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add gnomad constraints and mirna targets to variant annotation #190

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merged 5 commits into from
Sep 9, 2020
Merged

add gnomad constraints and mirna targets to variant annotation #190

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523a92b
add gnomad constraints and mirna targets to variant annotation
julie-sullivan Sep 3, 2020
3c5a7f5
change model to show targeted genes instead of mirnas
julie-sullivan Sep 7, 2020
7b55c73
move mirna from avro, we only need the targeted gene id
julie-sullivan Sep 8, 2020
830df71
rename to be mirnaTargets for clarity
julie-sullivan Sep 8, 2020
0be6ed3
remove transcript supportLevel, it's going in the flags instead
julie-sullivan Sep 9, 2020
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19 changes: 19 additions & 0 deletions biodata-models/src/main/avro/variantAnnotation.avdl
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Expand Up @@ -7,6 +7,7 @@ protocol VariantAnnotations {

enum ExpressionCall {UP, DOWN}

// deprecated
record ClinVar {
union { null, string } accession;
union { null, string } clinicalSignificance;
Expand All @@ -15,13 +16,15 @@ protocol VariantAnnotations {
union { null, string } reviewStatus;
}

// deprecated
record Gwas {
union { null, string } snpIdCurrent;
union { null, array<string> } traits;
union { null, double } riskAlleleFrequency;
union { null, string } reportedGenes;
}

// deprecated
record Cosmic {
union { null, string } mutationId;
union { null, string } primarySite;
Expand All @@ -34,6 +37,7 @@ protocol VariantAnnotations {
union { null, string } mutationSomaticStatus;
}

// deprecated
record VariantTraitAssociation {
union { null, array<ClinVar> } clinvar;
union { null, array<Gwas> } gwas;
Expand Down Expand Up @@ -62,6 +66,19 @@ protocol VariantAnnotations {
union { null, float } pvalue;
}

record Constraint {
union { null, string } source;
union { null, string } method;
union { null, string } name;
union { null, double } value;
}

record GeneMirnaTarget {
union { null, string } id;
union { null, string } name;
union { null, string } biotype;
}

record GeneTraitAssociation {
string id;
string name;
Expand Down Expand Up @@ -203,6 +220,8 @@ protocol VariantAnnotations {
union { null, array<Expression> } geneExpression;
union { null, array<GeneTraitAssociation> } geneTraitAssociation;
union { null, array<GeneDrugInteraction> } geneDrugInteraction;
union { null, array<Constraint> } geneConstraints;
union { null, array<GeneMirnaTarget> } geneMirnaTargets;
union { null, VariantTraitAssociation } variantTraitAssociation;
union { null, array<EvidenceEntry> } traitAssociation;
union { null, array<Score> } functionalScore;
Expand Down
103 changes: 0 additions & 103 deletions biodata-models/src/main/java/org/opencb/biodata/models/core/Constraint.java
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18 changes: 10 additions & 8 deletions biodata-models/src/main/java/org/opencb/biodata/models/core/GeneAnnotation.java
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Expand Up @@ -22,6 +22,8 @@
import org.opencb.biodata.models.variant.avro.Expression;
import org.opencb.biodata.models.variant.avro.GeneDrugInteraction;
import org.opencb.biodata.models.variant.avro.GeneTraitAssociation;
import org.opencb.biodata.models.variant.avro.Constraint;


import java.util.List;

Expand All @@ -32,18 +34,18 @@ public class GeneAnnotation {
private List<GeneTraitAssociation> diseases;
private List<GeneDrugInteraction> drugs;
private List<Constraint> constraints;
private List<MiRnaTarget> targets;
private List<MirnaTarget> mirnaTargets;

public GeneAnnotation() {
}

public GeneAnnotation(List<Expression> expression, List<GeneTraitAssociation> diseases,
List<GeneDrugInteraction> drugs, List<Constraint> constraints, List<MiRnaTarget> targets) {
List<GeneDrugInteraction> drugs, List<Constraint> constraints, List<MirnaTarget> mirnaTargets) {
this.expression = expression;
this.diseases = diseases;
this.drugs = drugs;
this.constraints = constraints;
this.targets = targets;
this.mirnaTargets = mirnaTargets;
}

