From 714b71bd21c6bbda51c2dbde4866f24ad1d015b8 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 4 May 2021 14:54:12 +0200 Subject: [PATCH] updated pubmed --- .../sx/ebi/SparkCreateBaselineDataFrame.scala | 1 - .../dnetlib/dhp/sx/ebi/model/PMArticle.java | 35 + .../eu/dnetlib/dhp/sx/ebi/model/PMGrant.java | 42 + .../dnetlib/dhp/sx/ebi/model/PMParser.scala | 53 +- .../dnetlib/dhp/sx/ebi/model/PMSubject.java | 41 + .../eu/dnetlib/sx/pangaea/PangaeaUtils.scala | 3 - .../SparkGeneratePanagaeaDataset.scala | 2 +- .../sx/pubmed/oozie_app/config-default.xml | 19 + .../dhp/sx/pubmed/oozie_app/workflow.xml | 40 + .../dhp/sx/pubmed/pangaea_to_dataset.json | 4 + .../java/eu/dnetlib/dhp/sx/ebi/TestEBI.scala | 12 +- .../eu/dnetlib/dhp/sx/ebi/pubmed.xml | 5188 +++++++++++++++++ 12 files changed, 5431 insertions(+), 9 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMGrant.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMSubject.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/pangaea_to_dataset.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/ebi/pubmed.xml 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 77e03c9b3..1cb49ab59 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 @@ -33,7 +33,6 @@ object SparkCreateBaselineDataFrame { implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal]) implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor]) val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline",2000) - val ds:Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i =>{ val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes())) new PMParser(xml) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMArticle.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMArticle.java index 75d4628e6..1627c9cbb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMArticle.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMArticle.java @@ -8,10 +8,33 @@ import java.util.List; public class PMArticle implements Serializable { private String pmid; + private String doi; private String date; private PMJournal journal; private String title; private String description; + private String language; + private final List subjects = new ArrayList<>(); + private final List publicationTypes = new ArrayList<>(); + + public List getPublicationTypes() { + return publicationTypes; + } + + private final List grants = new ArrayList<>(); + + public List getGrants() { + return grants; + } + + public String getDoi() { + return doi; + } + + public void setDoi(String doi) { + this.doi = doi; + } + private List authors = new ArrayList<>(); public String getPmid() { @@ -61,4 +84,16 @@ public class PMArticle implements Serializable { public void setAuthors(List authors) { this.authors = authors; } + + public List getSubjects() { + return subjects; + } + + public String getLanguage() { + return language; + } + + public void setLanguage(String language) { + this.language = language; + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMGrant.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMGrant.java new file mode 100644 index 000000000..928cba8fe --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMGrant.java @@ -0,0 +1,42 @@ + +package eu.dnetlib.dhp.sx.ebi.model; + +public class PMGrant { + + private String grantID; + private String agency; + private String country; + + public PMGrant() { + } + + public PMGrant(String grantID, String agency, String country) { + this.grantID = grantID; + this.agency = agency; + this.country = country; + } + + public String getGrantID() { + return grantID; + } + + public void setGrantID(String grantID) { + this.grantID = grantID; + } + + public String getAgency() { + return agency; + } + + public void setAgency(String agency) { + this.agency = agency; + } + + public String getCountry() { + return country; + } + + public void setCountry(String country) { + this.country = country; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMParser.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMParser.scala index 903eba134..eb9863a60 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMParser.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMParser.scala @@ -1,4 +1,6 @@ package eu.dnetlib.dhp.sx.ebi.model + +import scala.xml.MetaData import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader} class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] { @@ -12,24 +14,61 @@ class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] { tmp } + def extractAttributes(attrs:MetaData, key:String):String = { + + val res = attrs.get(key) + if (res.isDefined) { + val s =res.get + if (s != null && s.nonEmpty) + s.head.text + else + null + } + else null + } + + + def validate_Date(year:String, month:String, day:String):String = { + try { + f"${year.toInt}-${month.toInt}%02d-${day.toInt}%02d" + + } catch { + case _: Throwable =>null + } + } def generateNextArticle():PMArticle = { + + var currentSubject:PMSubject = null var currentAuthor: PMAuthor = null var currentJournal: PMJournal = null + var currentGrant: PMGrant = null var currNode: String = null var currentYear = "0" var currentMonth = "01" var currentDay = "01" + var currentArticleType:String = null + + + + + while (xml.hasNext) { xml.next match { - case EvElemStart(_, label, _, _) => + case EvElemStart(_, label, attrs, _) => currNode = label + label match { case "PubmedArticle" => currentArticle = new PMArticle case "Author" => currentAuthor = new PMAuthor case "Journal" => currentJournal = new PMJournal + case "Grant" => currentGrant = new PMGrant + case "PublicationType" | "DescriptorName" => + currentSubject = new PMSubject + currentSubject.setMeshId(extractAttributes(attrs, "UI")) + case "ArticleId" => currentArticleType = extractAttributes(attrs,"IdType") case _ => } case EvElemEnd(_, label) => @@ -37,8 +76,12 @@ class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] { case "PubmedArticle" => return currentArticle case "Author" => currentArticle.getAuthors.add(currentAuthor) case "Journal" => currentArticle.setJournal(currentJournal) - case "DateCompleted" => currentArticle.setDate(s"$currentYear-$currentMonth-$currentDay") + case "Grant" => currentArticle.getGrants.add(currentGrant) + case "PubMedPubDate" => if (currentArticle.getDate== null) + currentArticle.setDate(validate_Date(currentYear,currentMonth,currentDay)) case "PubDate" => currentJournal.setDate(s"$currentYear-$currentMonth-$currentDay") + case "DescriptorName" => currentArticle.getSubjects.add(currentSubject) + case "PublicationType" =>currentArticle.getPublicationTypes.add(currentSubject) case _ => } case EvText(text) => @@ -57,12 +100,18 @@ class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] { currentArticle.setDescription(currentArticle.getDescription + text.trim) } case "PMID" => currentArticle.setPmid(text.trim) + case "ArticleId" => if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim) + case "Language" => currentArticle.setLanguage(text.trim) case "ISSN" => currentJournal.setIssn(text.trim) + case "GrantID" => currentGrant.setGrantID(text.trim) + case "Agency" => currentGrant.setAgency(text.trim) + case "Country" => if (currentGrant != null) currentGrant.setCountry(text.trim) case "Year" => currentYear = text.trim case "Month" => currentMonth = text.trim case "Day" => currentDay = text.trim case "Volume" => currentJournal.setVolume( text.trim) case "Issue" => currentJournal.setIssue (text.trim) + case "PublicationType" | "DescriptorName" => currentSubject.setValue(text.trim) case "LastName" => { if (currentAuthor != null) currentAuthor.setLastName(text.trim) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMSubject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMSubject.java new file mode 100644 index 000000000..fd79e1cde --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMSubject.java @@ -0,0 +1,41 @@ + +package eu.dnetlib.dhp.sx.ebi.model; + +public class PMSubject { + private String value; + private String meshId; + private String registryNumber; + + public PMSubject() { + } + + public PMSubject(String value, String meshId, String registryNumber) { + this.value = value; + this.meshId = meshId; + this.registryNumber = registryNumber; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public String getMeshId() { + return meshId; + } + + public void setMeshId(String meshId) { + this.meshId = meshId; + } + + public String getRegistryNumber() { + return registryNumber; + } + + public void setRegistryNumber(String registryNumber) { + this.registryNumber = registryNumber; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/PangaeaUtils.