1

rq turtle/ttl

Count the number of features with the same ISDB and SIRIUS annotations

Use at

• https://enpkg.commons-lab.org/graphdb/repositories/ENPKG

PREFIX enpkg: <https://enpkg.commons-lab.org/kg/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT (COUNT(?feature) AS ?count) 
WHERE
    {
        ?lcms enpkg:has_massive_doi ?massive_doi .
        # FILTER(regex(str(?massive_doi), "MSV000087728")) # MassIVE id filter, MSV000087728 is pf1600, MSV000093464 is 337 Korean medicinal plants, if you want to query both you can pipe "MSV000087728|MSV000093464". You can apply or not these filters by ucommenting/commenting this line.
        ?lcms enpkg:has_lcms_feature_list ?feature_list .
        ?feature_list enpkg:has_lcms_feature ?feature .
        ?feature enpkg:has_sirius_annotation ?sirius_annotation .
            ?sirius_annotation rdf:type enpkg:SiriusStructureAnnotation .
            ?sirius_annotation enpkg:has_InChIkey2D ?sirius_ik2d .
        ?feature enpkg:has_isdb_annotation ?isdb_annotation .
            ?isdb_annotation rdf:type enpkg:IsdbAnnotation .
            ?isdb_annotation enpkg:has_InChIkey2D ?isdb_ik2d .
    FILTER(?isdb_ik2d = ?sirius_ik2d) .
    }

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v9("?count")
  v6("?feature"):::projected 
  v5("?feature_list")
  v8("?isdb_annotation")
  v1("?isdb_ik2d")
  v3("?lcms")
  v4("?massive_doi")
  v7("?sirius_annotation")
  v2("?sirius_ik2d")
  c6(["enpkg:SiriusStructureAnnotation"]):::iri 
  c9(["enpkg:IsdbAnnotation"]):::iri 
  f0[["?isdb_ik2d = ?sirius_ik2d"]]
  f0 --> v1
  f0 --> v2
  v3 --"enpkg:has_massive_doi"-->  v4
  v3 --"enpkg:has_lcms_feature_list"-->  v5
  v5 --"enpkg:has_lcms_feature"-->  v6
  v6 --"enpkg:has_sirius_annotation"-->  v7
  v7 --"a"-->  c6
  v7 --"enpkg:has_InChIkey2D"-->  v2
  v6 --"enpkg:has_isdb_annotation"-->  v8
  v8 --"a"-->  c9
  v8 --"enpkg:has_InChIkey2D"-->  v1
  bind2[/"count(?feature)"/]
  v6 --o bind2
  bind2 --as--o v9