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#######  additional file 1  ########
#### examples of SPARQL queries ####
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###Author: Adrien Coulet, Stanford University & University of Nancy
###Date: November 16th, 2010
###Last modification: January 18th, 2011
###Location: http://www.loria.fr/~coulet/jbs_material/additional_file_1.txt

#####################
###SPARQL endpoint###
#####################
http://sparql.bioontology.org/webui/

#####################
###loaded resource###
#####################
http://www.loria.fr/~coulet/jbs_material/phare.pd.owl

###############
###graph URI###
###############
rmi:phare.owl#pd

####################
###SPARQL queries###
####################

###all triples###
select $x $y $z
from <rmi:phare.owl#pd> 
where $x $y $z;

###all triples with the gene uchl1 as a subject###
select $y $z
from <rmi:phare.owl#pd> 
where <http://www.stanford.edu/~coulet/phare.owl#uchl1> $y $z;

###all sentences where the gene UCHL1 is subject of a relation
select $y
from <rmi:phare.owl#pd> 
where $rel <http://www.w3.org/2000/01/rdf-schema#comment> $y
and $rel <owl:annotatedSource> <http://www.stanford.edu/~coulet/phare.owl#uchl1>;

###relations and their provenance where uchl1 gene is subject
select $r $o $provenance
from <rmi:phare.owl#pd> 
where  $rel <http://www.w3.org/2000/01/rdf-schema#comment> $provenance
and ($rel <owl:annotatedSource> <http://www.stanford.edu/~coulet/phare.owl#uchl1>
     and $rel <owl:annotatedProperty> $r
     and $rel <owl:annotatedTarget> $o);

###all objects associated with a Variant###
select $x $z
from <rmi:phare.owl#pd>
where 
$x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.stanford.edu/~coulet/phare.owl#Variant>
and
$x <http://www.stanford.edu/~coulet/phare.owl#isAssociatedWith> $z;

###all triples with the variant of the gene apoe as a subject###
select $y $z
from <rmi:phare.owl#pd> 
where <http://www.stanford.edu/~coulet/phare.owl#apoe_variant> $y $z;

###all objects associated with parkinson=disease###
select $x
from <rmi:phare.owl#pd>
where $x <http://www.stanford.edu/~coulet/phare.owl#isAssociatedWith> <http://www.stanford.edu/~coulet/phare.owl#parkinson=disease>;


#######################
###loaded resource 2###
#######################
http://www.loria.fr/~coulet/jbs_material/phare.vip.owl

###############
###graph URI###
###############
rmi:phare.owl#vip
###load <http://www.loria.fr/~coulet/jbs_material/phare.vip.owl> into <rmi:phare.owl#vip>;###

######################
###SPARQL queries 2###
######################

#####all drugs that interact with gene SULT1A1######
###n.b. interact is synonym of is_associated_with###
select $x from <rmi:phare.owl#vip> where $x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.stanford.edu/~coulet/phare.owl#Drug>
and <http://www.stanford.edu/~coulet/phare.owl#sult1a1> <http://www.stanford.edu/~coulet/phare.owl#is_associated_with> $x;
select $x from <rmi:phare.owl#vip> where $x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.stanford.edu/~coulet/phare.owl#Drug>
and $x <http://www.stanford.edu/~coulet/phare.owl#is_associated_with>
 <http://www.stanford.edu/~coulet/phare.owl#sult1a1>;

####everything that interacts with a drug target####
###n.b. interact is synonym of is_associated_with###
select $x from <rmi:phare.owl#vip> where $y <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.stanford.edu/~coulet/ptgs2.owl#DrugTarget>
and $y <http://www.stanford.edu/~coulet/phare.owl#is_associated_with> $x;
select $x from <rmi:phare.owl#vip> where $y <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.stanford.edu/~coulet/phare.owl#DrugTarget>
and $x <http://www.stanford.edu/~coulet/phare.owl#is_associated_with> $y;