SparqlA

Sparq allows querying external server. Understanding of RDF is usefull

query 1 - all wet macular degeneration trials

doInstall <- F;toInstall <-c("SPARQL");if(doInstall){install.packages(toInstall)};lapply(toInstall,library, character.only = T)

## Loading required package: XML
## Loading required package: RCurl
## Loading required package: bitops

## [[1]]
##  [1] "SPARQL"    "RCurl"     "bitops"    "XML"       "stats"    
##  [6] "graphics"  "grDevices" "utils"     "datasets"  "methods"  
## [11] "base"

endpoint<-'http://clinicaltrials.bio2rdf.org/sparql'
qs<-'
  PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
  PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
  PREFIX dc: <http://purl.org/dc/elements/1.1/>
  PREFIX dct: <http://purl.org/dc/terms/>
  PREFIX ct: <http://bio2rdf.org/clinicaltrials:>
  PREFIX ctv: <http://bio2rdf.org/clinicaltrials_vocabulary:>
  
  SELECT *
  WHERE {
      ?x ctv:condition-mesh  <http://bio2rdf.org/clinicaltrials_resource:4938444ea4887b824f41147e31329e6c>. #wet AMD 
      ?x <http://bio2rdf.org/bio2rdf_vocabulary:identifier> ?xid.
      ?x rdfs:label ?label.
      ?x ctv:phase [rdfs:label ?phase].
  OPTIONAL {
      ?x ctv:firstreceived-results-date ?res_date.
          }
  }
'
#no line breaks
print(qs)

## [1] "\n  PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n  PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>\n  PREFIX dc: <http://purl.org/dc/elements/1.1/>\n  PREFIX dct: <http://purl.org/dc/terms/>\n  PREFIX ct: <http://bio2rdf.org/clinicaltrials:>\n  PREFIX ctv: <http://bio2rdf.org/clinicaltrials_vocabulary:>\n  \n  SELECT *\n  WHERE {\n      ?x ctv:condition-mesh  <http://bio2rdf.org/clinicaltrials_resource:4938444ea4887b824f41147e31329e6c>. #wet AMD \n      ?x <http://bio2rdf.org/bio2rdf_vocabulary:identifier> ?xid.\n      ?x rdfs:label ?label.\n      ?x ctv:phase [rdfs:label ?phase].\n  OPTIONAL {\n      ?x ctv:firstreceived-results-date ?res_date.\n          }\n  }\n"

#nicer format
cat(qs)

## 
##   PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
##   PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
##   PREFIX dc: <http://purl.org/dc/elements/1.1/>
##   PREFIX dct: <http://purl.org/dc/terms/>
##   PREFIX ct: <http://bio2rdf.org/clinicaltrials:>
##   PREFIX ctv: <http://bio2rdf.org/clinicaltrials_vocabulary:>
##   
##   SELECT *
##   WHERE {
##       ?x ctv:condition-mesh  <http://bio2rdf.org/clinicaltrials_resource:4938444ea4887b824f41147e31329e6c>. #wet AMD 
##       ?x <http://bio2rdf.org/bio2rdf_vocabulary:identifier> ?xid.
##       ?x rdfs:label ?label.
##       ?x ctv:phase [rdfs:label ?phase].
##   OPTIONAL {
##       ?x ctv:firstreceived-results-date ?res_date.
##           }
##   }

#actual query
#rs<-SPARQL(endpoint, qs)

#what is the structure of the result set

#str(rs)
#result set is a
#ttr<-(rs$results)
#print(ttr)
#ttr$xid
#how many rows
#nrow(ttr)

query 2 MeSH query

see https://www.nlm.nih.gov/pubs/techbull/mj15/mj15_mesh_rdf.html for more info

endpoint <-'http://id.nlm.nih.gov/mesh/sparql'
qs<-"
PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#>
PREFIX mesh: <http://id.nlm.nih.gov/mesh/>

SELECT DISTINCT ?predicate
FROM <http://id.nlm.nih.gov/mesh>
WHERE {

  ?s ?predicate ?o
  
}
ORDER BY ?p

"

cat(qs)

## 
## PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#>
## PREFIX mesh: <http://id.nlm.nih.gov/mesh/>
## 
## SELECT DISTINCT ?predicate
## FROM <http://id.nlm.nih.gov/mesh>
## WHERE {
## 
##   ?s ?predicate ?o
##   
## }
## ORDER BY ?p

#formats can be different, however the result has formatting code in it
#rs<-SPARQL(url=endpoint, query=qs,format='csv')

#default XML looks good
ttr<-SPARQL(url=endpoint, query=qs)$results

#str(rs)
str(ttr)

