diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala index b74d5d6960..b9f2b8501a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala @@ -577,6 +577,8 @@ val REL_TYPE_VALUE:String = "resultResult" rel.setSource(id) rel.setTarget(s"unresolved::${r.relatedIdentifier}::${r.relatedIdentifierType}") + rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava) + rel.getCollectedfrom.asScala.map(c => c.getValue)(collection.breakOut) rel })(collection breakOut) } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 7dd07b1c47..f033c6d816 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -142,6 +142,7 @@ case object Crossref2Oaf { result.setDateofacceptance(asField(issuedDate)) } else { + // TODO: take the oldest date between publishedPrint and publishedOnline result.setDateofacceptance(asField(createdDate.getValue)) } result.setRelevantdate(List(createdDate, postedDate, acceptedDate, publishedOnlineDate, publishedPrintDate).filter(p => p != null).asJava) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala new file mode 100644 index 0000000000..77e93d4d49 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -0,0 +1,272 @@ +package eu.dnetlib.dhp.sx.bio + +import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils +import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Instance, KeyValue, Oaf, Relation, StructuredProperty} +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.{compact, parse, render} + +import scala.collection.JavaConverters._ + +object BioDBToOAF { + + case class EBILinkItem(id: Long, links: String) {} + + case class EBILinks(relType: String, date: String, title: String, pmid: String, targetPid: String, targetPidType: String, targetUrl: String) {} + + val dataInfo: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9") + + val PDB_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue("10|opendoar____::d1c373ab1570cfb9a7dbb53c186b37a2", "Protein Data Bank") + val UNIPROT_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue("10|re3data_____::296e1abaf1302897a6838d3588cd0310", "UniProtKB/Swiss-Prot") + val SUBJ_CLASS = "Keywords" + UNIPROT_COLLECTED_FROM.setDataInfo(dataInfo) + PDB_COLLECTED_FROM.setDataInfo(dataInfo) + + val EBI_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue("10|opendoar____::83e60e09c222f206c725385f53d7e567c", "EMBL-EBIs Protein Data Bank in Europe (PDBe)") + + + case class UniprotDate(date: String, date_info: String) {} + + def uniprotToOAF(input: String): List[Oaf] = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json = parse(input) + val pid = (json \ "pid").extract[String] + + val d = new Dataset + + d.setPid( + List( + OafMapperUtils.structuredProperty(pid, "uniprot", "uniprot", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo) + ).asJava + ) + + d.setDataInfo(dataInfo) + d.setId(OafMapperUtils.createOpenaireId(50, s"uniprot_____::$pid", true)) + d.setCollectedfrom(List(UNIPROT_COLLECTED_FROM).asJava) + + val title: String = (json \ "title").extractOrElse[String](null) + + if (title != null) + d.setTitle(List(OafMapperUtils.structuredProperty(title, ModelConstants.MAIN_TITLE_QUALIFIER, dataInfo)).asJava) + + d.setOriginalId(List(pid).asJava) + val i = new Instance + + i.setPid(d.getPid) + i.setUrl(List(s"https://www.uniprot.org/uniprot/$pid").asJava) + i.setInstancetype(OafMapperUtils.qualifier("0046", "Bioentity", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)) + + i.setCollectedfrom(UNIPROT_COLLECTED_FROM) + d.setInstance(List(i).asJava) + + val dates: List[UniprotDate] = for { + JObject(dateOBJ) <- json \ "dates" + JField("date", JString(date)) <- dateOBJ + JField("date_info", JString(date_info)) <- dateOBJ + } yield UniprotDate(date, date_info) + + val subjects: List[String] = (json \\ "subjects").extractOrElse[List[String]](null) + + + if (subjects != null) { + d.setSubject( + subjects.map(s => + OafMapperUtils.structuredProperty(s, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, null) + ).asJava) + } + + + if (dates.nonEmpty) { + val i_date = dates.find(d => d.date_info.contains("entry version")) + if (i_date.isDefined) { + i.setDateofacceptance(OafMapperUtils.field(i_date.get.date, dataInfo)) + d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, dataInfo)) + } + val relevant_dates: List[StructuredProperty] = dates.filter(d => !d.date_info.contains("entry version")) + .map(date => OafMapperUtils.structuredProperty(date.date, "UNKNOWN", "UNKNOWN", ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, dataInfo)) + if (relevant_dates != null && relevant_dates.nonEmpty) + d.setRelevantdate(relevant_dates.asJava) + d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, dataInfo)) + } + + + val references_pmid: List[String] = for { + JObject(reference) <- json \ "references" + JField("PubMed", JString(pid)) <- reference + } yield pid + + val references_doi: List[String] = for { + JObject(reference) <- json \ "references" + JField(" DOI", JString(pid)) <- reference + } yield pid + + + if (references_pmid != null && references_pmid.nonEmpty) { + val rel = createRelation(references_pmid.head, "pmid", d.getId, UNIPROT_COLLECTED_FROM, "relationship", "isRelatedTo") + rel.getCollectedfrom + List(d, rel) + } + else if (references_doi != null && references_doi.nonEmpty) { + val rel = createRelation(references_doi.head, "doi", d.getId, UNIPROT_COLLECTED_FROM, "relationship", "isRelatedTo") + List(d, rel) + } + + + else + List(d) + } + + def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType:String, relClass:String):Relation = { + + val rel = new Relation + rel.setCollectedfrom(List(PDB_COLLECTED_FROM).asJava) + rel.setDataInfo(dataInfo) + + rel.setRelType("resultResult") + rel.setSubRelType(subRelType) + rel.setRelClass(relClass) + + rel.setSource(sourceId) + rel.setTarget(s"unresolved::$pid::$pidType") + + rel.getTarget.startsWith("unresolved") + rel.setCollectedfrom(List(collectedFrom).asJava) + rel + + } + + + def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue): Relation = { + createRelation(pid,pidType,sourceId,collectedFrom, "supplement","IsSupplementTo") + } + + + def pdbTOOaf(input: String): List[Oaf] = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json = parse(input) + val pdb = (json \ "pdb").extract[String].toLowerCase + + if (pdb.isEmpty) + return List() + + val d = new Dataset + + d.setPid( + List( + OafMapperUtils.structuredProperty(pdb, "pdb", "Protein Data Bank Identifier", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo) + ).asJava + ) + + d.setCollectedfrom(List(PDB_COLLECTED_FROM).asJava) + d.setDataInfo(dataInfo) + d.setId(OafMapperUtils.createOpenaireId(50, s"pdb_________::$pdb", true)) + d.setOriginalId(List(pdb).asJava) + + val title = (json \ "title").extractOrElse[String](null) + + if (title == null) + return List() + d.setTitle(List(OafMapperUtils.structuredProperty(title, ModelConstants.MAIN_TITLE_QUALIFIER, dataInfo)).asJava) + + val authors: List[String] = (json \ "authors").extractOrElse[List[String]](null) + + if (authors != null) { + val convertedAuthors = authors.zipWithIndex.map { a => + + val res = new Author + res.setFullname(a._1) + res.setRank(a._2 + 1) + res + } + + d.setAuthor(convertedAuthors.asJava) + } + + val i = new Instance + + i.setPid(d.getPid) + i.setUrl(List(s"https://www.rcsb.org/structure/$pdb").asJava) + i.setInstancetype(OafMapperUtils.qualifier("0046", "Bioentity", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)) + + i.setCollectedfrom(PDB_COLLECTED_FROM) + d.setInstance(List(i).asJava) + + val pmid = (json \ "pmid").extractOrElse[String](null) + + if (pmid != null) + List(d, createSupplementaryRelation(pmid, "pmid", d.getId, PDB_COLLECTED_FROM)) + else + List(d) + } + + + def extractEBILinksFromDump(input: String): EBILinkItem = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json = parse(input) + + val pmid = (json \ "publication" \ "pmid").extract[String] + val links = (json \ "links").extract[JObject] + EBILinkItem(pmid.toLong, compact(render(links))) + } + + + def EBITargetLinksFilter(input: EBILinks): Boolean = { + + input.targetPidType.equalsIgnoreCase("ena") || input.targetPidType.equalsIgnoreCase("pdb") || input.targetPidType.equalsIgnoreCase("uniprot") + + } + + + def parse_ebi_links(input: String): List[EBILinks] = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json = parse(input) + val pmid = (json \ "request" \ "id").extract[String] + for { + JObject(link) <- json \\ "Link" + JField("Target", JObject(target)) <- link + JField("RelationshipType", JObject(relType)) <- link + JField("Name", JString(relation)) <- relType + JField("PublicationDate", JString(publicationDate)) <- link + JField("Title", JString(title)) <- target + JField("Identifier", JObject(identifier)) <- target + JField("IDScheme", JString(idScheme)) <- identifier + JField("IDURL", JString(idUrl)) <- identifier + JField("ID", JString(id)) <- identifier + + } yield EBILinks(relation, publicationDate, title, pmid, id, idScheme, idUrl) + } + + + def convertEBILinksToOaf(input: EBILinks): List[Oaf] = { + val d = new Dataset + d.setCollectedfrom(List(EBI_COLLECTED_FROM).asJava) + d.setDataInfo(dataInfo) + d.setTitle(List(OafMapperUtils.structuredProperty(input.title, ModelConstants.MAIN_TITLE_QUALIFIER, dataInfo)).asJava) + + val nsPrefix = input.targetPidType.toLowerCase.padTo(12, '_') + + d.setId(OafMapperUtils.createOpenaireId(50, s"$nsPrefix::${input.targetPid.toLowerCase}", true)) + d.setOriginalId(List(input.targetPid.toLowerCase).asJava) + + + d.setPid( + List( + OafMapperUtils.structuredProperty(input.targetPid.toLowerCase, input.targetPidType.toLowerCase, "Protein Data Bank Identifier", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo) + ).asJava + ) + + val i = new Instance + + i.setPid(d.getPid) + i.setUrl(List(input.targetUrl).asJava) + i.setInstancetype(OafMapperUtils.qualifier("0046", "Bioentity", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)) + + i.setCollectedfrom(EBI_COLLECTED_FROM) + d.setInstance(List(i).asJava) + i.setDateofacceptance(OafMapperUtils.field(input.date, dataInfo)) + d.setDateofacceptance(OafMapperUtils.field(input.date, dataInfo)) + + List(d, createRelation(input.pmid, "pmid", d.getId, EBI_COLLECTED_FROM,"relationship", "isRelatedTo")) + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala deleted file mode 100644 index a37c6529f5..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala +++ /dev/null @@ -1,84 +0,0 @@ -package eu.dnetlib.dhp.sx.bio - -import eu.dnetlib.dhp.schema.common.ModelConstants -import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils -import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Instance, KeyValue, Oaf, Relation} -import org.json4s.DefaultFormats -import org.json4s.jackson.JsonMethods.parse - -import scala.collection.JavaConverters._ -object PDBToOAF { - - val dataInfo: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9") - - val collectedFrom: KeyValue = OafMapperUtils.keyValue("10|opendoar____::d1c373ab1570cfb9a7dbb53c186b37a2", "Protein Data Bank") - - def convert(input:String):List[Oaf]= { - implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats - lazy val json = parse(input) - val pdb = (json \ "pdb").extract[String].toLowerCase - - if (pdb.isEmpty) - return List() - - val d = new Dataset - - d.setPid( - List( - OafMapperUtils.structuredProperty(pdb, "pdb", "pdb", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES,dataInfo) - ).asJava - ) - - d.setCollectedfrom(List(collectedFrom).asJava) - d.setDataInfo(dataInfo) - d.setId(OafMapperUtils.createOpenaireId(50,s"pdb_________::$pdb", true)) - d.setOriginalId(List(pdb).asJava) - - val title = (json \ "title").extractOrElse[String](null) - - if (title== null) - return List() - d.setTitle(List(OafMapperUtils.structuredProperty(title, ModelConstants.MAIN_TITLE_QUALIFIER, dataInfo)).asJava) - - - val authors:List[String] = (json \ "authors").extractOrElse[List[String]](null) - - if (authors!= null) - { - val convertedAuthors = authors.zipWithIndex.map{a => - - val res = new Author - res.setFullname(a._1) - res.setRank(a._2+1) - res - } - - d.setAuthor(convertedAuthors.asJava) - } - - val i = new Instance - - i.setPid(d.getPid) - i.setUrl(List(s"https://www.rcsb.org/structure/$pdb").asJava) - i.setInstancetype(OafMapperUtils.qualifier("0046", "Bioentity", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE)) - - i.setCollectedfrom(collectedFrom) - d.setInstance(List(i).asJava) - val pmid = (json \ "pmid").extractOrElse[String](null) - - if (pmid != null) { - val rel = new Relation - rel.setCollectedfrom(List(collectedFrom).asJava) - rel.setDataInfo(dataInfo) - - rel.setRelType("resultResult") - rel.setSubRelType("supplement") - rel.setRelClass("IsSupplementTo") - - rel.setSource(d.getId) - rel.setTarget(s"unresolved::$pmid::pmid") - return List(d,rel) - } - List(d) - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala new file mode 100644 index 0000000000..9b14f3419c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala @@ -0,0 +1,44 @@ +package eu.dnetlib.dhp.sx.bio + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.{Oaf, Result} +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + +object SparkTransformBioDatabaseToOAF { + + def main(args: Array[String]): Unit = { + val conf: SparkConf = new SparkConf() + val log: Logger = LoggerFactory.getLogger(getClass) + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/bio_to_oaf_params.json"))) + parser.parseArgument(args) + val database: String = parser.get("database") + log.info("database: {}", database) + + val dbPath: String = parser.get("dbPath") + log.info("dbPath: {}", database) + val targetPath: String = parser.get("targetPath") + log.info("targetPath: {}", database) + + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + val sc = spark.sparkContext + + implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) + + + database.toUpperCase() match { + case "UNIPROT" => + spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).write.mode(SaveMode.Overwrite).save(targetPath) + case "PDB"=> + spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).write.mode(SaveMode.Overwrite).save(targetPath) + } + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkAddLinkUpdates.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkAddLinkUpdates.scala index 8471c3a4e0..294cd97add 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkAddLinkUpdates.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkAddLinkUpdates.scala @@ -165,13 +165,13 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin def main(args: Array[String]): Unit = { val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateEBIDataFrame.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json"))) parser.parseArgument(args) val spark: SparkSession = SparkSession .builder() .config(conf) - .appName(SparkCreateEBIDataFrame.getClass.getSimpleName) + .appName(SparkEBILinksToOaf.getClass.getSimpleName) .master(parser.get("master")).getOrCreate() diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateBaselineDataFrame.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateBaselineDataFrame.scala index 1c961d1a43..27dd4adba4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateBaselineDataFrame.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateBaselineDataFrame.scala @@ -41,7 +41,7 @@ object SparkCreateBaselineDataFrame { def main(args: Array[String]): Unit = { val conf: SparkConf = new SparkConf() val log: Logger = LoggerFactory.getLogger(getClass) - val parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateEBIDataFrame.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/ebi/baseline_to_oaf_params.json"))) parser.parseArgument(args) val isLookupUrl: String = parser.get("isLookupUrl") log.info("isLookupUrl: {}", isLookupUrl) @@ -52,7 +52,7 @@ object SparkCreateBaselineDataFrame { SparkSession .builder() .config(conf) - .appName(SparkCreateEBIDataFrame.getClass.getSimpleName) + .appName(SparkEBILinksToOaf.getClass.getSimpleName) .master(parser.get("master")).getOrCreate() import spark.implicits._ diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateEBIDataFrame.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateEBIDataFrame.scala deleted file mode 100644 index 9fc9704460..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateEBIDataFrame.scala +++ /dev/null @@ -1,86 +0,0 @@ -package eu.dnetlib.dhp.sx.ebi - -import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset} -import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} -import eu.dnetlib.dhp.sx.graph.parser.{DatasetScholexplorerParser, PublicationScholexplorerParser} -import eu.dnetlib.scholexplorer.relation.RelationMapper -import org.apache.commons.io.IOUtils -import org.apache.spark.SparkConf -import org.apache.spark.rdd.RDD -import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} -import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} -import org.slf4j.{Logger, LoggerFactory} - -import scala.collection.JavaConverters._ - -object SparkCreateEBIDataFrame { - - - def main(args: Array[String]): Unit = { - val logger: Logger = LoggerFactory.getLogger(SparkCreateEBIDataFrame.getClass) - val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateEBIDataFrame.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json"))) - parser.parseArgument(args) - val spark: SparkSession = - SparkSession - .builder() - .config(conf) - .appName(SparkCreateEBIDataFrame.getClass.getSimpleName) - .master(parser.get("master")).getOrCreate() - - val sc = spark.sparkContext - - - val workingPath = parser.get("workingPath") - val relationMapper = RelationMapper.load - - implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) - implicit val datasetEncoder: Encoder[DLIDataset] = Encoders.kryo(classOf[DLIDataset]) - implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo(classOf[DLIPublication]) - implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation]) - -// logger.info("Extract Publication and relation from publication_xml") -// val oafPubsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/publication_xml").map(s => -// { -// new ObjectMapper().readValue(s, classOf[String]) -// }).flatMap(s => { -// val d = new PublicationScholexplorerParser -// d.parseObject(s, relationMapper).asScala.iterator}) -// -// val mapper = new ObjectMapper() -// mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) -// spark.createDataset(oafPubsRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/oaf") -// -// logger.info("Extract Publication and relation from dataset_xml") -// val oafDatsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/dataset_xml").map(s => -// { -// new ObjectMapper().readValue(s, classOf[String]) -// }).flatMap(s => { -// val d = new DatasetScholexplorerParser -// d.parseObject(s, relationMapper).asScala.iterator}) - -// spark.createDataset(oafDatsRDD).write.mode(SaveMode.Append).save(s"$workingPath/oaf") - val dataset: Dataset[DLIDataset] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[DLIDataset]).map(d => d.asInstanceOf[DLIDataset]) - val publication: Dataset[DLIPublication] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[DLIPublication]).map(d => d.asInstanceOf[DLIPublication]) - val relations: Dataset[Relation] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[Relation]).map(d => d.asInstanceOf[Relation]) - publication.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, pubEncoder)) - .groupByKey(_._1)(Encoders.STRING) - .agg(EBIAggregator.getDLIPublicationAggregator().toColumn) - .map(p => p._2) - .write.mode(SaveMode.Overwrite).save(s"$workingPath/publication") - - dataset.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datasetEncoder)) - .groupByKey(_._1)(Encoders.STRING) - .agg(EBIAggregator.getDLIDatasetAggregator().toColumn) - .map(p => p._2) - .write.mode(SaveMode.Overwrite).save(s"$workingPath/dataset") - - relations.map(d => (s"${d.getSource}::${d.getRelType}::${d.getTarget}", d))(Encoders.tuple(Encoders.STRING, relEncoder)) - .groupByKey(_._1)(Encoders.STRING) - .agg(EBIAggregator.getRelationAggregator().toColumn) - .map(p => p._2) - .write.mode(SaveMode.Overwrite).save(s"$workingPath/relation") - - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkEBILinksToOaf.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkEBILinksToOaf.scala new file mode 100644 index 0000000000..250b285ff6 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkEBILinksToOaf.scala @@ -0,0 +1,40 @@ +package eu.dnetlib.dhp.sx.ebi + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.Oaf +import eu.dnetlib.dhp.sx.bio.BioDBToOAF +import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} +object SparkEBILinksToOaf { + + def main(args: Array[String]): Unit = { + val log: Logger = LoggerFactory.getLogger(SparkEBILinksToOaf.getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(SparkEBILinksToOaf.getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + val sourcePath = parser.get("sourcePath") + log.info(s"sourcePath -> $sourcePath") + val targetPath = parser.get("targetPath") + log.info(s"targetPath -> $targetPath") + + import spark.implicits._ + implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) + val ebLinks:Dataset[EBILinkItem] = spark.read.load(sourcePath).as[EBILinkItem].filter(l => l.links!= null) + + ebLinks.flatMap(j =>BioDBToOAF.parse_ebi_links(j.links)) + .repartition(4000) + .filter(p => BioDBToOAF.EBITargetLinksFilter(p)) + .flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)) + .write.mode(SaveMode.Overwrite).save(targetPath) + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/SparkGeneratePanagaeaDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/SparkGeneratePanagaeaDataset.scala index bd98e1cdb7..24ed089689 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/SparkGeneratePanagaeaDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/SparkGeneratePanagaeaDataset.scala @@ -1,7 +1,7 @@ package eu.dnetlib.sx.pangaea import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.sx.ebi.SparkCreateEBIDataFrame +import eu.dnetlib.dhp.sx.ebi.SparkEBILinksToOaf import org.apache.spark.rdd.RDD import org.apache.spark.{SparkConf, SparkContext} import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/bio_to_oaf_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/bio_to_oaf_params.json new file mode 100644 index 0000000000..76d0bfd6d5 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/bio_to_oaf_params.json @@ -0,0 +1,6 @@ +[ + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"db", "paramLongName":"database", "paramDescription": "should be PDB or UNIPROT", "paramRequired": true}, + {"paramName":"p", "paramLongName":"dbPath", "paramDescription": "the path of the database to transform", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the OAF target path ", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/oozie_app/config-default.xml