virtuoso - Property Path equivalent to OPTION(TRANSITIVE) statement in SPARQL -

-

i'm naive user trying replicate query results in following type of string:

derives_from (epithelial cell , (part_of (uterine cervix , (part_of (homo sapiens , (has disease adenocarcinoma)))))

i'm @ hackathon, have no ontology/sparql expert, , we're trying these related fields out of ontology , solr. we're desperate!

the webpage http://www.ontobee.org/ontology/clo?iri=http://purl.obolibrary.org/obo/clo_000368) helpfully provides sparql queries used on page. think relevant query:

prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix owl: <http://www.w3.org/2002/07/owl#> select distinct ?ref ?refp ?label ?o <http://purl.obolibrary.org/obo/merged/clo> {     ?ref ?refp ?o .     filter ( ?refp in ( owl:equivalentclass, rdfs:subclassof ) ) .     optional { ?ref rdfs:label ?label } .     {         {             select ?s ?o <http://purl.obolibrary.org/obo/merged/clo> {                 ?o ?p ?s .                 filter ( ?p in ( rdf:first, rdf:rest, owl:intersectionof, owl:unionof, owl:somevaluesfrom, owl:hasvalue, owl:allvaluesfrom, owl:complementof, owl:inverseof, owl:onclass, owl:onproperty ) )             }         }         option ( transitive, t_in( ?s ), t_out( ?o ), t_step( ?s ) ?link ).         filter ( ?s= <http://purl.obolibrary.org/obo/clo_0003684> )     } } order ?label

however, can't run check, because sparql endpoint doesn't support virtuoso. http://sparql.bioontology.org so, spits error on option(transitive). can show me equivalent standard pathway language? there varying pathway lengths between target nodes.

virtuoso's transitivity operator more powerful standard sparql provides, in general case not possible express same thing in single standard sparql query. however, believe in case is possible.

the following property path equivalent (disclaimer, haven't tested query, should give general idea):

?o (rdf:first|rdf:rest|owl:intersectionof|owl:unionof|owl:somevaluesfrom|owl:hasvalue|owl:allvaluesfrom|owl:complementof|owl:inverseof|owl:onclass|owl:onproperty)+ ?s .

the full query become this:

prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix owl: <http://www.w3.org/2002/07/owl#> select distinct ?ref ?refp ?label ?o <http://purl.obolibrary.org/obo/merged/clo> {     ?ref ?refp ?o .     filter ( ?refp in ( owl:equivalentclass, rdfs:subclassof ) ) .     optional { ?ref rdfs:label ?label } .     {         {             select ?s ?o <http://purl.obolibrary.org/obo/merged/clo> {                     ?o (rdf:first|rdf:rest|owl:intersectionof|owl:unionof|owl:somevaluesfrom|owl:hasvalue|owl:allvaluesfrom|owl:complementof|owl:inverseof|owl:onclass|owl:onproperty)+ ?s .             }         }         filter ( ?s= <http://purl.obolibrary.org/obo/clo_0003684> )     } } order ?label

note, way, filter condition on variable ?s outside subselect, might make query bit of performance hog. since not using ?s anywhere else in query, can simplify part of query further, eliminating filter, so:

    {         {             select ?o <http://purl.obolibrary.org/obo/merged/clo> {                     ?o (rdf:first|rdf:rest|owl:intersectionof|owl:unionof|owl:somevaluesfrom|owl:hasvalue|owl:allvaluesfrom|owl:complementof|owl:inverseof|owl:onclass|owl:onproperty)+ <http://purl.obolibrary.org/obo/clo_0003684> .             }         }     }

Comments

Post a Comment

Popular posts from this blog

how to insert data php javascript mysql with multiple array session 2 -

-
i have method method discussed , successful data entered 1 when more 1 can not database this programs my php form : <form class="form-horizontal" id="form-produk"> <div class="control-group" > <label class="control-label" for="kelas">kategori</label> <div class="controls"> <select class='form-control' name='id_kategori'> <?php $tampil=mysql_query("select * kategori order nama_kategori"); if ($id_kat==0){ echo "<option value=0 selected>- pilih kategori -</option>"; } while($w=mysql_fetch_array($tampil)){ if ($id_kat==$w[id_kategori]){ echo "<option value=$w[id_kategori] selected>$w[nama_kategori]</option>"; } else{ echo "<option value=$w[id_kategori]>$...
Read more

multithreading - Exception in Application constructor -

-
i wanna write snake game javafx , there exception don't know , want know how fix it. ( know it's not complete yet ) and want know , class extends application ( start override ) main in other programs? see , here not static void main bc didn't need, if want add main shoud do? it's exeption... exception in application constructor exception in thread "main" java.lang.nosuchmethodexception: main_snake.main([ljava.lang.string;) @ java.lang.class.getmethod(class.java:1819) @ com.intellij.rt.execution.application.appmain.main(appmain.java:125) and code : import javafx.animation.animationtimer; import javafx.application.application; import javafx.event.eventhandler; import javafx.scene.scene; import javafx.scene.canvas.canvas; import javafx.scene.canvas.graphicscontext; import javafx.scene.input.keyevent; import javafx.scene.layout.borderpane; import javafx.scene.paint.color; import javafx.stage.stage; import java.util.arraylist; /** * creat...
Read more

windows - CertCreateCertificateContext returns CRYPT_E_ASN1_BADTAG / 8009310b -

-
i realize similar post others (e.g. this one ), there details missing posts might significant case. to start with, here's simplified program: #include "stdafx.h" #include <windows.h> #include <wincrypt.h> int _tmain(int argc, _tchar* argv[]) { // usage: certextract certpath char keyfile[] = "c:\\certificates\\public.crt"; byte lp[65536]; security_attributes sa; handle hkeyfile; dword bytes; pccert_context certcontext; sa.nlength = sizeof(sa); sa.lpsecuritydescriptor = null; sa.binherithandle = false; hkeyfile = createfile(keyfile, generic_read, file_share_read, &sa, open_existing, file_attribute_normal, null); if (hkeyfile) { if (readfile(hkeyfile, lp, getfilesize(hkeyfile, null), &bytes, null) && bytes > 0) { certcontext = certcreatecertificatecontext(x509_asn_encoding, lp, bytes); if (certcontext) { printf("yay...
Read more