## 'data.frame':    1 obs. of  46 variables:
##  $ predicate   : chr "<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>"
##  $ predicate.1 : chr "<http://www.w3.org/2000/01/rdf-schema#label>"
##  $ predicate.2 : chr "<http://id.nlm.nih.gov/mesh/vocab#note>"
##  $ predicate.3 : chr "<http://id.nlm.nih.gov/mesh/vocab#concept>"
##  $ predicate.4 : chr "<http://id.nlm.nih.gov/mesh/vocab#dateCreated>"
##  $ predicate.5 : chr "<http://id.nlm.nih.gov/mesh/vocab#dateRevised>"
##  $ predicate.6 : chr "<http://id.nlm.nih.gov/mesh/vocab#frequency>"
##  $ predicate.7 : chr "<http://id.nlm.nih.gov/mesh/vocab#identifier>"
##  $ predicate.8 : chr "<http://id.nlm.nih.gov/mesh/vocab#indexerConsiderAlso>"
##  $ predicate.9 : chr "<http://id.nlm.nih.gov/mesh/vocab#mappedTo>"
##  $ predicate.10: chr "<http://id.nlm.nih.gov/mesh/vocab#parentTreeNumber>"
##  $ predicate.11: chr "<http://id.nlm.nih.gov/mesh/vocab#pharmacologicalAction>"
##  $ predicate.12: chr "<http://id.nlm.nih.gov/mesh/vocab#preferredConcept>"
##  $ predicate.13: chr "<http://id.nlm.nih.gov/mesh/vocab#preferredMappedTo>"
##  $ predicate.14: chr "<http://id.nlm.nih.gov/mesh/vocab#preferredTerm>"
##  $ predicate.15: chr "<http://id.nlm.nih.gov/mesh/vocab#previousIndexing>"
##  $ predicate.16: chr "<http://id.nlm.nih.gov/mesh/vocab#source>"
##  $ predicate.17: chr "<http://id.nlm.nih.gov/mesh/vocab#broaderConcept>"
##  $ predicate.18: chr "<http://id.nlm.nih.gov/mesh/vocab#casn1_label>"
##  $ predicate.19: chr "<http://id.nlm.nih.gov/mesh/vocab#narrowerConcept>"
##  $ predicate.20: chr "<http://id.nlm.nih.gov/mesh/vocab#registryNumber>"
##  $ predicate.21: chr "<http://id.nlm.nih.gov/mesh/vocab#relatedConcept>"
##  $ predicate.22: chr "<http://id.nlm.nih.gov/mesh/vocab#relatedRegistryNumber>"
##  $ predicate.23: chr "<http://id.nlm.nih.gov/mesh/vocab#scopeNote>"
##  $ predicate.24: chr "<http://id.nlm.nih.gov/mesh/vocab#term>"
##  $ predicate.25: chr "<http://id.nlm.nih.gov/mesh/vocab#allowableQualifier>"
##  $ predicate.26: chr "<http://id.nlm.nih.gov/mesh/vocab#annotation>"
##  $ predicate.27: chr "<http://id.nlm.nih.gov/mesh/vocab#broaderDescriptor>"
##  $ predicate.28: chr "<http://id.nlm.nih.gov/mesh/vocab#dateEstablished>"
##  $ predicate.29: chr "<http://id.nlm.nih.gov/mesh/vocab#hasDescriptor>"
##  $ predicate.30: chr "<http://id.nlm.nih.gov/mesh/vocab#hasQualifier>"
##  $ predicate.31: chr "<http://id.nlm.nih.gov/mesh/vocab#historyNote>"
##  $ predicate.32: chr "<http://id.nlm.nih.gov/mesh/vocab#onlineNote>"
##  $ predicate.33: chr "<http://id.nlm.nih.gov/mesh/vocab#publicMeSHNote>"
##  $ predicate.34: chr "<http://id.nlm.nih.gov/mesh/vocab#seeAlso>"
##  $ predicate.35: chr "<http://id.nlm.nih.gov/mesh/vocab#treeNumber>"
##  $ predicate.36: chr "<http://id.nlm.nih.gov/mesh/vocab#useInstead>"
##  $ predicate.37: chr "<http://id.nlm.nih.gov/mesh/vocab#abbreviation>"
##  $ predicate.38: chr "<http://id.nlm.nih.gov/mesh/vocab#considerAlso>"
##  $ predicate.39: chr "<http://id.nlm.nih.gov/mesh/vocab#altLabel>"
##  $ predicate.40: chr "<http://id.nlm.nih.gov/mesh/vocab#broaderQualifier>"
##  $ predicate.41: chr "<http://id.nlm.nih.gov/mesh/vocab#entryVersion>"
##  $ predicate.42: chr "<http://id.nlm.nih.gov/mesh/vocab#lexicalTag>"
##  $ predicate.43: chr "<http://id.nlm.nih.gov/mesh/vocab#prefLabel>"
##  $ predicate.44: chr "<http://id.nlm.nih.gov/mesh/vocab#sortVersion>"
##  $ predicate.45: chr "<http://id.nlm.nih.gov/mesh/vocab#thesaurusID>"

#result is not a well behaved data.frame (wide instead of long)
#print(ttr)