andrawaag
/ constructSOExample.sparql
Created
June 13, 2013 11:58
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| CONSTRUCT {?externalEnsemblId <skos:relatedMatch> ?dbPrimaryAcc . | |
| ?dbPrimaryAcc <DC.source> ?dbName .} | |
| WHERE { | |
| ?xref a <xref> . | |
| ?xref <hasDbprimary_acc> ?dbPrimaryAcc . | |
| ?xref <hasDisplayLabel> ?dbDisplayLabel . | |
| ?xref <hasExternalDbId> ?externalDbId . | |
| ?xref <hasInternalEnsemblId> ?internalEnsemblId . | |
| ?externalDbId <hasDbName> ?dbName . | |
| ?internalEnsemblId <hasExternalEnsemblId> ?externalEnsemblId . |
andrawaag
/ countryEducationalInstitutes.sparql
Created
July 3, 2013 13:51
Get the list of educationalInstitutes per country
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| SELECT DISTINCT ?Country count(?EducationalInstitute) as ?noInstitutes | |
| WHERE { | |
| ?Country <http://dbpedia.org/property/gdpNominal> ?Nominalgdp . | |
| ?Country <http://dbpedia.org/property/gdpNominalYear> ?gdpNominalYear . | |
| ?Country <http://dbpedia.org/property/gdpPppPerCapita> ?gdpPppPerCapita . | |
| ?Country <http://dbpedia.org/property/gdpPpp> ?gdpPpp . | |
| ?EducationalInstitute <http://dbpedia.org/property/country> ?Country . | |
| ?EducationalInstitute <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://schema.org/EducationalOrganization> .} ORDER BY ?noInstitutes |
andrawaag
/ getSparqlAsRDF.pl
Created
July 11, 2013 10:50
Get all mouse pathways. This perl scripts returns the uri through identifiers.org, a link the rdf version of the pathway and a url for the wiki entry of the specific revision currently loading in the triple store of wikipathways
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| #!/usr/bin/perl | |
| use LWP::Simple; | |
| use URI::Escape; | |
| my $sparql = "SELECT DISTINCT ?wpIdentifier ?pathway ?page | |
| WHERE { | |
| ?pathway dc:title ?title . | |
| ?pathway wp:organism ?organism . | |
| ?pathway foaf:page ?page . | |
| ?pathway dc:identifier ?wpIdentifier . |
andrawaag
/ getSparqlAsCSV.pl
Created
July 11, 2013 10:59
This perl scripts returns the results of a sparql query to return Pathway elements that don't contain no DataSource or Identifier
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| #!/usr/bin/perl | |
| use LWP::Simple; | |
| use URI::Escape; | |
| my $sparql = "SELECT DISTINCT ?wpIdentifier ?elementneedsattention ?elementLabel | |
| WHERE { | |
| ?pathway dc:title ?title . | |
| ?elementneedsattention a gpml:requiresCurationAttention . | |
| ?elementneedsattention dcterms:isPartOf ?pathway . | |
| ?elementneedsattention rdfs:label ?elementLabel . |
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| % Language Definition for GPML | |
| \usepackage{color} | |
| \definecolor{gray}{rgb}{0.4,0.4,0.4} | |
| \definecolor{darkblue}{rgb}{0.0,0.0,0.6} | |
| \definecolor{cyan}{rgb}{0.0,0.6,0.6} | |
| \lstset{ | |
| basicstyle=\ttfamily, | |
| columns=fullflexible, | |
| showstringspaces=false, |
andrawaag
/ FedSparqlwithbash.sh
Created
November 13, 2013 16:21
