwinLongitudegt
lt/recordgt ltrecordgt ltdarwinInstitutionCo
degtINSlt/darwinInstitutionCodegt
ltdarwinCollectionCodegtCOLlt/darwinCollectionCodegt
ltdarwinCatalogNumbergt27907lt/darwinCatalog
Numbergt ltdarwinScientificNamegtRubus
brasiliensislt/darwinScientificNamegt
ltdarwinLatitudegt-23.412lt/darwinLatitudegt
ltdarwinLongitudegt-46.7899lt/darwinLongitudegt
lt/recordgt ltrecordgt ltdarwinInstitutionCo
degtINSlt/darwinInstitutionCodegt
ltdarwinCollectionCodegtCOLlt/darwinCollectionCodegt
ltdarwinCatalogNumbergt27908lt/darwinCatalog
Numbergt ltdarwinScientificNamegtRubus
urticaefoliuslt/darwinScientificNamegt
ltdarwinLatitudegt-23.412lt/darwinLatitudegt
ltdarwinLongitudegt-46.7899lt/darwinLongitudegt
lt/recordgt lt/contentgt ltdiagnosticsgt
ltdiagnostic code"STATUS_INTERVAL"
severity"info"gt3600lt/diagnosticgt ltdiagnostic
code"STATUS_DATA" severity"info"gt191,1,1lt/diagno
sticgt ltdiagnostic code"MATCH_COUNT"
severity"info"gt26lt/diagnosticgt ltdiagnostic
code"RECORD_COUNT" severity"info"gt3lt/diagnosticgt
ltdiagnostic code"END_OF_RECORDS"
severity"info"gtfalselt/diagnosticgt
lt/diagnosticsgt lt/responsegt
Request
Response
6
DiGIR-BioCASe Protocol and Nested Networks
Get full set of Soy Bean crop descriptors.
User
Get standard plant genetic resource Passport data
for all crop types.
Get complete ABCD documents from each BioCASe
provider
Get Darwin Core records where darwinCountry
equals Madagascar from any provider.
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GBIF Central Data Services (Future)
8
GBIF Data Portal
9
GBIF Data Portal
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GBIF Data Portal