forked from D-Net/dnet-hadoop
added subjects to oaf generation
This commit is contained in:
parent
db831e6f43
commit
afe84c4244
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@ -40,19 +40,14 @@ case class CreatorType(
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case class TitleType(title: Option[String], titleType: Option[String], lang: Option[String]) {}
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case class SubjectType(subject: Option[String], subjectScheme: Option[String]) {}
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case class SubjectType(
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schemeURI: Option[String],
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value: Option[String],
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subjectScheme: Option[String]
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) {}
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case class DescriptionType(descriptionType: Option[String], description: Option[String]) {}
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case class FundingReferenceType(
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funderIdentifierType: Option[String],
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awardTitle: Option[String],
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awardUri: Option[String],
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funderName: Option[String],
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funderIdentifier: Option[String],
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awardNumber: Option[String]
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) {}
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case class DateType(date: Option[String], dateType: Option[String]) {}
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case class OAFRelations(relation: String, inverse: String, relType: String)
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@ -158,9 +158,23 @@ object BioschemaToOAFTransformation {
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.asJava
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)
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val publisher = (json \\ "publisher").extractOrElse[String](null)
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if (publisher != null)
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result.setPublisher(OafMapperUtils.field(publisher, null))
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val subjects = (json \\ "subjects").extract[List[SubjectType]]
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result.setSubject(
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subjects
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.filter(s => s.value.nonEmpty && s.subjectScheme.nonEmpty && s.schemeURI.nonEmpty)
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.map(s =>
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OafMapperUtils.structuredProperty(
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s.value.get,
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s.subjectScheme.get,
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s.schemeURI.get,
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ModelConstants.DNET_SUBJECT_TYPOLOGIES,
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ModelConstants.DNET_SUBJECT_TYPOLOGIES,
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null
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)
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)
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.asJava
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)
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val instance = result.getInstance().get(0)
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@ -1,10 +1,5 @@
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{"id":"PED00001#P38634_A_1","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00001#P38634_A_1","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:20399186","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/P38634","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:P38634"}],"descriptions":[],"titles":[{"title":"Protein SIC1"}],"dates":[{"date":"2021-12-10T11:11:09","dateType":"Collected"}]}
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{"id":"PED00002#O14558_A_0","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00002#O14558_A_0","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:24382496","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/O14558","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:O14558"}],"descriptions":[],"titles":[{"title":"Heat shock protein beta-6"}],"dates":[{"date":"2021-12-10T11:11:14","dateType":"Collected"}]}
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{"id":"PED00002#O14558_B_0","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00002#O14558_B_0","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:24382496","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/O14558","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:O14558"}],"descriptions":[],"titles":[{"title":"Heat shock protein beta-6"}],"dates":[{"date":"2021-12-10T11:11:14","dateType":"Collected"}]}
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{"id":"PED00003#Q16143_A_0","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00003#Q16143_A_0","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:25389903","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/Q16143","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:Q16143"}],"descriptions":[],"titles":[{"title":"Beta-synuclein"}],"dates":[{"date":"2021-12-10T11:11:17","dateType":"Collected"}]}
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{"id":"PED00004#O43806_A_0","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00004#O43806_A_0","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:16214166","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/O43806","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:O43806"}],"descriptions":[],"titles":[{"title":"Cyclin-dependent kinase inhibitor 1B"}],"dates":[{"date":"2021-12-10T11:11:22","dateType":"Collected"}]}
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{"id":"PED00005#O14558_A_0","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00005#O14558_A_0","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:24382496","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/O14558","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:O14558"}],"descriptions":[],"titles":[{"title":"Heat shock protein beta-6"}],"dates":[{"date":"2021-12-10T11:11:24","dateType":"Collected"}]}
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{"id":"PED00005#O14558_B_0","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00005#O14558_B_0","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:24382496","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/O14558","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:O14558"}],"descriptions":[],"titles":[{"title":"Heat shock protein beta-6"}],"dates":[{"date":"2021-12-10T11:11:24","dateType":"Collected"}]}
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{"id":"PED00006#P37840_A_1","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00006#P37840_A_1","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:25389903","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/P37840","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:P37840"}],"descriptions":[],"titles":[{"title":"Alpha-synuclein"}],"dates":[{"date":"2021-12-10T11:11:27","dateType":"Collected"}]}
