Biodiversity Consensus

Environmental Context (ENVO)

Observations automatically linked to environmental features via OpenStreetMap and ENVO.

Environmental SPARQL Queries

PREFIX sio: 
PREFIX rdfs: 
PREFIX envo: 

SELECT ?obs ?envLabel
WHERE {
  ?obs sio:is-located-in ?env .
  ?env a ?envClass ;
       rdfs:label ?envLabel .

  # Federate to OntoBee to check if ?envClass is a subclass of Desert
  SERVICE  {
    ?envClass rdfs:subClassOf* envo:00000098 .
  }
}
LIMIT 10
                

PREFIX sio: 
PREFIX rdfs: 

SELECT ?obs ?envLabel ?osmLink
WHERE {
  ?obs sio:is-located-in ?env .
  ?env rdfs:label ?envLabel ;
       rdfs:seeAlso ?osmLink .
  FILTER(CONTAINS(STR(?osmLink), "openstreetmap.org"))
}
LIMIT 10
                

Genomic Interoperability

Taxa in this project linked to external biological databases via NCBI IDs.

UniProt Federation Samples

These queries demonstrate how to link local taxa to the remote UniProt SPARQL endpoint.

PREFIX up: 
PREFIX sio: 
PREFIX rdfs: 
PREFIX ex: 

SELECT ?taxon ?protein ?name ?function
WHERE {
  ?taxon rdfs:subClassOf+ sio:Taxon .
  FILTER(REGEX(STR(?taxon), "NCBITaxon_"))
  BIND(STRAFTER(STR(?taxon), "NCBITaxon_") AS ?ncbi_id)

  SERVICE  {
    BIND(IRI(CONCAT("http://purl.uniprot.org/taxonomy/", ?ncbi_id)) AS ?up_taxon)
    ?protein up:organism ?up_taxon ;
             up:recommendedName/up:fullName ?name ;
             up:annotation ?anno .
    ?anno a up:Function_Annotation ;
          rdfs:comment ?function .
  }
}
LIMIT 5
                

PREFIX up: 
PREFIX sio: 
PREFIX rdfs: 
PREFIX skos: 

SELECT ?taxon ?gene ?geneName
WHERE {
  ?taxon rdfs:subClassOf+ sio:Taxon .
  FILTER(REGEX(STR(?taxon), "NCBITaxon_"))
  BIND(STRAFTER(STR(?taxon), "NCBITaxon_") AS ?ncbi_id)

  SERVICE  {
    BIND(IRI(CONCAT("http://purl.uniprot.org/taxonomy/", ?ncbi_id)) AS ?up_taxon)
    ?protein up:organism ?up_taxon ;
             up:encodedBy ?gene .
    ?gene skos:prefLabel ?geneName .
  }
}
LIMIT 5
                

PREFIX up: 
PREFIX sio: 
PREFIX rdfs: 
PREFIX rdf: 

SELECT ?taxon ?protein ?length
WHERE {
  ?taxon rdfs:subClassOf+ sio:Taxon .
  FILTER(REGEX(STR(?taxon), "NCBITaxon_"))
  BIND(STRAFTER(STR(?taxon), "NCBITaxon_") AS ?ncbi_id)

  SERVICE  {
    BIND(IRI(CONCAT("http://purl.uniprot.org/taxonomy/", ?ncbi_id)) AS ?up_taxon)
    ?protein up:organism ?up_taxon ;
             up:sequence ?seq .
    ?seq rdf:value ?seqValue .
    BIND(STRLEN(?seqValue) AS ?length)
  }
}
LIMIT 5
                

Community Analysis

Taxonomic Change Analysis

Analysis of how agents modify existing identifications (Causal Chain).