forked from D-Net/dnet-hadoop
added ped test with doi citation; fix pmid pid type
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@ -2,12 +2,12 @@
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<parameters>
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<property>
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<name>mainPath</name>
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<value>/data/bioschema/mobidb</value>
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<value>/data/bioschema/ped</value>
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<description>the working path of Bioschema stores</description>
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</property>
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<property>
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<name>datasourceKey</name>
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<value>mobidb</value>
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<value>ped</value>
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<description>the key that identifies the datasource (eg ped, disprot, mobidb)</description>
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</property>
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<property>
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@ -62,7 +62,7 @@ class BioschemaModelConstants extends Serializable {}
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object BioschemaModelConstants {
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val PROTEIN_RESOURCETYPE: Qualifier =
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qualifier("protein", "protein", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)
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qualifier("0047", "Protein", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)
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val DATA_INFO: DataInfo = OafMapperUtils.dataInfo(
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false,
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@ -73,35 +73,35 @@ object BioschemaModelConstants {
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"0.9"
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)
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val PED_PREFIX: String = "ped_________"
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val DISPROT_PREFIX: String = "disprot_____"
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val MOBIDB_PREFIX: String = "mobidb______"
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val PED_PREFIX: String = "fsh_____3595"
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val DISPROT_PREFIX: String = "fsh_____1904"
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val MOBIDB_PREFIX: String = "fsh_____2176"
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val resolvedURLPattern: Map[String, String] = Map(
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"https://identifiers.org/pubmed:" -> "pubmed",
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"https://identifiers.org/pubmed:" -> "pmid",
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"http://purl.uniprot.org/uniprot/" -> "uniprot",
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"https://identifiers.org/uniprot:" -> "uniprot",
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"https://identifiers.org/disprot:" -> "disprot",
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"https://identifiers.org/mobidb:" -> "mobidb"
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"https://identifiers.org/mobidb:" -> "mobidb",
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"https://doi.org/" -> "doi"
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)
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//TODO create DatasourceId and update those value
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val collectedFromMap: Map[String, KeyValue] = {
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val PEDCollectedFrom: KeyValue = OafMapperUtils.keyValue(
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"10|ped_________::pedDatasourceId",
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"10|fairsharing_::c0e8517b1fe0b5270f3f41d4b56d6118",
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"Protein Ensemble Database"
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)
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PEDCollectedFrom.setDataInfo(DATA_INFO)
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val DISPROTCollectedFrom: KeyValue = OafMapperUtils.keyValue(
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"10|disprot_____::disprotDatasourceId",
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"DisProt, the database of intrinsically disordered proteins"
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"10|fairsharing_::c91591a8d461c2869b9f535ded3e213e",
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"Database of Protein Disorder"
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)
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DISPROTCollectedFrom.setDataInfo(DATA_INFO)
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val MOBIDBCollectedFrom: KeyValue = OafMapperUtils.keyValue(
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"10|mobidb______::mobidbDatasourceId",
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"MobiDB, a database of protein disorder and mobility annotations"
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"10|fairsharing_::0234c510bc6d908b28c70ff313743079",
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"MobiDB"
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)
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MOBIDBCollectedFrom.setDataInfo(DATA_INFO)
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@ -0,0 +1,80 @@
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{
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"id": "PED00180#Q9KPH3_A_0",
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"types": {
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"resourceType": "Protein",
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"resourceTypeGeneral": "Dataset"
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},
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"creators": [],
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"identifiers": [
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{
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"identifier": "https://proteinensemble.org/PED00180#Q9KPH3_A_0",
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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://doi.org/10.1016/j.jsb.2020.107573",
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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/Q9KPH3",
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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:Q9KPH3"
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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": "PED00180#Q9KPH3_A_0 - Structural ensemble of protein DciA from Vibrio cholerae (1-157) "
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}
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],
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"dates": [
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{
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"date": "2022-05-10T18:03:43",
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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:00125",
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"value": "SAXS",
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"subjectScheme": "IDPO:00125"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl#IDPO:00224",
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"value": "GROMACS",
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"subjectScheme": "IDPO:00224"
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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:00185",
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"value": "FM",
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"subjectScheme": "IDPO:00185"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl:00213",
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"value": "EOM",
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"subjectScheme": "IDPO:00213"
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},
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{
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"schemeURI": "https://disprot.org/assets/data/IDPO_v0.2.owl:00214",
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"value": "GAJOE",
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"subjectScheme": "IDPO:00214"
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}
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]
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}
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@ -99,4 +99,17 @@ class BioschemaDataciteToOAFTest {
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println("----------------------------")
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})
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}
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@Test
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def testPEDDoiCitationMapping(): Unit = {
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val record = Source
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.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/bioschema/ped_doi_citation.json"))
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.mkString
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val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
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val res: List[Oaf] = BioschemaToOAFTransformation.generateOAF(record, true, "ped", "protein")
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res.foreach(r => {
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println(mapper.writeValueAsString(r))
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println("----------------------------")
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})
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}
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}
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