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{"id":"PED00006#Q16143_A_0","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00006#Q16143_A_0","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:25389903","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/Q16143","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:Q16143"}],"descriptions":[],"titles":[{"title":"Beta-synuclein"}],"dates":[{"date":"2021-12-10T11:11:27","dateType":"Collected"}]}
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{"id":"PED00006#Q16143_A_2","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00006#Q16143_A_2","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:25389903","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/Q16143","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:Q16143"}],"descriptions":[],"titles":[{"title":"Beta-synuclein"}],"dates":[{"date":"2021-12-10T11:11:27","dateType":"Collected"}]}
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{"id":"PED00111#O75880_A_1","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00111#O75880_A_1","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:16735468","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/O75880","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:O75880"}],"descriptions":[],"titles":[{"title":"PED00111#O75880_A_1 - Structural ensemble of the C-terminal region of Sco1 (132-301), apo structure."}],"dates":[{"date":"2021-12-10T11:17:16","dateType":"Collected"}],"subjects":[{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00120","value":"NMR","subjectScheme":"IDPO:00120"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00141","value":"TOCSY","subjectScheme":"IDPO:00141"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00143","value":"NOESY","subjectScheme":"IDPO:00143"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00147","value":"HSQC","subjectScheme":"IDPO:00147"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00153","value":"HNHA","subjectScheme":"IDPO:00153"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00154","value":"HNCO","subjectScheme":"IDPO:00154"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00155","value":"HNCA","subjectScheme":"IDPO:00155"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00156","value":"HNCACO","subjectScheme":"IDPO:00156"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00157","value":"HNCOCA","subjectScheme":"IDPO:00157"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00158","value":"HNCACB","subjectScheme":"IDPO:00158"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00160","value":"CBCACONH","subjectScheme":"IDPO:00160"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00164","value":"CBCANH","subjectScheme":"IDPO:00164"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00175","value":"NOE","subjectScheme":"IDPO:00175"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00228","value":"AMBER","subjectScheme":"IDPO:00228"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl:00190","value":"DYANA","subjectScheme":"IDPO:00190"}]}
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{"id":"PED00112#P19634_A_1","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00112#P19634_A_1","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:24840010","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/P19634","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:P19634"}],"descriptions":[],"titles":[{"title":"PED00112#P19634_A_1 - Structural ensemble of the TM VI-VII of the nhe1 isoform of the sodium/hydrogen exchanger (226-274)"}],"dates":[{"date":"2021-12-10T11:17:20","dateType":"Collected"}],"subjects":[{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00120","value":"NMR","subjectScheme":"IDPO:00120"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00141","value":"TOCSY","subjectScheme":"IDPO:00141"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00143","value":"NOESY","subjectScheme":"IDPO:00143"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00147","value":"HSQC","subjectScheme":"IDPO:00147"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00167","value":"chemical shift","subjectScheme":"IDPO:00167"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl:00188","value":"Structure calculation","subjectScheme":"IDPO:00188"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl:00202","value":"NMRpipe","subjectScheme":"IDPO:00202"}]}
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{"id":"PED00113#P04156_A_0","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00113#P04156_A_0","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/P04156","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:P04156"}],"descriptions":[],"titles":[{"title":"PED00113#P04156_A_0 - Structural ensemble of major prion protein (173-195)"}],"dates":[{"date":"2021-12-10T11:17:24","dateType":"Collected"}],"subjects":[{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00120","value":"NMR","subjectScheme":"IDPO:00120"}]}
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{"id":"PED00114#P27958_A_0","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00114#P27958_A_0","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsCitedBy","relatedIdentifier":"https://identifiers.org/pubmed:15247283","relatedIdentifierType":"URL"},{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/P27958","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:P27958"}],"descriptions":[],"titles":[{"title":"PED00114#P27958_A_0 - Structural ensemble of the membrane anchor domain of the nonstructural protein 5A (NS5A) of hepatitis C virus (1973-2003), in 50% tfe"}],"dates":[{"date":"2021-12-10T11:17:27","dateType":"Collected"}],"subjects":[{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00120","value":"NMR","subjectScheme":"IDPO:00120"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00141","value":"TOCSY","subjectScheme":"IDPO:00141"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00143","value":"NOESY","subjectScheme":"IDPO:00143"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00147","value":"HSQC","subjectScheme":"IDPO:00147"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00175","value":"NOE","subjectScheme":"IDPO:00175"},{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl:00194","value":"X-PLOR","subjectScheme":"IDPO:00194"}]}
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{"id":"PED00115#P04156_A_0","types":{"resourceType":"Protein","resourceTypeGeneral":"Dataset"},"creators":[],"identifiers":[{"identifier":"https://proteinensemble.org/PED00115#P04156_A_0","identifierType":"URL"}],"relatedIdentifiers":[{"relationType":"IsIdenticalTo","relatedIdentifier":"http://purl.uniprot.org/uniprot/P04156","relatedIdentifierType":"URL"}],"alternateIdentifiers":[{"alternateIdentifier":"https://identifiers.org/uniprot:P04156"}],"descriptions":[],"titles":[{"title":"PED00115#P04156_A_0 - Structural ensemble of major prion protein (173-195), mutant D178N"}],"dates":[{"date":"2021-12-10T11:17:30","dateType":"Collected"}],"subjects":[{"schemeURI":"https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00120","value":"NMR","subjectScheme":"IDPO:00120"}]}
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@ -1,5 +1,5 @@
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{
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"id": "PED00001#P38634_A_1",
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"id": "PED00111#O75880_A_1",
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"types": {
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"resourceType": "Protein",
