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Updating examples to latest schemas
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@agbeltran
agbeltran committed Sep 6, 2016
1 parent abc307f commit 70130fb
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Showing 5 changed files with 419 additions and 342 deletions.
8 changes: 4 additions & 4 deletions code/validate_instances.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,8 @@ def validate_instance(path, filename, error_printing):

path = "../examples"
validate_instance(path, "SBGrid-179.json", 2)
#validate_instance(path, "ClinicalTrials.gov-NCT00001372.json", 2)
#validate_instance(path, "PDB-5AEM.json", 2)
#validate_instance(path, "Uniprot-P77967.json", 2)
#validate_instance(path, "DBgap-phs000979.v1.p1.json", 2)
validate_instance(path, "ClinicalTrials.gov-NCT00001372.json", 2)
validate_instance(path, "PDB-5AEM.json", 2)
validate_instance(path, "Uniprot-P77967.json", 2)
validate_instance(path, "DBgap-phs000979.v1.p1.json", 2)

62 changes: 29 additions & 33 deletions examples/ClinicalTrials.gov-NCT00001372.json
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Original file line number Diff line number Diff line change
Expand Up @@ -34,14 +34,14 @@
}
],
"keywords": [
{ "value": "Systemic Lupus Erythematosus", "ontologyTermIRI" : "" },
{ "value": "Natural History", "ontologyTermIRI" : "" },
{ "value": "Lupus Nephritis", "ontologyTermIRI" : "" },
{ "value": "Lupus", "ontologyTermIRI" : "" },
{ "value": "Systemic Lupus", "ontologyTermIRI" : "" },
{ "value": "SLE", "ontologyTermIRI" : "" }
{ "value": "Systemic Lupus Erythematosus", "valueIRI" : "" },
{ "value": "Natural History", "valueIRI" : "" },
{ "value": "Lupus Nephritis", "valueIRI" : "" },
{ "value": "Lupus", "valueIRI" : "" },
{ "value": "Systemic Lupus", "valueIRI" : "" },
{ "value": "SLE", "valueIRI" : "" }
],
"isCitedBy" : [
"primaryPublications" : [
{
"identifiers": [
{
Expand All @@ -52,7 +52,7 @@
"title": "Part 2: Dermatologic and joint disease, the antiphospholipid antibody syndrome, pregnancy and hormonal therapy, morbidity and mortality, and pathogenesis.",
"type" : {
"value" : "Review",
"ontologyTermIRI" : ""
"valueIRI" : ""
},
"publicationVenue" : "Ann Intern Med. ",
"dates" : [
Expand Down Expand Up @@ -99,7 +99,7 @@
"title": "Accelerated in vitro apoptosis of lymphocytes from patients with systemic lupus erythematosus.",
"type" : {
"value" : "article",
"ontologyTermIRI" : ""
"valueIRI" : ""
},
"publicationVenue" : "J Immunol.",
"dates" : [
Expand Down Expand Up @@ -134,7 +134,7 @@
"title": "Autoantigens targeted in systemic lupus erythematosus are clustered in two populations of surface structures on apoptotic keratinocytes.",
"type" : {
"value" : "article",
"ontologyTermIRI" : ""
"valueIRI" : ""
},
"publicationVenue" : "J Exp Med.",

Expand Down Expand Up @@ -166,12 +166,12 @@
"name" : "Expression data from Adipose Stem Cells (ASC) from morbidly obese and non-obese individuals",
"types" : [{
"value" : "Observational",
"ontologyTermIRI" : ""
"valueIRI" : ""
}],
"extraProperties" : [
{ "category" : "study design", "categoryIRI": "", "values" : [ "N/A" ] , "valuesIRI" : []},
{ "category" : "recruitment status", "values" : ["recruiting"] , "valuesIRI" : [""]},
{ "category" : "estimated enrollment ", "values" : ["100000"] , "valuesIRI" : [""]}
{ "category" : "study design", "categoryIRI": "", "values" : [ "N/A" ] },
{ "category" : "recruitment status", "values" : [ "recruiting" ] },
{ "category" : "estimated enrollment ", "values" : [ "100000" ] }

],
"isAboutBiologicalEntity": [
Expand Down Expand Up @@ -214,18 +214,18 @@
"postalAddress" : "concatenate (<city>Bethesda</city> <state>Maryland</state> <zip>20892</zip> <country>United States</country>)",
"roles" : [{
"value": "sponsor",
"ontologyTermIRI": ""
"valueIRI": ""
}]
}
],
"roles" : [
{
"value" : "principal investigator" ,
"ontologyTermIRI" : ""
"valueIRI" : ""
},
{
"value" : "backup contact" ,
"ontologyTermIRI" : ""
"valueIRI" : ""
}
]
},
Expand All @@ -240,14 +240,14 @@
"postalAddress" : "concatenate (<city>Bethesda</city> <state>Maryland</state> <zip>20892</zip> <country>United States</country>)",
"roles" : [{
"value" : "sponsor",
"ontologyTermIRI" : ""
"valueIRI" : ""
}]
}
],
"roles" : [
{
"value" : "overall contact" ,
"ontologyTermIRI" : ""
"valueIRI" : ""
}
]
}
Expand Down Expand Up @@ -277,23 +277,21 @@
"date": "1999-11-03",
"type": {
"value": "creation",
"ontologyTermIRI" : ""
"valueIRI" : ""
}
},
{
"date": "2016-05-19",
"type": {
"value": "modification",
"ontologyTermIRI" : ""
"valueIRI" : ""
}
}
],
"accessModalities" : [
{
"access" : {
"landingPage": "https://clinicaltrials.gov/",
"accessURL" : "https://clinicaltrials.gov/show/NCT00001372?displayxml=true"
}
],
},
"conformsTo": [
{
"identifiers": [
Expand All @@ -305,7 +303,7 @@
"name": "XSD",
"type": {
"value": "xml schema",
"ontologyTermIRI" : ""
"valueIRI" : ""
}
},
{
Expand All @@ -318,12 +316,11 @@
"name": "XML",
"type": {
"value": "format",
"ontologyTermIRI" : ""
"valueIRI" : ""
}
}
],
"storedIn" : [
{
"storedIn" : {
"identifiers": [
{
"identifier": "https://clinicaltrials.gov/ct2/home",
Expand All @@ -345,16 +342,15 @@
"types" :[
{
"value" : "primary repository",
"ontologyTermIRI" : ""
"valueIRI" : ""
}
],
"version": ""
}
],
},
"size": -1,
"unit" : {
"value" : "megabyte",
"ontologyTermIRI" : "http://purl.obolibrary.org/obo/UO_0000235"
"valueIRI" : "http://purl.obolibrary.org/obo/UO_0000235"
}
}
]
Expand Down

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