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| curl "http://sparql.bioontology.org/sparql/?query=PREFIX+omv%3A+%3Chttp%3A%2F%2Fomv.ontoware.org%2F2005%2F05%2Fontology%23%3E%0D%0APREFIX+rdfs%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0D%0APREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%0D%0ASELECT+DISTINCT+%3Fdisease+%3Flabel+%3Ftype+%0D%0AWHERE+%7B%0D%0A%09%0D%0A++++++++%3Fdisease+rdfs%3Alabel+%3Flabel+.%0D%0A++++++++%3Fdisease+rdf%3Atype+%3Chttp%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23Concept%3E+.%0D%0A%7D%0D%0A%0D%0A++++++++&apikey=d3419539-f429-4450-9097-8dd123acadd0&format=txt | |
| “ \ | |
| |grep name=\"disease\”\ | |
| |sed "s/<binding name=\"disease\"><uri>/</“\ | |
| |sed "s/<\/uri><\/binding>/>/“\ | |
| |grep EFO \ | |
| |for efo in `xargs`; \ | |
| do curl "http://sparql.wikipathways.org/?default-graph-uri=&query=PREFIX+identifiers%3A%3Chttp%3A%2F%2Fidentifiers.org%2Fensembl%2F%3E%0D%0APREFIX+atlas%3A+%3Chttp%3A%2F%2Frdf.ebi.ac.uk%2Fresource%2Fatlas%2F%3E%0D%0APREFIX+atlasterms%3A+%3Chttp%3A%2F%2Frdf.ebi.ac.uk%2Fterms%2Fatlas%2 |
andrawaag
/ leprosyInAmerica.r
Last active
January 31, 2024 07:14
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| library(SPARQL) | |
| library(ggplot2) | |
| library(rworldmap) | |
| wdqs <- "https://query.wikidata.org/bigdata/namespace/wdq/sparql" | |
| query = "PREFIX wd: <http://www.wikidata.org/entity/> | |
| PREFIX wdt: <http://www.wikidata.org/prop/direct/> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX p: <http://www.wikidata.org/prop/> | |
| PREFIX v: <http://www.wikidata.org/prop/statement/> |
andrawaag
/ DifExInsullinSIgnalling.R
Last active
October 4, 2015 21:29
Differentially expressed Genes in a pathway on Insulin Signaling in case of Diabetes Mellitus
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| library(SPARQL) | |
| library(ggplot2) | |
| wpSparql <- "http://sparql.wikipathways.org" | |
| ebiSparql <- "https://www.ebi.ac.uk/rdf/services/atlas/sparql" | |
| efoPathwaysQuery <- "PREFIX identifiers: <http://identifiers.org/ensembl/> | |
| PREFIX atlas: <http://rdf.ebi.ac.uk/resource/atlas/> | |
| PREFIX atlasterms: <http://rdf.ebi.ac.uk/terms/atlas/> | |
| PREFIX efo: <http://www.ebi.ac.uk/efo/> | |
| PREFIX foaf: <http://xmlns.com/foaf/0.1/> | |
| PREFIX dcterms: <http://purl.org/dc/terms/> |
andrawaag
/ TuberculosisinWikidata.R
Last active
December 7, 2015 14:51
Get a spatial map in R on Number of cases of Tuberculosis in Wikidata added the SWAT4LS tutorial
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| library(SPARQL) | |
| library(ggplot2) | |
| library(rworldmap) | |
| wdqs <- "https://query.wikidata.org/bigdata/namespace/wdq/sparql" | |
| query <- "PREFIX wd: <http://www.wikidata.org/entity/> | |
| PREFIX wdt: <http://www.wikidata.org/prop/direct/> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX p: <http://www.wikidata.org/prop/> | |
| PREFIX v: <http://www.wikidata.org/prop/statement/> |
andrawaag
/ WIkidataMalariaCounts.R
Created
December 7, 2015 14:54
Get a spatial map in R on Number of cases of Malaria in Wikidata added the SWAT4LS tutorial
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| library(SPARQL) | |
| library(ggplot2) | |
| library(rworldmap) | |
| wdqs <- "https://query.wikidata.org/bigdata/namespace/wdq/sparql" | |
| query <- "PREFIX wd: <http://www.wikidata.org/entity/> | |
| PREFIX wdt: <http://www.wikidata.org/prop/direct/> | |
| PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> | |
| PREFIX p: <http://www.wikidata.org/prop/> | |
| PREFIX v: <http://www.wikidata.org/prop/statement/> |