org.monarchinitiative.phenol.io.annotations.hpo.OrphanetXML2HpoDiseaseModelParser Maven / Gradle / Ivy
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phenol-io contains the generic I/O functionality for ontologies
package org.monarchinitiative.phenol.io.annotations.hpo;
import org.monarchinitiative.phenol.annotations.hpo.HpoAnnotationEntry;
import org.monarchinitiative.phenol.annotations.hpo.HpoAnnotationModel;
import org.monarchinitiative.phenol.base.HpoAnnotationModelException;
import org.monarchinitiative.phenol.base.PhenolRuntimeException;
import org.monarchinitiative.phenol.formats.hpo.HpoFrequencyTermIds;
import org.monarchinitiative.phenol.ontology.data.Ontology;
import org.monarchinitiative.phenol.ontology.data.TermId;
import java.io.FileInputStream;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.*;
import javax.xml.namespace.QName;
import javax.xml.stream.XMLEventReader;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamException;
import javax.xml.stream.events.Attribute;
import javax.xml.stream.events.EndElement;
import javax.xml.stream.events.StartElement;
import javax.xml.stream.events.XMLEvent;
/**
* This class is an XML parser for the Orphanet file with HPO-based disease annotations
* ({@code en_product4_HPO.xml} (see http://www.orphadata.org/). Note that the section of the
* XML that denotes an individual HPO annotation with frequency is like this
*
*
*
* HP:0010535
* Sleep apnea
*
*
* 453313
* Occasional (29-5%)
*
*
*
* That is, one line of the annotation is contained with an {@code HPODisorderAssociation} node.
* Each disease begins like this
*
*
* 437
* Hypophosphatemic rickets
*
*
* (...)
*
* That is, we extract the Orphanumber and the name and then there is a list of annotations.
* @author Peter Robinson
*/
public class OrphanetXML2HpoDiseaseModelParser {
/** Path to {@code en_product4_HPO.xml} file. */
private final String orphanetXmlPath;
/** Reference to the HPO Ontology. */
private final Ontology ontology;
/** A String of the form ORPHA:orphadata[2019-01-05] that we will use as the biocuration entry. */
private final String orphanetBiocurationString;
/** A map of diseases parsed from Orphanet. */
private final Map orphanetDiseaseMap = new HashMap<>();
/** If true, replace obsolete term ids without throwing Exception. */
private boolean replaceObsoleteTermId;
public OrphanetXML2HpoDiseaseModelParser(String xmlpath, Ontology onto, boolean tolerant) {
orphanetXmlPath = xmlpath;
this.ontology = onto;
this.replaceObsoleteTermId=tolerant;
String todaysDate = getTodaysDate();
orphanetBiocurationString=String.format("ORPHA:orphadata[%s]", todaysDate);
try {
parse();
} catch (XMLStreamException | IOException e) {
e.printStackTrace();
}
}
public Map getOrphanetDiseaseMap() { return this.orphanetDiseaseMap; }
/**
* Transform the Orphanet codes into HPO Frequency TermId's.
*
* The frequency ids are
*
* - Excluded (0%): Orphanet id 28440
* - Frequent (79-30%): Orphanet id: 28419
* - Obligate (100%): Orphanet id: 28405
* - Occasional (29-5%): Orphanet id: 28426
* - Very frequent (99-80%): Orphanet id 28412
* - Very rare : Orphanet id 28433
*
* @param fstring An Orphanet id (attribute in XML file) corresponding to a frequency category
* @return corresponding HPO Frequency TermId
*/
private TermId string2frequency(String fstring) throws PhenolRuntimeException {
switch (fstring) {
case "28405": return HpoFrequencyTermIds.ALWAYS_PRESENT;// Obligate
case "28412": return HpoFrequencyTermIds.VERY_FREQUENT;
case "28419": return HpoFrequencyTermIds.FREQUENT;
case "28426": return HpoFrequencyTermIds.OCCASIONAL;
case "28433": return HpoFrequencyTermIds.VERY_RARE;
case "28440": return HpoFrequencyTermIds.EXCLUDED;
}
// the following should never happen, actually!