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"resourceTypeGeneral": "Dataset"
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@ -7,37 +7,114 @@
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"creators": [],
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"identifiers": [
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{
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"identifier": "https://proteinensemble.org/PED00001#P38634_A_1",
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"identifier": "https://proteinensemble.org/PED00111#O75880_A_1",
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"identifierType": "URL"
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}
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],
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"relatedIdentifiers": [
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{
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"relationType": "IsCitedBy",
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"relatedIdentifier": "https://identifiers.org/pubmed:20399186",
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"relatedIdentifier": "https://identifiers.org/pubmed:16735468",
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"relatedIdentifierType": "URL"
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},
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{
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"relationType": "IsIdenticalTo",
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"relatedIdentifier": "http://purl.uniprot.org/uniprot/P38634",
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"relatedIdentifier": "http://purl.uniprot.org/uniprot/O75880",
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"relatedIdentifierType": "URL"
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}
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],
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"alternateIdentifiers": [
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{
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"alternateIdentifier": "https://identifiers.org/uniprot:P38634"
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"alternateIdentifier": "https://identifiers.org/uniprot:O75880"
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}
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],
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"descriptions": [],
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"titles": [
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{
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"title": "Protein SIC1"
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"title": "PED00111#O75880_A_1 - Structural ensemble of the C-terminal region of Sco1 (132-301), apo structure."
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}
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],
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"dates": [
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{
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"date": "2021-12-10T11:11:09",
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"date": "2021-12-10T11:17:16",
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"dateType": "Collected"
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}
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],
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"subjects": [
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00120",
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"value": "NMR",
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"subjectScheme": "IDPO:00120"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00141",
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"value": "TOCSY",
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"subjectScheme": "IDPO:00141"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00143",
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"value": "NOESY",
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"subjectScheme": "IDPO:00143"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00147",
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"value": "HSQC",
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"subjectScheme": "IDPO:00147"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00153",
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"value": "HNHA",
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"subjectScheme": "IDPO:00153"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00154",
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"value": "HNCO",
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"subjectScheme": "IDPO:00154"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00155",
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"value": "HNCA",
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"subjectScheme": "IDPO:00155"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00156",
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"value": "HNCACO",
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"subjectScheme": "IDPO:00156"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00157",
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"value": "HNCOCA",
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"subjectScheme": "IDPO:00157"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00158",
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"value": "HNCACB",
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"subjectScheme": "IDPO:00158"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00160",
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"value": "CBCACONH",
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"subjectScheme": "IDPO:00160"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00164",
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"value": "CBCANH",
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"subjectScheme": "IDPO:00164"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00175",
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"value": "NOE",
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"subjectScheme": "IDPO:00175"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00228",
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"value": "AMBER",
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"subjectScheme": "IDPO:00228"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl:00190",
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"value": "DYANA",
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"subjectScheme": "IDPO:00190"
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}
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]
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}
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@ -50,13 +50,13 @@ class BioschemaDataciteToOAFTest {
|
|||
|
||||
val total_items = spark.read.text(targetPath).count()
|
||||
println(s"total_items: $total_items")
|
||||
assertTrue(total_items == 50)
|
||||
assertTrue(total_items == 21)
|
||||
|
||||
instance.generateBioschemaDataset(path, exportLinks = false, targetPath, "ped", "protein", spark)
|
||||
|
||||
val total_datasets = spark.read.text(targetPath).count()
|
||||
println(s"total_datasets: $total_datasets")
|
||||
assertTrue(total_datasets == 10)
|
||||
assertTrue(total_datasets == 5)
|
||||
|
||||
spark.stop()
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue