org.monarchinitiative.phenol.annotations.hpo.OrphanetXML2HpoDiseaseModelParser Maven / Gradle / Ivy
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phenol-annotation contains the annotation functionality for ontologies
package org.monarchinitiative.phenol.annotations.hpo;
import org.monarchinitiative.phenol.base.PhenolRuntimeException;
import org.monarchinitiative.phenol.annotations.constants.hpo.HpoFrequencyTermIds;
import org.monarchinitiative.phenol.ontology.data.Ontology;
import org.monarchinitiative.phenol.ontology.data.TermId;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.FileInputStream;
import java.io.IOException;
import java.text.SimpleDateFormat;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
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
* @deprecated to be removed in v3.0.0.
*/
@Deprecated(forRemoval = true)
public class OrphanetXML2HpoDiseaseModelParser {
private final static Logger logger = LoggerFactory.getLogger(OrphanetXML2HpoDiseaseModelParser.class);
/**
* 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 final boolean replaceObsoleteTermId;
private static final String DISORDER = "Disorder";
private static final String ORPHA_NUMBER = "OrphaNumber";
private static final String ORPHA_CODE = "OrphaCode";
private static final String NAME = "Name";
private static final String HPO_DISORDER_ASSOCIATION = "HPODisorderAssociation";
private static final String DIAGNOSTIC_CRITERIA = "DiagnosticCriteria";
private static final String DISORDER_TYPE = "DisorderType";
private static final String DISORDER_GROUP = "DisorderGroup";
private static final String EXPERT_LINK = "ExpertLink";
private static final String HPO_DISORDER_ASSOCIATION_LIST = "HPODisorderAssociationList";
private static final String HPO_DISORDER_SET_STATUS = "HPODisorderSetStatus";
private static final String HPO_DISORDER_SET_STATUS_LIST = "HPODisorderSetStatusList";
private static final String HPO_FREQUENCY = "HPOFrequency";
private static final String HPO = "HPO";
private static final String HPO_ID = "HPOId";
private static final String HPO_TERM = "HPOTerm";
private static final String JDBOR = "JDBOR";
private static final String AVAILABILITY = "Availability";
private static final String FULL_NAME = "FullName";
private static final String SHORT_IDENTIFIER = "ShortIdentifier";
private static final String LEGAL_CODE = "LegalCode";
private static final String LICENSE = "Licence";
private static final String SOURCE = "Source";
private static final String VALIDATION_DATE = "ValidationDate";
private static final String VALIDATION_STATUS = "ValidationStatus";
private static final String ONLINE = "Online";
/**
* These are the local names of the Orphanet product4.xml file.
*/
private final Set allowableXmlNodeNames = Stream.of(AVAILABILITY,
DIAGNOSTIC_CRITERIA,
DISORDER,
DISORDER_GROUP,
DISORDER_TYPE,
EXPERT_LINK,
FULL_NAME,
HPO_DISORDER_ASSOCIATION,
HPO_DISORDER_ASSOCIATION_LIST,
HPO_DISORDER_SET_STATUS,
HPO_DISORDER_SET_STATUS_LIST,
HPO_FREQUENCY,
HPO_ID,
HPO,
HPO_TERM,
JDBOR,
LEGAL_CODE,
LICENSE,
NAME,
ONLINE,
ORPHA_CODE,
ORPHA_NUMBER,
SOURCE,
SHORT_IDENTIFIER,
VALIDATION_DATE,
VALIDATION_STATUS)
.collect(Collectors.toCollection(HashSet::new));
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.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;
boolean inDisorderType = false;
boolean inDisorderGroup = 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();
String localName = startElement.getName().getLocalPart();
if (!allowableXmlNodeNames.contains(localName)) {
throw new PhenolRuntimeException("Unexpected XML Node in Orphanet product_4 XML: " + localName);
}
switch (localName) {
case DISORDER_TYPE:
inDisorderType = true;
break;
case ORPHA_CODE:
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 || inDisorderGroup || inDisorderType) {
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 DISORDER_GROUP:
inDisorderGroup = true;
break;
case HPO_ID:
xmlEvent = xmlEventReader.nextEvent();
currentHpoId = xmlEvent.asCharacters().getData();
break;
case HPO_TERM:
xmlEvent = xmlEventReader.nextEvent();
currentHpoTermLabel = xmlEvent.asCharacters().getData();
break;
case HPO_FREQUENCY:
// 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 DIAGNOSTIC_CRITERIA:
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 localPart = endElement.getName().getLocalPart();
switch (localPart) {
case HPO_FREQUENCY:
inFrequency = false;
break;
case DIAGNOSTIC_CRITERIA:
inDiagnosticCriterion = false;
break;
case HPO_DISORDER_ASSOCIATION:
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) {
logger.warn(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())
);
}
break;
case DISORDER_GROUP:
inDisorderGroup = false;
break;
case DISORDER_TYPE:
inDisorderType = false;
break;
case DISORDER:
TermId orphaDiseaseId = TermId.of(String.format("ORPHA:%s", currentOrphanumber));
HpoAnnotationModel model = new HpoAnnotationModel(String.format("ORPHA:%s", currentOrphanumber),
currentAnnotationEntryList);
orphanetDiseaseMap.put(orphaDiseaseId, model);
inDisorderType = false;
currentOrphanumber = null;
currentDiseaseName = null;
currentAnnotationEntryList.clear();
}
}
}
}
/**
* 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);
}
}
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