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135_plazi_proteome

rq turtle/ttl

Connect a taxonomic treatment collected by Plazi in their synospecies system. We connect by what is called the dwc:id-ENA property which is encoded as a xsd:string which is the naked identifier of an NCBI taxon concept. Which in UniProt is encoded as an IRI starting with `http://purl.uniprot.org/taxonomy/'. After converting the taxon identifier we can query for Proteomes in UniProt for that taxon.

Use at

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX trt:   <http://plazi.org/vocab/treatment#>
PREFIX dwc:   <http://rs.tdwg.org/dwc/terms/>
PREFIX dwcFP: <http://filteredpush.org/ontologies/oa/dwcFP#>
SELECT
  ?proteome 
  ?ncbiTaxon 
  ?treatment
WHERE 
{
  {
    SERVICE <https://lindas.admin.ch/query> {
      ?tc a dwcFP:TaxonConcept ;
          dwc:ID-ENA ?ena .
      ?treatment trt:augmentsTaxonConcept|trt:definesTaxonConcept ?tc ;
                 dwc:basisOfRecord ?mc .
      ?mc trt:gbifOccurrenceId ?occ .
    }
  }
  BIND(IRI(CONCAT('http://purl.uniprot.org/taxonomy/', ?ena)) AS ?ncbiTaxon)
  ?proteome a up:Proteome ;
            up:organism ?ncbiTaxon 
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v2("?ena")
  v4("?mc")
  v6("?ncbiTaxon"):::projected 
  v5("?occ")
  v7("?proteome"):::projected 
  v1("?tc")
  v3("?treatment"):::projected 
  c3([http://filteredpush.org/ontologies/oa/dwcFP#TaxonConcept]):::iri 
  c9(["up:Proteome"]):::iri 
  subgraph s1["https://lindas.admin.ch/query"]
    style s1 stroke-width:4px;
    v1 --"a"-->  c3
    v1 --http://rs.tdwg.org/dwc/terms/ID-ENA-->  v2
    subgraph union0[" Union "]
    subgraph union0l[" "]
      style union0l fill:#abf,stroke-dasharray: 3 3;
      v3 --http://plazi.org/vocab/treatment#definesTaxonConcept-->  v1
    end
    subgraph union0r[" "]
      style union0r fill:#abf,stroke-dasharray: 3 3;
      v3 --http://plazi.org/vocab/treatment#augmentsTaxonConcept-->  v1
    end
    union0r <== or ==> union0l
    end
    v3 --http://rs.tdwg.org/dwc/terms/basisOfRecord-->  v4
    v4 --http://plazi.org/vocab/treatment#gbifOccurrenceId-->  v5
  end
  bind0[/"concat('http://purl.uniprot.org/taxonomy/',?ena)"/]
  v2 --o bind0
  bind0 --as--o v6
  v7 --"a"-->  c9
  v7 --"up:organism"-->  v6