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/PangaeaUtils.scala index c57b1f7a9..bbd9124bd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/PangaeaUtils.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/sx/pangaea/PangaeaUtils.scala @@ -5,9 +5,6 @@ import org.apache.spark.sql.{Encoder, Encoders} import org.json4s import org.json4s.DefaultFormats import org.json4s.jackson.JsonMethods.parse - -import java.text.SimpleDateFormat -import java.util.Date import java.util.regex.Pattern import scala.language.postfixOps import scala.xml.{Elem, Node, XML} 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 88e5f2142..bd98e1cdb 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 @@ -24,7 +24,7 @@ object SparkGeneratePanagaeaDataset { SparkSession .builder() .config(conf) - .appName(SparkCreateEBIDataFrame.getClass.getSimpleName) + .appName(SparkGeneratePanagaeaDataset.getClass.getSimpleName) .master(parser.get("master")).getOrCreate() parser.getObjectMap.asScala.foreach(s => logger.info(s"${s._1} -> ${s._2}")) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/oozie_app/config-default.xml new file mode 100644 index 000000000..bdd48b0ab --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/oozie_app/config-default.xml @@ -0,0 +1,19 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/oozie_app/workflow.xml new file mode 100644 index 000000000..a940220da --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/oozie_app/workflow.xml @@ -0,0 +1,40 @@ + + + + baselineWorkingPath + the Baseline Working Path + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Convert Baseline to Dataset + eu.dnetlib.dhp.sx.ebi.SparkCreateBaselineDataFrame + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --workingPath${baselineWorkingPath} + --masteryarn + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/pangaea_to_dataset.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/pangaea_to_dataset.json new file mode 100644 index 000000000..366f1426e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/pubmed/pangaea_to_dataset.json @@ -0,0 +1,4 @@ +[ + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "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/test/java/eu/dnetlib/dhp/sx/ebi/TestEBI.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/ebi/TestEBI.scala index 92e14895d..098291a32 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/ebi/TestEBI.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/ebi/TestEBI.scala @@ -1,16 +1,24 @@ package eu.dnetlib.dhp.sx.ebi +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.sx.ebi.model.PMParser import org.junit.jupiter.api.Test +import scala.io.Source +import scala.xml.pull.XMLEventReader + class TestEBI { -// @Test + @Test def testEBIData() = { - SparkAddLinkUpdates.main("-mt local[*] -w /home/sandro/Downloads".split(" ")) + val inputXML = Source.fromInputStream(getClass.getResourceAsStream("pubmed.xml")).mkString + val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes())) + val mapper = new ObjectMapper() + new PMParser(xml).foreach(s =>println(mapper.writeValueAsString(s))) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/ebi/pubmed.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/ebi/pubmed.xml new file mode 100644 index 000000000..22da07e29 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/ebi/pubmed.xml @@ -0,0 +1,5188 @@ + + + + + + 1 + + 1976 + 01 + 16 + + + 2019 + 02 + 08 + +
+ + 0006-2944 + + 13 + 2 + + 1975 + Jun + + + Biochemical medicine + Biochem Med + + Formate assay in body fluids: application in methanol poisoning. + + 117-26 + + + + Makar + A B + AB + + + McMartin + K E + KE + + + Palese + M + M + + + Tephly + T R + TR + + + eng + + + MC_UU_12013/5 + MRC + United Kingdom + + + + Journal Article + Research Support, U.S. Gov't, P.H.S. + +
+ + United States + Biochem Med + 0151424 + 0006-2944 + + + + 0 + Formates + + + 142M471B3J + Carbon Dioxide + + + EC 1.2.- + Aldehyde Oxidoreductases + + + Y4S76JWI15 + Methanol + + + IM + + + Aldehyde Oxidoreductases + metabolism + + + Animals + + + Body Fluids + analysis + + + Carbon Dioxide + blood + + + Formates + blood + poisoning + + + Haplorhini + + + Humans + + + Hydrogen-Ion Concentration + + + Kinetics + + + Methanol + blood + + + Methods + + + Pseudomonas + enzymology + + + + + + + 1975 + 6 + 1 + + + 1975 + 6 + 1 + 0 + 1 + + + 1975 + 6 + 1 + 0 + 0 + + + ppublish + + 1 + 10.1016/0006-2944(75)90147-7 + + + + + + 2 + + 1976 + 01 + 10 + + + 2019 + 06 + 12 + +
