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phenol-annotation contains the annotation functionality for ontologies
package org.monarchinitiative.phenol.annotations.io.hpo;
import org.monarchinitiative.phenol.annotations.base.Sex;
import org.monarchinitiative.phenol.annotations.formats.AnnotationReference;
import org.monarchinitiative.phenol.annotations.formats.EvidenceCode;
import org.monarchinitiative.phenol.annotations.formats.hpo.HpoFrequency;
import org.monarchinitiative.phenol.annotations.formats.hpo.HpoOnset;
import org.monarchinitiative.phenol.base.PhenolException;
import org.monarchinitiative.phenol.base.PhenolRuntimeException;
import org.monarchinitiative.phenol.ontology.data.Identified;
import org.monarchinitiative.phenol.ontology.data.TermId;
import java.util.Arrays;
import java.util.List;
import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors;
/**
* Represent an HPO Term together with a Frequency and an Onset and modifiers. This is intended to
* be used to represent a disease annotation.
*
* @author Peter Robinson
* @version 0.1.3 (2018-03-12)
*/
public class HpoAnnotationLine implements Identified {
/**
* The annotated {@link TermId}.
*/
private final TermId diseaseId;
private final String diseaseName;
private final boolean isNegated;
private final TermId phenotypeTermId;
private final List annotationReferences;
/**
* The characteristic age of onset of a feature in a certain disease.
*/
private final HpoOnset onset;
private final String frequency;
/**
* Phenotype associated with sex.
*/
private final Sex sex;
/**
* List of modifiers of this annotation. List can be empty but cannot be null
*/
private final List modifiers;
private final Aspect aspect;
/**
* A list of curators that created/updated this line, e.g. {@code HPO:probinson[2017-06-16];HPO:iea[2009-02-17]}.
*/
private final List curators;
public static HpoAnnotationLine of(TermId diseaseId,
String diseaseName,
boolean isNegated,
TermId phenotypeTermId,
List annotationReferences,
HpoOnset onset,
String frequency,
Sex sex,
List modifiers,
Aspect aspect,
List curators) {
return new HpoAnnotationLine(diseaseId,
diseaseName,
isNegated,
phenotypeTermId,
annotationReferences,
onset,
frequency,
sex,
modifiers,
aspect,
curators);
}
public static HpoAnnotationLine of(String line) throws PhenolException {
try {
String[] fields = line.split("\t");
TermId diseaseId = TermId.of(fields[0]);
String diseaseName = fields[1];
boolean isNegated = fields[2].equalsIgnoreCase("NOT");
TermId phenotype = TermId.of(fields[3]);
EvidenceCode code = EvidenceCode.parse(fields[5]);
List annotationReferences = Arrays.stream(fields[4].split(";"))
.filter(token -> !token.isBlank())
.map(reference -> AnnotationReference.of(TermId.of(reference), code))
.collect(Collectors.toList());
HpoOnset onsetId = HpoOnset.fromHpoIdString(fields[6])
.orElse(null);
String frequency = fields[7];
Sex sex = Sex.parse(fields[8]).orElse(null);
List modifiers = Arrays.stream(fields[9].split(";"))
.filter(token -> !token.isBlank())
.map(TermId::of)
.collect(Collectors.toList());
Aspect aspect = Aspect.parse(fields[10]).orElse(null);
List curators = Arrays.stream(fields[11].split(";"))
.map(String::trim)
.collect(Collectors.toList());
return of(diseaseId, diseaseName, isNegated, phenotype, annotationReferences, onsetId, frequency, sex, modifiers, aspect, curators);
} catch (PhenolRuntimeException e) {
throw new PhenolException(String.format("Exception [%s] parsing line: %s",e.getMessage(), line));
}
}
/**
* @param diseaseId Disease identifier, e.g. OMIM:123456
* @param diseaseName Name of the disease, e.g. "LEIGH SYNDROME; LS"
* @param isNegated Is the HPO ID negated?
* @param phenotypeTermId Hpo ID of the line {@link TermId}
* @param annotationReferences List of references (e.g., PMID or OMIM) that support this annotation
* @param onset The onset of the feature in the disease
* @param frequency Annotation frequency
* @param sex Phenotype associated with sex
* @param modifiers list of modifiers (list can be empty but not null)
* @param aspect The type of the phenotype (P,I,M,C)
* @param curators The curators and dates of curation of this annotation
*/
private HpoAnnotationLine(TermId diseaseId,
String diseaseName,
boolean isNegated,
TermId phenotypeTermId,
List annotationReferences,
HpoOnset onset,
String frequency,
Sex sex,
List modifiers,
Aspect aspect,
List curators) {
this.diseaseId = Objects.requireNonNull(diseaseId);
this.diseaseName = Objects.requireNonNull(diseaseName);
this.isNegated = isNegated;
this.phenotypeTermId = Objects.requireNonNull(phenotypeTermId, "Term ID must not be null");
this.frequency = Objects.requireNonNull(frequency, "Annotation frequency must not be null");
this.onset = onset; // nullable
this.modifiers = Objects.requireNonNull(modifiers, "Modifiers must not be null");
this.annotationReferences = Objects.requireNonNull(annotationReferences);
this.sex = sex; // nullable
this.aspect = Objects.requireNonNull(aspect);
this.curators = Objects.requireNonNull(curators);
}
/**
* @return {@link TermId} corresponding to the {@code HPO_ID} column (the same as {@link #phenotypeTermId()})
* and not the {@link #diseaseId()}.
*/
@Override
public TermId id() {
return phenotypeTermId();
}
public TermId diseaseId() {
return diseaseId;
}
public String diseaseName() {
return diseaseName;
}
public boolean isNegated() {
return isNegated;
}
public TermId phenotypeTermId() {
return phenotypeTermId;
}
/**
* @return The annotating {@link HpoFrequency}.
*/
public String frequency() {
return frequency;
}
/**
* @return the {@link HpoOnset} object representing the age of onset of the feature (or null if not onset is available)
*/
public Optional onset() {
return Optional.ofNullable(onset);
}
public List modifiers() {
return modifiers;
}
public List annotationReferences() {
return annotationReferences;
}
public Sex sex() {
return sex;
}
public Aspect aspect() {
return aspect;
}
public List curators() {
return curators;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
HpoAnnotationLine that = (HpoAnnotationLine) o;
return isNegated == that.isNegated && Objects.equals(diseaseId, that.diseaseId) && Objects.equals(diseaseName, that.diseaseName) && Objects.equals(phenotypeTermId, that.phenotypeTermId) && Objects.equals(annotationReferences, that.annotationReferences) && onset == that.onset && Objects.equals(frequency, that.frequency) && sex == that.sex && Objects.equals(modifiers, that.modifiers) && aspect == that.aspect && Objects.equals(curators, that.curators);
}
@Override
public int hashCode() {
return Objects.hash(diseaseId, diseaseName, isNegated, phenotypeTermId, annotationReferences, onset, frequency, sex, modifiers, aspect, curators);
}
@Override
public String toString() {
return "HpoAnnotationLine{" +
"diseaseId=" + diseaseId +
", diseaseName='" + diseaseName + '\'' +
", isNegated=" + isNegated +
", phenotypeTermId=" + phenotypeTermId +
", annotationReferences=" + annotationReferences +
", onset=" + onset +
", frequency='" + frequency + '\'' +
", sex=" + sex +
", modifiers=" + modifiers +
", aspect=" + aspect +
", curators=" + curators +
'}';
}
}
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