From b260fee7877f3fea971dbaa39aef0c5c227c78a7 Mon Sep 17 00:00:00 2001 From: miconis Date: Wed, 22 Jul 2020 17:29:48 +0200 Subject: [PATCH] implementation of the dedup_id generation using pids to make the graph more stable --- .../eu/dnetlib/dhp/oa/dedup/DatePicker.java | 2 +- .../dhp/oa/dedup/DedupRecordFactory.java | 96 ++++++++++++++++--- .../eu/dnetlib/dhp/oa/dedup/Identifier.java | 55 +++++++++++ .../java/eu/dnetlib/dhp/oa/dedup/PidType.java | 54 +++++++++++ .../dhp/oa/dedup/EntityMergerTest.java | 27 +++++- .../dnetlib/dhp/oa/dedup/SparkDedupTest.java | 41 ++++---- .../dhp/dedup/json/publication_merge3.json | 3 + 7 files changed, 237 insertions(+), 41 deletions(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Identifier.java create mode 100644 dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/PidType.java create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge3.json diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java index 70fb2cc5b..d6b8bf71c 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DatePicker.java @@ -114,7 +114,7 @@ public class DatePicker { } } - private static boolean inRange(final String date) { + public static boolean inRange(final String date) { final int year = Integer.parseInt(substringBefore(date, "-")); return year >= YEAR_LB && year <= YEAR_UB; } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java index 8028d5a94..7f04afe8a 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java @@ -1,11 +1,12 @@ package eu.dnetlib.dhp.oa.dedup; -import java.io.Serializable; -import java.util.Collection; -import java.util.Iterator; -import java.util.List; - +import com.fasterxml.jackson.databind.DeserializationFeature; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.common.collect.Lists; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import org.apache.commons.lang.StringUtils; import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapGroupsFunction; import org.apache.spark.sql.Dataset; @@ -13,15 +14,12 @@ import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; import org.slf4j.LoggerFactory; - -import com.fasterxml.jackson.databind.DeserializationFeature; -import com.fasterxml.jackson.databind.ObjectMapper; -import com.google.common.collect.Lists; - -import eu.dnetlib.dhp.schema.common.ModelSupport; -import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; +import java.text.ParseException; +import java.text.SimpleDateFormat; +import java.util.*; + public class DedupRecordFactory { private static final Logger log = LoggerFactory.getLogger(DedupRecordFactory.class); @@ -77,15 +75,23 @@ public class DedupRecordFactory { String id, Iterator> entities, long ts, DataInfo dataInfo, Class clazz) throws IllegalAccessException, InstantiationException { + SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd"); + T entity = clazz.newInstance(); final Collection dates = Lists.newArrayList(); final List> authors = Lists.newArrayList(); + final List bestPids = Lists.newArrayList(); //best pids list entities .forEachRemaining( t -> { T duplicate = t._2(); + + StructuredProperty bestPid = bestPid(duplicate.getPid()); + if (bestPid != null) + bestPids.add(new Identifier(bestPid, extractDate(duplicate, sdf), PidType.classidValueOf(bestPid.getQualifier().getClassid()))); + entity.mergeFrom(duplicate); if (ModelSupport.isSubClass(duplicate, Result.class)) { Result r1 = (Result) duplicate; @@ -94,6 +100,7 @@ public class DedupRecordFactory { if (r1.getDateofacceptance() != null) dates.add(r1.getDateofacceptance().getValue()); } + }); // set authors and date @@ -102,10 +109,73 @@ public class DedupRecordFactory { ((Result) entity).setAuthor(AuthorMerger.merge(authors)); } - entity.setId(id); + Identifier bestPid = winnerPid(bestPids); + if (bestPid == null) + entity.setId(id); + else + entity.setId(id.split("\\|")[0] + "|" + createPrefix(bestPid.getPid().getQualifier().getClassid()) + "::" + DedupUtility.md5(bestPid.getPid().getValue())); + entity.setLastupdatetimestamp(ts); entity.setDataInfo(dataInfo); return entity; } + + //pick the best pid from the list (consider date and pidtype) + public static Identifier winnerPid(List pids) { + if (pids == null || pids.size() == 0) + return null; + Optional bp = pids.stream() + .filter(pid -> pid.getType() != PidType.undefined) + .max(Identifier::compareTo); + return bp.orElse(null); + } + + //pick the best pid from the entity + public static StructuredProperty bestPid(List pids) { + + if (pids == null || pids.size() == 0) + return null; + Optional bp = pids.stream() + .filter(pid -> PidType.classidValueOf(pid.getQualifier().getClassid()) != PidType.undefined) + .max(Comparator.comparing(pid -> PidType.classidValueOf(pid.getQualifier().getClassid()))); + + return bp.orElse(null); + } + + //create the prefix (length = 12): dedup_+ pidType + public static String createPrefix(String pidType) { + + StringBuilder prefix = new StringBuilder("dedup_" + pidType); + + while (prefix.length() < 12) { + prefix.append("_"); + } + return prefix.toString().substring(0, 12); + + } + + //extracts the date from the record. If the date is not available or is not wellformed, it returns a base date: 00-01-01 + public static Date extractDate(T duplicate, SimpleDateFormat sdf){ + + String date = "2000-01-01"; + if (ModelSupport.isSubClass(duplicate, Result.class)) { + Result result = (Result) duplicate; + if (isWellformed(result.getDateofacceptance())){ + date = result.getDateofacceptance().getValue(); + } + } + + try { + return sdf.parse(date); + } catch (ParseException e) { + return new Date(); + } + + } + + public static boolean isWellformed(Field date) { + return date != null && StringUtils.isNotBlank(date.getValue()) && date.getValue().matches("\\d{4}-\\d{2}-\\d{2}") && DatePicker.inRange(date.getValue()); + } + } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Identifier.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Identifier.java new file mode 100644 index 000000000..3d92900ca --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/Identifier.java @@ -0,0 +1,55 @@ +package eu.dnetlib.dhp.oa.dedup; + +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +import java.io.Serializable; +import java.util.Date; + +public class Identifier implements Serializable, Comparable{ + + StructuredProperty pid; + Date date; + PidType type; + + public Identifier(StructuredProperty pid, Date date, PidType type) { + this.pid = pid; + this.date = date; + this.type = type; + } + + public StructuredProperty getPid() { + return pid; + } + + public void setPid(StructuredProperty pidValue) { + this.pid = pid; + } + + public Date getDate() { + return date; + } + + public void setDate(Date date) { + this.date = date; + } + + public PidType getType() { + return type; + } + + public void setType(PidType type) { + this.type = type; + } + + @Override + public int compareTo(Identifier i) { + //priority in comparisons: 1) pidtype, 2) date + if (this.getType().compareTo(i.getType()) == 0){ //same type + return this.getDate().compareTo(date); + } + else { + return this.getType().compareTo(i.getType()); + } + + } +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/PidType.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/PidType.java new file mode 100644 index 000000000..c0af44b1e --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/PidType.java @@ -0,0 +1,54 @@ +package eu.dnetlib.dhp.oa.dedup; + +public enum PidType { + + //from the less to the more important + undefined, + orcid, + ror, + grid, + pdb, + arXiv, + pmid, + doi; + + public static PidType classidValueOf(String s){ + try { + return PidType.valueOf(s); + } + catch (Exception e) { + return PidType.undefined; + } + } + +} + +//dnet:pid_types +//"actrn" +//"nct" +//"euctr" +//"epo_id" +//"gsk" +//"GeoPass" +//"GBIF" +//"isrctn" +//"ISNI" +//"jprn" +//"mag_id" +//"oai" +//"orcid" +//"PANGAEA" +//"epo_nr_epodoc" +//"UNKNOWN" +//"VIAF" +//"arXiv" +//"doi" +//"grid" +//"info:eu-repo/dai" +//"orcidworkid" +//"pmc" +//"pmid" +//"urn" +//"who" +//"drks" +//"pdb" \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index 3fb9d1751..b3cb7b9d9 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -22,10 +22,11 @@ public class EntityMergerTest implements Serializable { List> publications; List> publications2; + List> publications3; String testEntityBasePath; DataInfo dataInfo; - String dedupId = "dedup_id"; + String dedupId = "00|dedup_id::1"; Publication pub_top; @BeforeEach @@ -38,6 +39,8 @@ public class EntityMergerTest implements Serializable { publications = readSample(testEntityBasePath + "/publication_merge.json", Publication.class); publications2 = readSample(testEntityBasePath + "/publication_merge2.json", Publication.class); + publications3 = readSample(testEntityBasePath + "/publication_merge3.json", Publication.class); + pub_top = getTopPub(publications); @@ -54,6 +57,9 @@ public class EntityMergerTest implements Serializable { .entityMerger(dedupId, softwares.iterator(), 0, dataInfo, Software.class); assertEquals(merged.getBestaccessright().getClassid(), "OPEN SOURCE"); + + assertEquals(merged.getId(), "00|dedup_doi___::0968af610a356656706657e4f234b340"); + } @Test @@ -62,7 +68,8 @@ public class EntityMergerTest implements Serializable { Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class); - assertEquals(dedupId, pub_merged.getId()); + // verify id + assertEquals(pub_merged.getId(), "00|dedup_doi___::0968af610a356656706657e4f234b340"); assertEquals(pub_merged.getJournal(), pub_top.getJournal()); assertEquals(pub_merged.getBestaccessright(), pub_top.getBestaccessright()); @@ -117,11 +124,25 @@ public class EntityMergerTest implements Serializable { Publication pub_merged = DedupRecordFactory .