+ + 1090-2104 + + 66 + 4 + + 1975 + Oct + 27 + + + Biochemical and biophysical research communications + Biochem Biophys Res Commun + + Delineation of the intimate details of the backbone conformation of pyridine nucleotide coenzymes in aqueous solution. + + 1173-9 + + + + Bose + K S + KS + + + Sarma + R H + RH + + + eng + + Journal Article + Research Support, U.S. Gov't, Non-P.H.S. + Research Support, U.S. Gov't, P.H.S. + +
+ + United States + Biochem Biophys Res Commun + 0372516 + 0006-291X + + + + 0U46U6E8UK + NAD + + + 53-59-8 + NADP + + + IM + + + Biochem Pharmacol. 1975 Aug 15;24(16):1517-21 + 8 + + + + + Fourier Analysis + + + Magnetic Resonance Spectroscopy + + + Models, Molecular + + + Molecular Conformation + + + NAD + analogs & derivatives + + + NADP + + + Structure-Activity Relationship + + + Temperature + + + + + + + 1975 + 10 + 27 + + + 1975 + 10 + 27 + 0 + 1 + + + 1975 + 10 + 27 + 0 + 0 + + + ppublish + + 2 + 0006-291X(75)90482-9 + 10.1016/0006-291x(75)90482-9 + + + + + + 3 + + 1976 + 01 + 10 + + + 2019 + 06 + 12 + +
+ + 0006-291X + + 66 + 4 + + 1975 + Oct + 27 + + + Biochemical and biophysical research communications + Biochem Biophys Res Commun + + Metal substitutions incarbonic anhydrase: a halide ion probe study. + + 1281-6 + + + + Smith + R J + RJ + + + Bryant + R G + RG + + + eng + + Journal Article + Research Support, U.S. Gov't, P.H.S. + +
+ + United States + Biochem Biophys Res Commun + 0372516 + 0006-291X + + + + 00BH33GNGH + Cadmium + + + EC 4.2.1.1 + Carbonic Anhydrases + + + FXS1BY2PGL + Mercury + + + J41CSQ7QDS + Zinc + + + IM + + + Animals + + + Binding Sites + + + Cadmium + + + Carbonic Anhydrases + metabolism + + + Cattle + + + Humans + + + Hydrogen-Ion Concentration + + + Magnetic Resonance Spectroscopy + + + Mercury + + + Protein Binding + + + Protein Conformation + + + Zinc + pharmacology + + + + + + + 1975 + 10 + 27 + + + 1975 + 10 + 27 + 0 + 1 + + + 1975 + 10 + 27 + 0 + 0 + + + ppublish + + 3 + 0006-291X(75)90498-2 + 10.1016/0006-291x(75)90498-2 + + + + + + 4 + + 1976 + 01 + 10 + + + 2019 + 06 + 12 + +
+ + 1090-2104 + + 66 + 4 + + 1975 + Oct + 27 + + + Biochemical and biophysical research communications + Biochem Biophys Res Commun + + Effect of chloroquine on cultured fibroblasts: release of lysosomal hydrolases and inhibition of their uptake. + + 1338-43 + + + + Wiesmann + U N + UN + + + DiDonato + S + S + + + Herschkowitz + N N + NN + + + eng + + + BB/C008219/1 + Biotechnology and Biological Sciences Research Council + United Kingdom + + + G1100377 + Medical Research Council + United Kingdom + + + G1100377 + MRC + United Kingdom + + + + Journal Article + +
+ + United States + Biochem Biophys Res Commun + 0372516 + 0006-291X + + + + 0 + Dextrans + + + 886U3H6UFF + Chloroquine + + + EC 3.1.6.- + Sulfatases + + + EC 3.1.6.8 + Cerebroside-Sulfatase + + + EC 3.2.1.31 + Glucuronidase + + + IM + + + Biological Transport + + + Cells, Cultured + + + Cerebroside-Sulfatase + metabolism + + + Chloroquine + pharmacology + + + Dextrans + metabolism + + + Fibroblasts + enzymology + metabolism + + + Glucuronidase + metabolism + + + Humans + + + Leukodystrophy, Metachromatic + enzymology + + + Lysosomes + drug effects + enzymology + + + Pinocytosis + drug effects + + + Skin + enzymology + + + Sulfatases + metabolism + + + + + + + 1975 + 10 + 27 + + + 1975 + 10 + 27 + 0 + 1 + + + 1975 + 10 + 27 + 0 + 0 + + + ppublish + + 4 + 0006-291X(75)90506-9 + 10.1016/0006-291x(75)90506-9 + + + + + + 5 + + 1976 + 01 + 10 + + + 2019 + 06 + 12 + +
+ + 1090-2104 + + 66 + 4 + + 1975 + Oct + 27 + + + Biochemical and biophysical research communications + Biochem Biophys Res Commun + + Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin. + + 1349-56 + + + + Hendrickson + W A + WA + + + Ward + K B + KB + + + eng + + Journal Article + +
