Difference between revisions of "Manuscript Details"

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−
=== Query 1 ===
+
== Query 1 ==
−
* SPARQL Query:
+
Query Goal: Show me proteins that are downregulated in the epimastigote stage and exist in a single metabolic pathway.
−
**
+
−
*Cuebee Query
+
−
**[http://jade.cs.uga.edu:8080/download/query1.avi| Query 1 in Cuebee]
+
−
 
+
−
 
+
−
 
+
−
=== Query 2 ===
+
 
==== SPARQL Query: ====
 
==== SPARQL Query: ====
 
  <nowiki>PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#>
 
  <nowiki>PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#>
Line 57: Line 50:
 
</nowiki>
 
</nowiki>
  
−
==== Cuebee Query ====
+
==== Cuebee Query: ====
−
**[http://jade.cs.uga.edu:8080/download/query2.avi| Query 2 in Cuebee]
+
[http://jade.cs.uga.edu:8080/download/query1.avi| Query 1]
  
  
  
−
=== Query 3 ===
+
== Query 2 ==
−
* SPARQL Query:
+
Query Goal: Give the gene knockout summaries, both for plasmid construction and strain creation, for all gene knockout targets that are 2-fold upregulated in amastigotes at the transcript level and that have orthologs in Leishmania but not in Trypanosoma brucei.
−
**
+
==== SPARQL Query: ====
−
*Cuebee Query
+
<nowiki>PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#>
−
**[http://jade.cs.uga.edu:8080/download/query3.avi| Query 3 in Cuebee]
+
PREFIX PATHWAY: <http://purl.org/obo/owlapi/pathway#>
 +
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 +
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 +
PREFIX so: <http://purl.org/obo/owl/sequence#>
 +
PREFIX owl: <http://www.w3.org/2002/07/owl#>
 +
PREFIX NCI: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
 +
PREFIX provenir: <http://knoesis.wright.edu/provenir/provenir.owl#>
 +
PREFIX ro: <http://obofoundry.org/ro/ro.owl#>
 +
PREFIX PLO: <http://paige.ctegd.uga.edu/ParasiteLifecycle.owl#>
 +
 
 +
SELECT DISTINCT ?gene ?KOStatus ?KOLog ?knockoutProject ?StrainID  ?StrainStatusURL ?strainSummary
 +
FROM <http://knoesis.wright.edu/tcruzi4>
 +
WHERE { GRAPH <http://knoesis.wright.edu/tcruzi4>
 +
{
 +
?knockout provenir:has_parameter ?gene .
 +
?knockout ro:part_of ?knockoutProject .
 +
?knockoutProject rdf:type BASE:knockout_project_protocol .
 +
?gene rdf:type so:gene .
 +
?StrainID provenir:has_parameter ?gene .
 +
?StrainID rdf:type BASE:strain_creation_protocol .
 +
?knockoutProject provenir:has_parameter ?Log .
 +
?Log rdf:type BASE:KOlog .
 +
?Log rdfs:label ?KOLog .
 +
?knockoutProject provenir:has_parameter ?StatusURL .
 +
?StatusURL rdf:type BASE:status .
 +
?StatusURL rdfs:label ?KOStatus .
 +
?microarray BASE:has_output_value ?logbase .
 +
?microarray rdf:type NCI:Microarray_Analysis .
 +
?microarray BASE:has_output_value ?gene .
 +
?logbase rdf:type BASE:log_base2_ratio .
 +
?logbase BASE:has_value ?log2ratio .
 +
?gene BASE:is_orthologous_to ?ortholog .
 +
?ortholog rdf:type so:gene .
 +
?ortholog ro:derives_from ?x .
 +
?x rdf:type PLO:organism .
 +
FILTER regex(?x, "LMA") .
 +
FILTER regex(?microarray, "amastigote") .
 +
FILTER (?log2ratio > 1) .
 +
OPTIONAL
 +
{?StrainID provenir:has_parameter ?StrainStatusURL .
 +
?StrainStatusURL rdf:type BASE:status. }
 +
OPTIONAL { ?StrainID provenir:has_parameter ?StrainSummaryURL .
 +
?StrainSummaryURL rdf:type BASE:strain_summary.
 +
?StrainSummaryURL rdfs:label ?strainSummary .
 +
}
 +
}
 +
}
 +
</nowiki>
 +
 
