SADI

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Publication of GBIF Data via SADI Semantic Web Services

a demo SADI Web Service was created showing how GBIF data can be served via SADI. The most obvious linkage into the current SADI virtual "meta-graph" was through Taxonomy, so a second service was constructed that extracts taxonmy information from the UniProt protein record. Nota bene - I have no faith that the GBIF service will function properly all the time (or ever). The way it traverses from NCBI Taxon ID to GBIF taxonConceptID is by retrieving the binomial species name from UniProt, then doing a species-name search in GBIF to get the GBIF taxonConceptID. I have no idea whether this is a "safe" operation, nor do I know the circumstances under which it will fail. Someone who knows the GBIF data should re-write this service appropriately.

To see these services in action, go to the CardioSHARE demonstration client and enter the following query


  PREFIX pred:   <http://sadiframework.org/ontologies/service_objects.owl#>
  PREFIX uniprot: <http://lsrn.org/UniProt:>
  SELECT ?taxon ?dw
  WHERE {
    	uniprot:Q39090 pred:fromNCBITaxon ?taxon .   
  	?taxon pred:includesCanadianSpeciesOccurrence ?dw
  }


I am publishing a small subset of the Darwin Core metadata about these Species Occurrences, including the latitude and longitude and earliest and latest collection dates (where available). The usual SPARQL query restriction tools can be applied, as in the following example where we only want observations higher than latitude 45':

  PREFIX pred:   <http://sadiframework.org/ontologies/service_objects.owl#>
  PREFIX uniprot: <http://lsrn.org/UniProt:>
  PREFIX to: <http://rs.tdwg.org/ontology/voc/TaxonOccurrence#>
  SELECT ?taxon ?dw ?lat
  WHERE {
       uniprot:Q39090 pred:fromNCBITaxon ?taxon .
       ?taxon pred:includesCanadianSpeciesOccurrence ?dw .
       ?dw to:decimalLatitude ?lat .
       FILTER (?lat > "45")
  }