+ + United States + Biochem Biophys Res Commun + 0372516 + 0006-291X + + + + 0 + Hemerythrin + + + 0 + Metalloproteins + + + 0 + Muscle Proteins + + + IM + + + Animals + + + Cnidaria + + + Computers + + + Hemerythrin + + + Metalloproteins + + + Models, Molecular + + + Muscle Proteins + + + Protein Conformation + + + Species Specificity + + + + + + + 1975 + 10 + 27 + + + 1975 + 10 + 27 + 0 + 1 + + + 1975 + 10 + 27 + 0 + 0 + + + ppublish + + 5 + 0006-291X(75)90508-2 + 10.1016/0006-291x(75)90508-2 + + + + + + 6 + + 1976 + 01 + 10 + + + 2019 + 06 + 12 + +
+ + 0006-291X + + 66 + 4 + + 1975 + Oct + 27 + + + Biochemical and biophysical research communications + Biochem Biophys Res Commun + + Studies of oxygen binding energy to hemoglobin molecule. + + 1424-31 + + + + Chow + Y W + YW + + + Pietranico + R + R + + + Mukerji + A + A + + + eng + + Journal Article + Research Support, U.S. Gov't, Non-P.H.S. + +
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+ + England + Biochem Pharmacol + 0101032 + 0006-2952 + + + + 0 + Proteins + + + 98600C0908 + Cycloheximide + + + EC 2.6.1.16 + Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + + + EC 2.7.- + Phosphotransferases + + + EC 3.1.1.6 + Acetylesterase + + + EC 6.2.1.- + Coenzyme A Ligases + + + EC 6.2.1.1 + Acetate-CoA Ligase + + + N08U5BOQ1K + Glucosamine + + + V956696549 + Acetylglucosamine + + + YQE403BP4D + Phenobarbital + + + IM + + + Acetate-CoA Ligase + metabolism + + + Acetylesterase + metabolism + + + Acetylglucosamine + + + Animals + + + Coenzyme A Ligases + metabolism + + + Cycloheximide + pharmacology + + + Glucosamine + + + Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing) + metabolism + + + Liver + drug effects + enzymology + + + Male + + + Phenobarbital + pharmacology + + + Phosphotransferases + metabolism + + + Proteins + metabolism + + + Rats + + + Stimulation, Chemical + + + + + + + 1975 + 9 + 15 + + + 1975 + 9 + 15 + 0 + 1 + + + 1975 + 9 + 15 + 0 + 0 + + + ppublish + + 15 + 0006-2952(75)90013-1 + 10.1016/0006-2952(75)90013-1 + + + + Clin Med (Lond). 2005 Jul-Aug;5(4):344-8 + + 16138488 + + + + Arch Dis Child. 2007 Jul;92(7):573-5 + + 17588971 + + + + Arch Dis Child. 2007 Dec;92(12):1143 + + 18032643 + + + + Pediatrics. 2010 Nov;126(5):851-5 + + 20956413 + + + + J Health Serv Res Policy. 2011 Apr;16(2):75-80 + + 21389060 + + + + BMJ. 2011 Apr 18;342:d2421 + + 21502273 + + + + Clin Med (Lond). 2011 Oct;11(5):420-1 + + 22034695 + + + + Bull Hist Med. 1998 Summer;72(2):246-78 + + 9628051 + + + + + + + + 16 + + 1976 + 01 + 23 + + + 2020 + 02 + 25 + +
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+ + 0006-2952 + + 24 + 18 + + 1975 + Sep + 15 + + + Biochemical pharmacology + Biochem Pharmacol + + Effects of 5,6-dihydroxytryptamine on tyrosine-hydroxylase activity in central catecholaminergic neurons of the rat. + + 1739-42 + + + + Renaud + B + B + + + Buda + M + M + + + Lewis + B D + BD + + + Pujol + J F + JF + + + eng + + + HERU1 + CSO_ + Chief Scientist Office + United Kingdom + + + + Journal Article + +
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+ + 0006-2952 + + 24 + 20 + + 1975 + Oct + 15 + + + Biochemical pharmacology + Biochem Pharmacol + + Inhibition of aldehyde reductase isoenzymes in human and rat brain. + + 1865-9 + + + + Ris + M M + MM + + + Deitrich + R A + RA + + + Von Wartburg + J P + JP + + + eng + + Journal Article + Research Support, U.S. Gov't, Non-P.H.S. + Research Support, U.S. Gov't, P.H.S. + +
+ + England + Biochem Pharmacol + 0101032 + 0006-2952 + + + + 0 + Anticonvulsants + + + 0 + Barbiturates + + + 0 + Hydantoins + + + 0 + Isoenzymes + + + 0 + Succinimides + + + 0U46U6E8UK + NAD + + + 53-59-8 + NADP + + + C8I4BVN78E + Glutethimide + + + EC 1.2.- + Aldehyde Oxidoreductases + + + IM + + + Aldehyde Oxidoreductases + antagonists & inhibitors + + + Animals + + + Anticonvulsants + pharmacology + + + Barbiturates + pharmacology + + + Brain + enzymology + + + Glutethimide + pharmacology + + + Humans + + + Hydantoins + pharmacology + + + In Vitro Techniques + + + Isoenzymes + antagonists & inhibitors + + + Kinetics + + + NAD + metabolism + + + NADP + pharmacology + + + Rats + + + Succinimides + pharmacology + + + + + + + 1975 + 10 + 15 + + + 1975 + 10 + 15 + 0 + 1 + + + 1975 + 10 + 15 + 0 + 0 + + + ppublish + + 18 + 0006-2952(75)90405-0 + 10.1016/0006-2952(75)90405-0 + + + + + + 19 + + 1976 + 01 + 29 + + + 2020 + 02 + 25 + +