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); + // verify id + assertEquals(pub_merged.getId(), "00|dedup_doi___::0ca46ff10b2b4c756191719d85302b14"); + assertEquals(pub_merged.getAuthor().size(), 27); - // insert assertions here } + @Test + public void publicationMergerTest3() throws InstantiationException, IllegalAccessException { + + Publication pub_merged = DedupRecordFactory + .entityMerger(dedupId, publications3.iterator(), 0, dataInfo, Publication.class); + + // verify id + assertEquals(pub_merged.getId(), "00|dedup_doi___::0ca46ff10b2b4c756191719d85302b14"); + + } + + public DataInfo setDI() { DataInfo dataInfo = new DataInfo(); dataInfo.setTrust("0.9"); diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java index fb5ebc099..35c4c7026 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java @@ -1,22 +1,12 @@ package eu.dnetlib.dhp.oa.dedup; -import static java.nio.file.Files.createTempDirectory; - -import static org.apache.spark.sql.functions.col; -import static org.apache.spark.sql.functions.count; -import static org.junit.jupiter.api.Assertions.assertEquals; -import static org.mockito.Mockito.lenient; - -import java.io.File; -import java.io.IOException; -import java.io.Serializable; -import java.net.URISyntaxException; -import java.nio.file.Paths; -import java.util.HashSet; -import java.util.Set; -import java.util.stream.Collectors; - +import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -35,16 +25,19 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -import eu.dnetlib.pace.util.MapDocumentUtil; import scala.Tuple2; +import java.io.File; +import java.io.IOException; +import java.io.Serializable; +import java.net.URISyntaxException; +import java.nio.file.Paths; + +import static java.nio.file.Files.createTempDirectory; +import static org.apache.spark.sql.functions.count; +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.mockito.Mockito.lenient; + @ExtendWith(MockitoExtension.class) @TestMethodOrder(MethodOrderer.OrderAnnotation.class) public class SparkDedupTest implements Serializable { diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge3.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge3.json new file mode 100644 index 000000000..c82c8c83e --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_merge3.json @@ -0,0 +1,3 @@ +{"id":"50|doajarticles::842fa3b99fcdccafb4d5c8a815f56efa","dateofcollection":"2020-04-06T12:22:31.216Z","title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Increased Expression of Herpes Virus-Encoded hsv1-miR-H18 and hsv2-miR-H9-5p in Cancer-Containing Prostate Tissue Compared to That in Benign Prostate Hyperplasia Tissue"}],"publisher":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Korean Continence Society"},"bestaccessright":null,"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"collectedfrom":[{"dataInfo":null,"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.5213/inj.1632552.276"}, {"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.5213/inj.1632552.27XXXXX"}],"author":[{"affiliation":null,"fullname":"Seok Joong Yun","name":null,"pid":[],"rank":1,"surname":null},{"affiliation":null,"fullname":"Pildu Jeong","name":null,"pid":[],"rank":2,"surname":null},{"affiliation":null,"fullname":"Ho Won Kang","name":null,"pid":[],"rank":3,"surname":null},{"affiliation":null,"fullname":"Helen Ki Shinn","name":null,"pid":[],"rank":4,"surname":null},{"affiliation":null,"fullname":"Ye-Hwan Kim","name":null,"pid":[],"rank":5,"surname":null},{"affiliation":null,"fullname":"Chunri Yan","name":null,"pid":[],"rank":6,"surname":null},{"affiliation":null,"fullname":"Young-Ki Choi","name":null,"pid":[],"rank":7,"surname":null},{"affiliation":null,"fullname":"Dongho Kim","name":null,"pid":[],"rank":8,"surname":null},{"affiliation":null,"fullname":"Dong Hee Ryu","name":null,"pid":[],"rank":9,"surname":null},{"affiliation":null,"fullname":"Yun-Sok Ha","name":null,"pid":[],"rank":10,"surname":null},{"affiliation":null,"fullname":"Tae-Hwan Kim","name":null,"pid":[],"rank":11,"surname":null},{"affiliation":null,"fullname":"Tae Gyun Kwon","name":null,"pid":[],"rank":12,"surname":null},{"affiliation":null,"fullname":"Jung Min Kim","name":null,"pid":[],"rank":13,"surname":null},{"affiliation":null,"fullname":"Sang Heon Suh","name":null,"pid":[],"rank":14,"surname":null},{"affiliation":null,"fullname":"Seon-Kyu Kim","name":null,"pid":[],"rank":15,"surname":null},{"affiliation":null,"fullname":"Seon-Young Kim","name":null,"pid":[],"rank":16,"surname":null},{"affiliation":null,"fullname":"Sang Tae Kim","name":null,"pid":[],"rank":17,"surname":null},{"affiliation":null,"fullname":"Won Tae Kim","name":null,"pid":[],"rank":18,"surname":null},{"affiliation":null,"fullname":"Ok-Jun Lee","name":null,"pid":[],"rank":19,"surname":null},{"affiliation":null,"fullname":"Sung-Kwon Moon","name":null,"pid":[],"rank":20,"surname":null},{"affiliation":null,"fullname":"Nam-Hyung Kim","name":null,"pid":[],"rank":21,"surname":null},{"affiliation":null,"fullname":"Isaac Yi Kim","name":null,"pid":[],"rank":22,"surname":null},{"affiliation":null,"fullname":"Jayoung Kim","name":null,"pid":[],"rank":23,"surname":null},{"affiliation":null,"fullname":"Hee-Jae Cha","name":null,"pid":[],"rank":24,"surname":null},{"affiliation":null,"fullname":"Yung-Hyun Choi","name":null,"pid":[],"rank":25,"surname":null},{"affiliation":null,"fullname":"Eun-Jong Cha","name":null,"pid":[],"rank":26,"surname":null},{"affiliation":null,"fullname":"Wun-Jae Kim","name":null,"pid":[],"rank":27,"surname":null}],"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"MicroRNAs"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Prostate Neoplasms"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Herpesviridae"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Prostate Hyperplasia"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Diseases of the genitourinary system. Urology"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"RC870-923"}],"description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Purpose: Previously, we reported the presence of virus-encoded microRNAs (miRNAs) in the urine of prostate cancer (CaP) patients. In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. Further studies will be required to elucidate the role of these miRNAs with respect to CaP and herpes viral infections."}],"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2016-06-01"},"embargoenddate":null,"resourcetype":null,"context":[],"instance":[{"accessright":{"classid":"OPEN","classname":"Open 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Neoplasms"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Herpesviridae"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"","classname":"","schemeid":"","schemename":""},"value":"Prostate Hyperplasia"}],"description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Purpose: Previously, we reported the presence of virus-encoded microRNAs (miRNAs) in the urine of prostate cancer (CaP) patients. In this study, we investigated the expression of two herpes virus-encoded miRNAs in prostate tissue. Methods: A total of 175 tissue samples from noncancerous benign prostatic hyperplasia (BPH), 248 tissue samples from patients with CaP and BPH, and 50 samples from noncancerous surrounding tissues from these same patients were analyzed for the expression of two herpes virus-encoded miRNAs by real-time polymerase chain reaction (PCR) and immunocytochemistry using nanoparticles as molecular beacons. Results: Real-time reverse transcription-PCR results revealed significantly higher expression of hsv1-miR-H18 and hsv2-miRH9- 5p in surrounding noncancerous and CaP tissues than that in BPH tissue (each comparison, P<0.001). Of note, these miRNA were expressed equivalently in the CaP tissues and surrounding noncancerous tissues. Moreover, immunocytochemistry clearly demonstrated a significant enrichment of both hsv1-miR-H18 and hsv2-miR-H9 beacon-labeled cells in CaP and surrounding noncancerous tissue compared to that in BPH tissue (each comparison, P<0.05 for hsv1-miR-H18 and hsv2- miR-H9). Conclusions: These results suggest that increased expression of hsv1-miR-H18 and hsv2-miR-H95p might be associated with tumorigenesis in the prostate. Further studies will be required to elucidate the role of these miRNAs with respect to CaP and herpes viral infections."}],"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk","classname":"sysimport:crosswalk","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2016-06-01"},"embargoenddate":null,"resourcetype":null,"context":[],"instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":{"dataInfo":null,"key":"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357","value":"PubMed 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