throw new PhenolRuntimeException("[ERROR] Could not find TermId for Orphanet frequency {}. "+
"This indicates a serious and unexpected error, please report to the developers"+ fstring);
}
/**
* This method performs the XML parse of the Orphanet file
* @throws XMLStreamException If there is an XML stream issue
* @throws IOException If the file cannot be opened
*/
@SuppressWarnings("ConstantConditions")
private void parse() throws XMLStreamException , IOException {
XMLInputFactory xmlInputFactory = XMLInputFactory.newInstance();
XMLEventReader xmlEventReader = xmlInputFactory.createXMLEventReader(new FileInputStream(orphanetXmlPath));
boolean inFrequency = false;
boolean inDiagnosticCriterion = false;
String currentHpoId=null;
String currentHpoTermLabel=null;
TermId currentFrequencyTermId=null;
String currentOrphanumber=null;
String currentDiseaseName=null;
List currentAnnotationEntryList=new ArrayList<>();
while (xmlEventReader.hasNext()) {
XMLEvent xmlEvent = xmlEventReader.nextEvent();
if (xmlEvent.isStartElement()) {
StartElement startElement = xmlEvent.asStartElement();
switch (startElement.getName().getLocalPart()) {
case "Disorder":
// no op
break;
case "OrphaNumber":
if (inFrequency || inDiagnosticCriterion) {
continue;
} // Orphanumbers are used for the Disorder but also for the Frequency nodes
xmlEvent = xmlEventReader.nextEvent();
currentOrphanumber = xmlEvent.asCharacters().getData();
break;
case "Name":
if (inFrequency || inDiagnosticCriterion) {
continue;
} // skip, we have no need to parse the name of the frequency element
// since we get the class from the attribute "id"
xmlEvent = xmlEventReader.nextEvent();
currentDiseaseName = xmlEvent.asCharacters().getData();
break;
case "HPOId":
xmlEvent = xmlEventReader.nextEvent();
currentHpoId = xmlEvent.asCharacters().getData();
break;
case "HPOTerm":
xmlEvent = xmlEventReader.nextEvent();
currentHpoTermLabel = xmlEvent.asCharacters().getData();
break;
case "HPOFrequency":
// if we are here, then we can grab the frequency from the id attribute.
Attribute idAttr = startElement.getAttributeByName(new QName("id"));
if (idAttr != null) {
currentFrequencyTermId = string2frequency(idAttr.getValue());
}
inFrequency = true;
break;
case "DiagnosticCriteria":
inDiagnosticCriterion=true;
break;
case "HPO":
// no-op, no need to get the id attribute from this node
break;
case "JDBOR":
// no-op, no need to do anything for the very top level node
break;
default:
// no-op, no need to do anything for many node types!
break;
}
} else if (xmlEvent.isEndElement()) {
EndElement endElement = xmlEvent.asEndElement();
String endElementName = endElement.getName().getLocalPart();
if ( endElementName.equals("HPOFrequency")) {
inFrequency = false;
} else if ( endElementName.equals("DiagnosticCriteria")) {
inDiagnosticCriterion = false;
} else if (endElementName.equals("HPODisorderAssociation")) {
// We should have data for HPO Id, HPo Label, and a Frequency term
try {
HpoAnnotationEntry entry = HpoAnnotationEntry.fromOrphaData(
String.format("ORPHA:%s", currentOrphanumber),
currentDiseaseName,
currentHpoId,
currentHpoTermLabel,
currentFrequencyTermId,
ontology,
orphanetBiocurationString,
replaceObsoleteTermId);
currentHpoId = null;
currentHpoTermLabel = null;
currentFrequencyTermId = null;// reset
currentAnnotationEntryList.add(entry);
} catch (HpoAnnotationModelException e) {
System.err.println(String.format("Parse error for %s [ORPHA:%s] HPOid: %s (%s)",
currentDiseaseName != null ? currentDiseaseName : "n/a",
currentOrphanumber != null ? currentOrphanumber : "n/a",
currentHpoId != null ? currentHpoId : "n/a",
e.getMessage())
);
}
} else if (endElementName.equals("Disorder")) {
TermId orphaDiseaseId = TermId.of(String.format("ORPHA:%s",currentOrphanumber));
HpoAnnotationModel model = new HpoAnnotationModel(String.format("ORPHA:%s", currentOrphanumber),
currentAnnotationEntryList);
orphanetDiseaseMap.put(orphaDiseaseId,model);
currentOrphanumber=null;
currentDiseaseName=null;
currentAnnotationEntryList.clear();
} else if (endElementName.equals("JDBOR")) {
// no-op all done
}
}
}
}
/** We are using this to supply a date created value for the Orphanet annotations.
* After some research, no better way of getting the current date was found.
* @return A String such as 2018-02-22
*/
private String getTodaysDate() {
Date date = new Date();
return new SimpleDateFormat("yyyy-MM-dd").format(date);
}
}