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Copy pathbuild-the-dataset-tree-in-mdc.rq
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build-the-dataset-tree-in-mdc.rq
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prefix obo: <http://purl.obolibrary.org/obo/>
prefix dc: <http://purl.org/dc/elements/1.1/>
select distinct ?datasetOrSubclass ?datasetOrSubclassLabel ?x ?datasetPrefTerm ?title ?formatSpecLabel ?accessPage ?version ?doi ?doiURL ?identifier ?synopsis ?licenseName ?licenseUrl ?documentationDescription ?documentationUrl ?websiteUrl ?developerName ?pubAbout ?pubThatUsedRelease ?olympus
from <http://www.pitt.edu/obc/ide/apollo-sv>
from <http://www.pitt.edu/obc/ide/classes-and-indexing-instances>
from <http://www.pitt.edu/obc/ide/article-instances>
from <http://www.pitt.edu/obc/ide/article-deleted-instances>
from <http://ide.obc.io/auth>
from <http://www.pitt.edu/obc/mdc/content>
where {
#the item (?x) is in the MIDAS Digital Commons
<http://www.pitt.edu/obc/IDE_ARTICLES_12000070095> obo:BFO_0000174 ?x .
#the item (?x) is an instance of a class (?datasetOrSubclass)
?x rdf:type ?datasetOrSubclass .
#the class (?datasetOrSubclass) is either "data set" or some descendant of "data set"
?datasetOrSubclass rdfs:subClassOf* obo:IAO_0000100 .
#get the label of the class
?datasetOrSubclass rdfs:label ?datasetOrSubclassLabel .
#get the editor preferred term of the data set
?x obo:IAO_0000111 ?datasetPrefTerm .
#if there is a title annotation, get the title of the data set
OPTIONAL { ?x dc:title ?title } .
#get URL to data set access page if present
OPTIONAL { ?x obo:ERO_0000480 ?accessPage } .
#get version if present
OPTIONAL { ?y rdf:type obo:APOLLO_SV_00000108 .
?y obo:IAO_0000219 ?x .
?y rdfs:label ?version } .
#get DOI if present
OPTIONAL { ?z rdf:type obo:OBI_0002110 .
?z obo:IAO_0000219 ?x .
?z rdfs:label ?doi } .
#get DOI URL if present
OPTIONAL { ?z rdf:type obo:OBI_0002110 .
?z obo:IAO_0000219 ?x .
?z obo:ERO_0000480 ?doiURL } .
#get other identifier if present
OPTIONAL { ?identifierInd rdf:type obo:IAO_0020000 .
?identifierInd obo:IAO_0000219 ?x .
?identifierInd rdfs:label ?identifier } .
#get human readable synopsis if present
OPTIONAL { ?x obo:APOLLO_SV_00000523 ?synopsis } .
#get license name if present
OPTIONAL { ?t rdf:type obo:APOLLO_SV_00000535 .
?t obo:BFO_0000050 ?x .
?t rdfs:label ?licenseName } .
#get license URL if present
OPTIONAL { ?t rdf:type obo:APOLLO_SV_00000535 .
?t obo:BFO_0000050 ?x .
?t obo:ERO_0000480 ?licenseUrl } .
#get documentation description if present
OPTIONAL { ?s rdf:type obo:IAO_0000310 .
?s obo:IAO_0000136 ?x .
?s rdfs:label ?documentationDescription } .
#get documentation URL if present
OPTIONAL { ?s rdf:type obo:IAO_0000310 .
?s obo:IAO_0000136 ?x .
?s obo:ERO_0000480 ?documentationUrl } .
#get website URL if present
OPTIONAL { ?o rdf:type obo:FBcv_0000667 .
?o obo:IAO_0000136 ?x .
?o obo:ERO_0000480 ?websiteUrl } .
#get developer(s) if any
OPTIONAL { ?r rdf:type obo:BFO_0000040 . #r is a material entity
?r obo:RO_0000053 ?q . #r is the bearer of q
?q rdf:type obo:OMRSE_00000038 . #q is a legal person role
?p rdf:type obo:APOLLO_SV_00000796 . #p is an instance of creating dataset
?p obo:RO_0002218 ?r . #p has active participant r
?p obo:OBI_0000299 ?x . #p has specified output the dataset
?r rdfs:label ?developerName } . #r has a label/name
#get publication(s) about if any
OPTIONAL { ?n obo:IAO_0000136 ?x .
?n rdf:type obo:IAO_0000311 .
?n rdfs:label ?pubAbout } .
#get publication(s) that used release if any
OPTIONAL { ?m obo:IAO_0000136 ?k . #m is about k
?k rdf:type obo:OBI_0000471 . #k is instance of study
?m rdf:type obo:IAO_0000311 . #m is instance of pub
?m dc:title ?pubThatUsedRelease . #m has label pubThatUsedRelease
?i obo:BFO_0000054 ?j . #i realized by j
?j rdf:type obo:OBIws_0000050 . #j is instance of code execution
?j obo:BFO_0000050 ?k . #j (execution) part of k (study)
?i rdf:type obo:APOLLO_SV_00000525 . #i instance of executable
?h obo:OBI_0000299 ?i . #i specified output of h
?h rdf:type obo:APOLLO_SV_00000524 . #h instance of compiling
?h obo:OBI_0000293 ?x #h has input the dtm
} .
#get data formats if any
OPTIONAL { ?datasetCreation obo:OBI_0000299 ?x . #creation of dataset has specified output the dataset
?datasetCreation obo:OBI_0000417 ?formatSpec . #creation of dataset achieves format spec objective
?datasetCreation rdf:type obo:APOLLO_SV_00000796 . #creation is instance of dataset creating
?formatSpec rdf:type obo:IAO_0000098 . #format spec is instance of data format spec
?formatSpec rdfs:label ?formatSpecLabel #format spec label
} .
#get RROO info if any
OPTIONAL {
?datasetConc rdf:type obo:IAO_0000015 . #the dataset concretization is an instance of information carrier
?x obo:RO_0000058 ?datasetConc . #and the dataset is concretized by dataset concretization
obo:IDE_0000000270 obo:RO_0000053 ?datasetConc . #and Olympus is the bearer of the dataset concretization
obo:IDE_0000000270 rdfs:label ?olympus #get label of Olympus individual
} .
#filter out punned individuals
FILTER ( ?x != obo:IAO_0000100 )
FILTER ( ?x != ?datasetOrSubclass )
FILTER ( ?datasetOrSubclass != obo:APOLLO_SV_00000522)
}