 +
==== Cuebee Query: ====
 +
[http://jade.cs.uga.edu:8080/download/query2.avi| Query 2]
 +
 
 +
 
 +
 
 +
== Query 3 ==
 +
Query Goal: Give the strain summary for all strains created through single or double knockout of a
 +
protein kinase gene.
 +
==== SPARQL Query: ====
 +
<nowiki>PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#>
 +
PREFIX PATHWAY: <http://purl.org/obo/owlapi/pathway#>
 +
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
 +
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 +
PREFIX so: <http://purl.org/obo/owl/sequence#>
 +
PREFIX owl: <http://www.w3.org/2002/07/owl#>
 +
PREFIX NCI: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
 +
PREFIX provenir: <http://knoesis.wright.edu/provenir/provenir.owl#>
 +
PREFIX ro: <http://obofoundry.org/ro/ro.owl#>
 +
 
 +
SELECT DISTINCT ?StrainID ?strainSummary
 +
WHERE { GRAPH <http://knoesis.wright.edu/tcruzi4>
 +
{
 +
?gene BASE:has_GO_annotation ?go_term .
 +
?go_term rdfs:label ?GOtermLable .
 +
?gene rdf:type so:gene .
 +
?go_term rdf:type BASE:GO_term .
 +
FILTER regex(?GOtermLable, "kinase") .
 +
FILTER regex(?GOtermLable, "protein") .
 +
?StrainID provenir:has_parameter ?gene .
 +
?StrainID rdf:type BASE:strain_creation_protocol .
 +
?StrainID provenir:has_parameter ?StrainSummaryURL .
 +
?StrainSummaryURL rdf:type BASE:strain_summary.
 +
?StrainSummaryURL rdfs:label ?strainSummary .
 +
}
 +
}
 +
</nowiki>
 +
 
 +
=== Cuebee Query: ====
 +
[http://jade.cs.uga.edu:8080/download/query3.avi| Query 3]

Revision as of 14:20, 9 June 2011

Query 1

Query Goal: Show me proteins that are downregulated in the epimastigote stage and exist in a single metabolic pathway.

SPARQL Query:

PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#>
PREFIX PATHWAY: <http://purl.org/obo/owlapi/pathway#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX so: <http://purl.org/obo/owl/sequence#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX NCI: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>

SELECT ?gene ?microarray ?pathwaylabel ?logbasevalue ?entry ?pathway
FROM <http://knoesis.wright.edu/tcruzi4>
WHERE { GRAPH <http://knoesis.wright.edu/tcruzi4>
{
?microarray BASE:has_output_value ?gene .
?microarray BASE:has_output_value ?logbase .
?microarray rdf:type NCI:Microarray_Analysis .
?logbase rdf:type BASE:log_base2_ratio .
?logbase BASE:has_value ?logbasevalue .
?gene rdf:type so:gene .
?entry owl:sameAs ?gene .
?entry rdf:type so:gene .
?entry BASE:involved_in ?pathway .
?pathway rdf:type BASE:pathway .
?pathway rdfs:label ?pathwaylabel
FILTER regex(?microarray , "epimastigote") .
FILTER (?logbasevalue < -1) .
{
	SELECT  ?gene count(?pathway)
	FROM <http://knoesis.wright.edu/tcruzi4>
	WHERE { GRAPH <http://knoesis.wright.edu/tcruzi4>
	{
	?microarray BASE:has_output_value ?gene .
           ?microarray rdf:type NCI:Microarray_Analysis .
	?gene rdf:type so:gene .
	?entry owl:sameAs ?gene .
	?entry rdf:type so:gene .
	?entry BASE:involved_in ?pathway .
	?pathway rdf:type BASE:pathway .
	?pathway rdfs:label ?pathwaylabel
	FILTER regex(?microarray , "epimastigote") .
	}
	}
	group by ?gene
	having count(?pathway) = 1
	}
}
}

Cuebee Query:

Query 1


Query 2

Query Goal: Give the gene knockout summaries, both for plasmid construction and strain creation, for all gene knockout targets that are 2-fold upregulated in amastigotes at the transcript level and that have orthologs in Leishmania but not in Trypanosoma brucei.

