Difference between revisions of "Manuscript Details"
From Knoesis wiki
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|title_background=#b0e2ff | |title_background=#b0e2ff | ||
|content= | |content= | ||
− | + | Cuebee Query: <br /> | |
− | [http://jade.cs.uga.edu:8080/download/query1.avi | + | [http://jade.cs.uga.edu:8080/download/query1.avi Query 1] |
− | + | SPARQL Query: | |
− | PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#> | + | <nowiki>PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#> |
PREFIX PATHWAY: <http://purl.org/obo/owlapi/pathway#> | PREFIX PATHWAY: <http://purl.org/obo/owlapi/pathway#> | ||
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> | ||
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} | } | ||
} | } | ||
+ | </nowiki> | ||
}} | }} | ||
− | + | {{block | |
− | + | |title=Query 2: 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. | |
− | + | |title_background=#b0e2ff | |
− | = | + | |content= |
− | [http://jade.cs.uga.edu:8080/download/query2.avi | + | Cuebee Query: <br /> |
+ | [http://jade.cs.uga.edu:8080/download/query2.avi Query 2] | ||
− | + | SPARQL Query: | |
<nowiki>PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#> | <nowiki>PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#> | ||
PREFIX PATHWAY: <http://purl.org/obo/owlapi/pathway#> | PREFIX PATHWAY: <http://purl.org/obo/owlapi/pathway#> | ||
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} | } | ||
</nowiki> | </nowiki> | ||
+ | }} | ||
− | + | {{block | |
− | + | |title=Query 3: Give the strain summary for all strains created through single or double knockout of a | |
− | + | ||
protein kinase gene. | protein kinase gene. | ||
+ | |title_background=#b0e2ff | ||
+ | |content= | ||
+ | Cuebee Query: <br /> | ||
+ | [http://jade.cs.uga.edu:8080/download/query3.avi Query 3] | ||
− | + | SPARQL Query: | |
− | + | ||
− | + | ||
− | + | ||
<nowiki>PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#> | <nowiki>PREFIX BASE: <http://knoesis.wright.edu/ParasiteExperiment.owl#> | ||
PREFIX PATHWAY: <http://purl.org/obo/owlapi/pathway#> | PREFIX PATHWAY: <http://purl.org/obo/owlapi/pathway#> | ||
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} | } | ||
</nowiki> | </nowiki> | ||
+ | }} |
Revision as of 15:05, 9 June 2011
Query 1: Show proteins that are downregulated in the epimastigote stage and exist in a single metabolic pathway. |
Cuebee Query: 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 } } } |
Query 2: 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. |
Cuebee Query: 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 . } } } |
Query 3: Give the strain summary for all strains created through single or double knockout of a
protein kinase gene. |
Cuebee Query: 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 . } } |