+ + 0006-2952 + + 24 + 20 + + 1975 + Oct + 15 + + + Biochemical pharmacology + Biochem Pharmacol + + Antidepressant drugs affect dopamine uptake. + + 1896-7 + + + + Halaris + A E + AE + + + Belendiuk + K T + KT + + + Freedman + D X + DX + + + eng + + Journal Article + Research Support, U.S. Gov't, Non-P.H.S. + +
+ + England + Biochem Pharmacol + 0101032 + 0006-2952 + + + + 0 + Antidepressive Agents + + + 0 + Central Nervous System Stimulants + + + VTD58H1Z2X + Dopamine + + + IM + + + Animals + + + Antidepressive Agents + pharmacology + + + Brain + drug effects + metabolism + + + Central Nervous System Stimulants + pharmacology + + + Depression, Chemical + + + Dopamine + metabolism + + + In Vitro Techniques + + + Male + + + Rats + + + + + + + 1975 + 10 + 15 + + + 1975 + 10 + 15 + 0 + 1 + + + 1975 + 10 + 15 + 0 + 0 + + + ppublish + + 19 + 0006-2952(75)90412-8 + 10.1016/0006-2952(75)90412-8 + + + + JAMA. 2001 Jun 13;285(22):2871-9 + + 11401608 + + + + Med Care. 2001 Aug;39(8 Suppl 2):II2-45 + + 11583120 + + + + Health Serv Manage Res. 2002 May;15(2):126-37 + + 12028801 + + + + Qual Saf Health Care. 2003 Dec;12(6):458-64 + + 14645763 + + + + J Am Soc Nephrol. 2004 Mar;15(3):754-60 + + 14978178 + + + + Lancet. 2004 Apr 3;363(9415):1147-54 + + 15064036 + + + + BMJ. 2005 Apr 2;330(7494):781-3 + + 15802723 + + + + J Am Coll Cardiol. 2005 Oct 4;46(7):1236-41 + + 16198837 + + + + Milbank Q. 2005;83(4):691-729 + + 16279964 + + + + JAMA. 2006 Jan 18;295(3):324-7 + + 16418469 + + + + N Engl J Med. 2006 Nov 30;355(22):2308-20 + + 17101617 + + + + J Eval Clin Pract. 2007 Apr;13(2):161-8 + + 17378860 + + + + N Engl J Med. 2007 Aug 9;357(6):608-13 + + 17687138 + + + + Qual Saf Health Care. 2007 Oct;16(5):387-99 + + 17913782 + + + + BMJ. 2008 Jun 28;336(7659):1491-4 + + 18577559 + + + + BMJ. 2008 Aug 13;337:a957 + + 18703659 + + + + JAMA. 2008 Dec 24;300(24):2913-5 + + 19109120 + + + + Clin Med (Lond). 2009 Apr;9(2):140-4 + + 19435119 + + + + BMJ. 2009 Nov 19;339:b4809 + + 19926689 + + + + BMJ. 2009 Nov 19;339:b4811 + + 19926690 + + + + BMJ. 2010 Mar 31;340:c1234 + + 20360220 + + + + BMJ. 2010 Apr 20;340:c2016 + + 20406861 + + + + BMJ. 2010 Apr 23;340:c2153 + + 20418546 + + + + N Engl J Med. 2010 Jul 1;363(1):45-53 + + 20463332 + + + + BMJ. 2010 Aug 13;341:c4078 + + 20709715 + + + + N Engl J Med. 2010 Dec 23;363(26):2477-81 + + 21142528 + + + + J Am Soc Nephrol. 2011 Feb;22(2):225-34 + + 21289212 + + + + BMJ. 2011 Feb 03;342:d199 + + 21292720 + + + + Clin Med (Lond). 2010 Dec;10(6):537-9 + + 21413472 + + + + Nephron Clin Pract. 2011;119(1):c10-7; discussion c17 + + 21659780 + + + + Kidney Int. 2011 Nov;80(10):1021-34 + + 21775971 + + + + Implement Sci. 2011 Oct 24;6:119 + + 22024188 + + + + BMJ. 2012 Mar 01;344:e1001 + + 22381521 + + + + Methods Inf Med. 2012;51(3):189-98 + + 22476327 + + + + Ann Intern Med. 1998 Feb 15;128(4):289-92 + + 9471932 + + + + Int J Qual Health Care. 1998 Oct;10(5):443-7 + + 9828034 + + + + + + + + 20 + + 1976 + 01 + 29 + + + 2020 + 02 + 25 + +
+ + 0006-2952 + + 24 + 20 + + 1975 + Oct + 15 + + + Biochemical pharmacology + Biochem Pharmacol + + Aggregation of blood platelets by adrenaline and its uptake. + + 1903-4 + + + + Barthel + W + W + + + Markwardt + F + F + + + eng + + Journal Article + +
+ + England + Biochem Pharmacol + 0101032 + 0006-2952 + + + + 436O5HM03C + Dihydroergotamine + + + 8NA5SWF92O + Lysergic Acid Diethylamide + + + YKH834O4BH + Epinephrine + + + IM + + + Animals + + + Blood Platelets + metabolism + + + Dihydroergotamine + pharmacology + + + Drug Interactions + + + Epinephrine + blood + pharmacology + + + In Vitro Techniques + + + Lysergic Acid Diethylamide + pharmacology + + + Platelet Aggregation + drug effects + + + Rabbits + + + + + + + 1975 + 10 + 15 + + + 1975 + 10 + 15 + 0 + 1 + + + 1975 + 10 + 15 + 0 + 0 + + + ppublish + + 20 + 0006-2952(75)90415-3 + 10.1016/0006-2952(75)90415-3 + + + + Int J Qual Health Care. 2008 Feb;20(1):22-30 + + 18073269 + + + + Qual Health Res. 2008 Mar;18(3):380-90 + + 18235161 + + + + N Engl J Med. 2009 Jan 29;360(5):491-9 + + 19144931 + + + + Med Educ. 1998 May;32(3):239-43 + + 9743776 + + + + + + + + 21 + + 1976 + 01 + 26 + + + 2017 + 03 + 22 + +
+ + 0004-4172 + + 25 + 9 + + 1975 + Sep + + + Arzneimittel-Forschung + Arzneimittelforschung + + [Biochemical studies on camomile components/III. In vitro studies about the antipeptic activity of (--)-alpha-bisabolol (author's transl)]. + + 1352-4 + + + (--)-alpha-Bisabolol has a primary antipeptic action depending on dosage, which is not caused by an alteration of the pH-value. The proteolytic activity of pepsin is reduced by 50 percent through addition of bisabolol in the ratio of 1/0.5. The antipeptic action of bisabolol only occurs in case of direct contact. In case of a previous contact with the substrate, the inhibiting effect is lost. + + + + Isaac + O + O + + + Thiemer + K + K + + + ger + + English Abstract + Journal Article + + Biochemische Untersuchungen von Kamilleninhaltsstoffen. III. In-vitro-Versuche über die antipeptische Wirkung des (-)-alpha-Bisabolols +
+ + Germany + Arzneimittelforschung + 0372660 + 0004-4172 + + + + 0 + Hemoglobins + + + 0 + Sesquiterpenes + + + 42HK56048U + Tyrosine + + + 5V2JDO056X + Trichloroacetic Acid + + + EC 3.4.23.1 + Pepsin A + + + IM + + + Dose-Response Relationship, Drug + + + Hemoglobins + metabolism + + + Hydrogen-Ion Concentration + + + In Vitro Techniques + + + Methods + + + Pepsin A + antagonists & inhibitors + metabolism + + + Plants, Medicinal + + + Sesquiterpenes + pharmacology + + + Spectrophotometry, Ultraviolet + + + Trichloroacetic Acid + + + Tyrosine + metabolism + + + + + + + 1975 + 9 + 1 + + + 1975 + 9 + 1 + 0 + 1 + + + 1975 + 9 + 1 + 0 + 0 + + + ppublish + + 21 + + + + + + 22 + + 1976 + 01 + 26 + + + 2020 + 02 + 25 + +
+ + 0004-4172 + + 25 + 9 + + 1975 + Sep + + + Arzneimittel-Forschung + Arzneimittelforschung + + [Demonstration of tumor inhibiting properties of a strongly immunostimulating low-molecular weight substance. Comparative studies with ifosfamide on the immuno-labile DS carcinosarcoma. Stimulation of the autoimmune activity for approx. 20 days by BA 1, a N-(2-cyanoethylene)-urea. Novel prophylactic possibilities]. + + 1369-79 + + + A report is given on the recent discovery of outstanding immunological properties in BA 1 [N-(2-cyanoethylene)-urea] having a (low) molecular mass M = 111.104. Experiments in 214 DS carcinosarcoma bearing Wistar rats have shown that BA 1, at a dosage of only about 12 percent LD50 (150 mg kg) and negligible lethality (1.7 percent), results in a recovery rate of 40 percent without hyperglycemia and, in one test, of 80 percent with hyperglycemia. Under otherwise unchanged conditions the reference substance ifosfamide (IF) -- a further development of cyclophosphamide -- applied without hyperglycemia in its most efficient dosage of 47 percent LD50 (150 mg kg) brought about a recovery rate of 25 percent at a lethality of 18 percent. (Contrary to BA 1, 250-min hyperglycemia caused no further improvement of the recovery rate.) However this comparison is characterized by the fact that both substances exhibit two quite different (complementary) mechanisms of action. Leucocyte counts made after application of the said cancerostatics and dosages have shown a pronounced stimulation with BA 1 and with ifosfamide, the known suppression in the post-therapeutic interval usually found with standard cancerostatics. In combination with the cited plaque test for BA 1, blood pictures then allow conclusions on the immunity status. Since IF can be taken as one of the most efficient cancerostatics--there is no other chemotherapeutic known up to now that has a more significant effect on the DS carcinosarcoma in rats -- these findings are of special importance. Finally, the total amount of leucocytes and lymphocytes as well as their time behaviour was determined from the blood picture of tumour-free rats after i.v. application of BA 1. The thus obtained numerical values clearly show that further research work on the prophylactic use of this substance seems to be necessary and very promising. + + + + Ardenne + M + M + + + Reitnauer + P G + PG + + + ger + + Comparative Study + English Abstract + Journal Article + + Nachweis krebshemmender Eigenschaften einer stark immunstimulierenden Verbindung kleiner Molekülmasse. Versuche am immunlabilen DS-Karzinosarkom im Vergleich mit Ifosfamid. Stimulierung der körpereigenen Abwehr über etwa 20 Tage durch BA 1, einen N-(2-Cyanthylen)-harnstoff. Neue prophylaktische Möglichkeiten +
+ + Germany + Arzneimittelforschung + 0372660 + 0004-4172 + + + + 0 + Antineoplastic Agents + + + 8N3DW7272P + Cyclophosphamide + + + 8W8T17847W + Urea + + + UM20QQM95Y + Ifosfamide + + + IM + + + Animals + + + Antineoplastic Agents + pharmacology + therapeutic use + + + Carcinosarcoma + drug therapy + + + Cyclophosphamide + analogs & derivatives + + + Drug Evaluation, Preclinical + + + Drug Tolerance + + + Erythrocyte Count + + + Hydrogen-Ion Concentration + + + Hyperglycemia + + + Ifosfamide + pharmacology + therapeutic use + + + Immunity + drug effects + + + Immunosuppression + + + Lethal Dose 50 + + + Leukocyte Count + + + Male + + + Mice + + + Neoplasms, Experimental + drug therapy + + + Rats + + + Stimulation, Chemical + + + Time Factors + + + Urea + analogs & derivatives + pharmacology + therapeutic use + + + + + + + 1975 + 9 + 1 + + + 1975 + 9 + 1 + 0 + 1 + + + 1975 + 9 + 1 + 0 + 0 + + + ppublish + + 22 + + + + Crit Care Med. 2006 Jul;34(7):1913-7 + + 16715038 + + + + Crit Care. 2007;11(2):R31 + + 17331245 + + + + J Am Soc Nephrol. 2010 Feb;21(2):345-52 + + 20019168 + + + + Am J Kidney Dis. 2010 Oct;56(4):651-60 + + 20673605 + + + + Blood Purif. 2010;30(2):120-6 + + 20714143 + + + + Nephrol Dial Transplant. 2011 Jul;26(7):2161-8 + + 21148028 + + + + Am J Kidney Dis. 2011 Feb;57(2):228-34 + + 21195518 + + + + Clin J Am Soc Nephrol. 2012 Apr;7(4):533-40 + + 22362062 + + + + QJM. 2012 Aug;105(8):729-40 + + 22408153 + + + + Clin J Am Soc Nephrol. 2012 May;7(5):712-9 + + 22422536 + + + + QJM. 2013 Apr;106(4):323-32 + + 23345468 + + + + J R Coll Physicians Edinb. 2013;43(1):37-8 + + 23516690 + + + + + + + + 23 + + 1976 + 01 + 26 + + + 2020 + 02 + 25 + +
+ + 0004-4172 + + 25 + 9 + + 1975 + Sep + + + Arzneimittel-Forschung + Arzneimittelforschung + + Effect of etafenone on total and regional myocardial blood flow. + + 1400-3 + + + The distribution of blood flow to the subendocardial, medium and subepicardial layers of the left ventricular free wall was studied in anaesthetized dogs under normoxic (A), hypoxic (B) conditions and under pharmacologically induced (etafenone) coronary vasodilation (C). Regional myocardial blood flow was determined by means of the particle distribution method. In normoxia a transmural gradient of flow was observed, with the subendocardial layers receiving a significantly higher flow rate compared with the subepicardial layers. In hypoxia induced vasodilation this transmural gradient of flow was persistent. In contrast a marked redistribution of regional flow was observed under pharmacologically induced vasodilation. The transmural gradient decreased. In contrast to some findings these experiments demonstrate that a considerable vasodilatory capacity exists in all layers of the myocardium and can be utilized by drugs. The differences observed for the intramural distribution pattern of flow under hypoxia and drug induced vasodilation support the hypothesis that this pattern reflects corresponding gradients of regional myocardial metabolism. + + + + Flohr + H + H + + + Breull + W + W + + + eng + + + G0700399 + Medical Research Council + United Kingdom + + + + Journal Article + +
+ + Germany + Arzneimittelforschung + 0372660 + 0004-4172 + + + + 0 + Propiophenones + + + 0 + Vasodilator Agents + + + 142M471B3J + Carbon Dioxide + + + S88TT14065 + Oxygen + + + IM + + + Animals + + + Blood Pressure + drug effects + + + Carbon Dioxide + blood + + + Cardiac Output + drug effects + + + Coronary Circulation + drug effects + + + Coronary Vessels + drug effects + + + Dogs + + + Heart Rate + drug effects + + + Heart Septum + + + Heart Ventricles + + + Hydrogen-Ion Concentration + + + Hypoxia + physiopathology + + + Oxygen + blood + + + Propiophenones + pharmacology + + + Vasodilator Agents + pharmacology + + + + + + + 1975 + 9 + 1 + + + 1975 + 9 + 1 + 0 + 1 + + + 1975 + 9 + 1 + 0 + 0 + + + ppublish + + 23 + + + + J Appl Psychol. 2001 Aug;86(4):730-40 + + 11519656 + + + + South Med J. 2005 May;98(5):528-32 + + 15954509 + + + + J Crit Care. 2008 Jun;23(2):167-72 + + 18538207 + + + + Med Educ. 2009 Jan;43(1):50-7 + + 19140997 + + + + Clin Med (Lond). 2009 Oct;9(5):417-20 + + 19886098 + + + + + + \ No newline at end of file