SPARQL Query:

PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#>
PREFIX PATHWAY: <http://purl.org/obo/owlapi/pathway#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX so: <http://purl.org/obo/owl/sequence#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX NCI: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX provenir: <http://knoesis.wright.edu/provenir/provenir.owl#>
PREFIX ro: <http://obofoundry.org/ro/ro.owl#>
PREFIX PLO: <http://paige.ctegd.uga.edu/ParasiteLifecycle.owl#>

SELECT DISTINCT ?gene ?KOStatus ?KOLog ?knockoutProject ?StrainID  ?StrainStatusURL ?strainSummary
FROM <http://knoesis.wright.edu/tcruzi4>
WHERE { GRAPH <http://knoesis.wright.edu/tcruzi4>
{
?knockout provenir:has_parameter ?gene .
?knockout ro:part_of ?knockoutProject .
?knockoutProject rdf:type BASE:knockout_project_protocol .
?gene rdf:type so:gene .
?StrainID provenir:has_parameter ?gene .
?StrainID rdf:type BASE:strain_creation_protocol .
?knockoutProject provenir:has_parameter ?Log .
?Log rdf:type BASE:KOlog .
?Log rdfs:label ?KOLog .
?knockoutProject provenir:has_parameter ?StatusURL .
?StatusURL rdf:type BASE:status .
?StatusURL rdfs:label ?KOStatus .
?microarray BASE:has_output_value ?logbase .
?microarray rdf:type NCI:Microarray_Analysis .
?microarray BASE:has_output_value ?gene .
?logbase rdf:type BASE:log_base2_ratio .
?logbase BASE:has_value ?log2ratio .
?gene BASE:is_orthologous_to ?ortholog .
?ortholog rdf:type so:gene .
?ortholog ro:derives_from ?x .
?x rdf:type PLO:organism .
FILTER regex(?x, "LMA") .
FILTER regex(?microarray, "amastigote") .
FILTER (?log2ratio > 1) .
 OPTIONAL
{?StrainID provenir:has_parameter ?StrainStatusURL .
 ?StrainStatusURL rdf:type BASE:status. }
OPTIONAL { ?StrainID provenir:has_parameter ?StrainSummaryURL .
 ?StrainSummaryURL rdf:type BASE:strain_summary.
 ?StrainSummaryURL rdfs:label ?strainSummary .
}
}
}

Cuebee Query:

Query 2


Query 3

Query Goal: Give the strain summary for all strains created through single or double knockout of a protein kinase gene.

SPARQL Query:

PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#>
PREFIX PATHWAY: <http://purl.org/obo/owlapi/pathway#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX so: <http://purl.org/obo/owl/sequence#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX NCI: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX provenir: <http://knoesis.wright.edu/provenir/provenir.owl#>
PREFIX ro: <http://obofoundry.org/ro/ro.owl#>

SELECT DISTINCT ?StrainID ?strainSummary
WHERE { GRAPH <http://knoesis.wright.edu/tcruzi4>
{
?gene BASE:has_GO_annotation ?go_term .
?go_term rdfs:label ?GOtermLable .
?gene rdf:type so:gene .
?go_term rdf:type BASE:GO_term .
FILTER regex(?GOtermLable, "kinase") .
FILTER regex(?GOtermLable, "protein") .
?StrainID provenir:has_parameter ?gene .
?StrainID rdf:type BASE:strain_creation_protocol .
?StrainID provenir:has_parameter ?StrainSummaryURL .
?StrainSummaryURL rdf:type BASE:strain_summary.
?StrainSummaryURL rdfs:label ?strainSummary .
}
}

Cuebee Query: =

Query 3

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