new file mode 100644 index 0000000000..bdd48b0ab2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/oozie_app/config-default.xml @@ -0,0 +1,19 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/oozie_app/workflow.xml new file mode 100644 index 0000000000..5948c579f2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/oozie_app/workflow.xml @@ -0,0 +1,111 @@ + + + + PDBPath + the PDB Database Working Path + + + + UNIPROTDBPath + the UNIPROT Database Working Path + + + + EBIDataset + the EBI Links Dataset Path + + + + targetPath + the Target Working dir path + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Convert PDB to OAF Dataset + eu.dnetlib.dhp.sx.bio.SparkTransformBioDatabaseToOAF + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=2000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --dbPath${PDBPath} + --databasePDB + --targetPath${targetPath}/pdb_OAF + + + + + + + + + yarn + cluster + Convert UNIPROT to OAF Dataset + eu.dnetlib.dhp.sx.bio.SparkTransformBioDatabaseToOAF + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=2000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --dbPath${UNIPROTDBPath} + --databaseUNIPROT + --targetPath${targetPath}/uniprot_OAF + + + + + + + + + yarn + cluster + Convert EBI Links to OAF Dataset + eu.dnetlib.dhp.sx.ebi.SparkEBILinksToOaf + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=2000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --sourcePath${EBIDataset} + --targetPath${targetPath}/ebi_OAF + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/baseline_to_oaf_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/baseline_to_oaf_params.json new file mode 100644 index 0000000000..4899fa76dd --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/baseline_to_oaf_params.json @@ -0,0 +1,5 @@ +[ + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"i", "paramLongName":"isLookupUrl","paramDescription": "isLookupUrl", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath","paramDescription": "the path of the sequencial file to read", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json index 4899fa76dd..8039131b26 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/ebi_to_df_params.json @@ -1,5 +1,5 @@ [ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"i", "paramLongName":"isLookupUrl","paramDescription": "isLookupUrl", "paramRequired": true}, - {"paramName":"w", "paramLongName":"workingPath","paramDescription": "the path of the sequencial file to read", "paramRequired": true} + {"paramName":"s", "paramLongName":"sourcePath","paramDescription": "the source Path", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath","paramDescription": "the oaf path ", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/workflow.xml index 7e63362428..3f442c5c65 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/workflow.xml @@ -54,7 +54,7 @@ cluster Create EBI DataSet - eu.dnetlib.dhp.sx.ebi.SparkCreateEBIDataFrame + eu.dnetlib.dhp.sx.ebi.SparkEBILinksToOaf dhp-graph-mapper-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/bio/pubmed/BioScholixTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/bio/pubmed/BioScholixTest.scala index f7a5bcd179..3a1f02c24c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/bio/pubmed/BioScholixTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/bio/pubmed/BioScholixTest.scala @@ -2,16 +2,21 @@ package eu.dnetlib.dhp.sx.bio.pubmed import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature} import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result} -import eu.dnetlib.dhp.sx.bio.PDBToOAF +import eu.dnetlib.dhp.sx.bio.BioDBToOAF +import eu.dnetlib.dhp.sx.ebi.SparkEBILinksToOaf import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.{BeforeEach, Test} import org.mockito.junit.jupiter.MockitoExtension +import java.io.{BufferedReader, FileInputStream, InputStream, InputStreamReader} +import java.util.zip.GZIPInputStream import scala.collection.JavaConverters._ import scala.io.Source import scala.xml.pull.XMLEventReader - +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse @ExtendWith(Array(classOf[MockitoExtension])) class BioScholixTest extends AbstractVocabularyTest{ @@ -23,6 +28,21 @@ class BioScholixTest extends AbstractVocabularyTest{ super.setUpVocabulary() } + class BufferedReaderIterator(reader: BufferedReader) extends Iterator[String] { + override def hasNext() = reader.ready + override def next() = reader.readLine() + } + + object GzFileIterator { + def apply(is: InputStream, encoding: String) = { + new BufferedReaderIterator( + new BufferedReader( + new InputStreamReader( + new GZIPInputStream( + is), encoding))) + } + } + @Test def testEBIData() = { @@ -60,7 +80,7 @@ class BioScholixTest extends AbstractVocabularyTest{ val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/pdb_dump")).mkString records.lines.foreach(s => assertTrue(s.nonEmpty)) - val result:List[Oaf]= records.lines.toList.flatMap(o => PDBToOAF.convert(o)) + val result:List[Oaf]= records.lines.toList.flatMap(o => BioDBToOAF.pdbTOOaf(o)) @@ -72,4 +92,62 @@ class BioScholixTest extends AbstractVocabularyTest{ } + + @Test + def testUNIprotToOAF():Unit = { + + assertNotNull(vocabularies) + assertTrue(vocabularies.vocabularyExists("dnet:publication_resource")) + + val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT) + mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false) + val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/uniprot_dump")).mkString + records.lines.foreach(s => assertTrue(s.nonEmpty)) + + val result:List[Oaf]= records.lines.toList.flatMap(o => BioDBToOAF.uniprotToOAF(o)) + + + + assertTrue(result.nonEmpty) + result.foreach(r => assertNotNull(r)) + + println(result.count(o => o.isInstanceOf[Relation])) + println(mapper.writeValueAsString(result.head)) + + } + + case class EBILinks(relType:String, date:String, title:String, pmid:String, targetPid:String, targetPidType:String) {} + + def parse_ebi_links(input:String):List[EBILinks] ={ + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json = parse(input) + val pmid = (json \ "publication" \"pmid").extract[String] + for { + JObject(link) <- json \\ "Link" + JField("Target",JObject(target)) <- link + JField("RelationshipType",JObject(relType)) <- link + JField("Name", JString(relation)) <- relType + JField("PublicationDate",JString(publicationDate)) <- link + JField("Title", JString(title)) <- target + JField("Identifier",JObject(identifier)) <- target + JField("IDScheme", JString(idScheme)) <- identifier + JField("ID", JString(id)) <- identifier + + } yield EBILinks(relation, publicationDate, title, pmid, id, idScheme) + } + + + @Test + def testEBILinksToOAF():Unit = { + val iterator = GzFileIterator(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi_links.gz"), "UTF-8") + val data = iterator.next() + + val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT) + mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false) + + val res = BioDBToOAF.parse_ebi_links(BioDBToOAF.extractEBILinksFromDump(data).links).filter(BioDBToOAF.EBITargetLinksFilter).flatMap(BioDBToOAF.convertEBILinksToOaf) + print(res.length) + + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/bio/ebi_links.gz b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/bio/ebi_links.gz new file mode 100644 index 0000000000..0da111c144 Binary files /dev/null and b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/bio/ebi_links.gz differ diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/bio/uniprot_dump b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/bio/uniprot_dump new file mode 100644 index 0000000000..6b8ed0d94a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/bio/uniprot_dump @@ -0,0 +1,6 @@ +{"pid": "Q6GZX4", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 41."}], "title": "Putative transcription factor 001R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": "Q6GZX3", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 42."}], "title": "Uncharacterized protein 002L;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": "Q197F8", "dates": [{"date": "16-JUN-2009", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "11-JUL-2006", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 27."}], "title": "Uncharacterized protein 002R;", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus."], "references": [{"PubMed": "16912294"}, {" DOI": "10.1128/jvi.00464-06"}]} +{"pid": "Q197F7", "dates": [{"date": "16-JUN-2009", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "11-JUL-2006", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 23."}], "title": "Uncharacterized protein 003L;", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus."], "references": [{"PubMed": "16912294"}, {" DOI": "10.1128/jvi.00464-06"}]} +{"pid": "Q6GZX2", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 36."}], "title": "Uncharacterized protein 3R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": "Q6GZX1", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 34."}], "title": "Uncharacterized protein 004R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]} \ No newline at end of file