@Override
Expand All @@ -53,7 +55,7 @@ public String toString() {
sb.append(", geneTraits=").append(diseases);
sb.append(", drugs=").append(drugs);
sb.append(", constraints=").append(constraints);
sb.append(", targets=").append(targets);
sb.append(", targets=").append(mirnaTargets);
sb.append('}');
return sb.toString();
}
Expand Down Expand Up @@ -94,12 +96,12 @@ public GeneAnnotation setConstraints(List<Constraint> constraints) {
return this;
}

public List<MiRnaTarget> getTargets() {
return targets;
public List<MirnaTarget> getMirnaTargets() {
return mirnaTargets;
}

public GeneAnnotation setTargets(List<MiRnaTarget> targets) {
this.targets = targets;
public GeneAnnotation setMirnaTargets(List<MirnaTarget> mirnaTargets) {
this.mirnaTargets = mirnaTargets;
return this;
}
}
14 changes: 7 additions & 7 deletions ...encb/biodata/models/core/MiRnaTarget.java → ...encb/biodata/models/core/MirnaTarget.java
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Expand Up @@ -21,7 +21,7 @@

import java.util.List;

public class MiRnaTarget {
public class MirnaTarget {

/**
* miRTarBase ID, e.g. MIRT735377
Expand All @@ -42,11 +42,11 @@ public class MiRnaTarget {



public MiRnaTarget() {
public MirnaTarget() {

}

public MiRnaTarget(String id, String source, String sourceId, List<TargetGene> targets) {
public MirnaTarget(String id, String source, String sourceId, List<TargetGene> targets) {
this.id = id;
this.source = source;
this.sourceId = sourceId;
Expand All @@ -68,7 +68,7 @@ public String getId() {
return id;
}

public MiRnaTarget setId(String id) {
public MirnaTarget setId(String id) {
this.id = id;
return this;
}
Expand All @@ -77,7 +77,7 @@ public String getSource() {
return source;
}

public MiRnaTarget setSource(String source) {
public MirnaTarget setSource(String source) {
this.source = source;
return this;
}
Expand All @@ -86,7 +86,7 @@ public String getSourceId() {
return sourceId;
}

public MiRnaTarget setSourceId(String sourceId) {
public MirnaTarget setSourceId(String sourceId) {
this.sourceId = sourceId;
return this;
}
Expand All @@ -95,7 +95,7 @@ public List<TargetGene> getTargets() {
return targets;
}

public MiRnaTarget setTargets(List<TargetGene> targets) {
public MirnaTarget setTargets(List<TargetGene> targets) {
this.targets = targets;
return this;
}
Expand Down
17 changes: 2 additions & 15 deletions biodata-models/src/main/java/org/opencb/biodata/models/core/Transcript.java
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Expand Up @@ -46,7 +46,6 @@ public class Transcript implements Serializable {
private String description;
private String version;
private String source;
private String supportLevel;
private List<Exon> exons;
private List<Xref> xrefs;
private List<TranscriptTfbs> tfbs;
Expand Down Expand Up @@ -113,7 +112,7 @@ public Transcript(String id, String name, String chromosome, int start, int end,
}

public Transcript(String id, String name, String biotype, String status, String source, String chromosome, Integer start, Integer end,
String strand, String version, String supportLevel, Integer codingRegionStart, Integer codingRegionEnd,
String strand, String version, Integer codingRegionStart, Integer codingRegionEnd,
Integer cdnaCodingStart, Integer cdnaCodingEnd, Integer cdsLength, String proteinId, String description,
List<Xref> xrefs, List<Exon> exons, List<TranscriptTfbs> tfbs, TranscriptAnnotation annotation) {
this.id = id;
Expand All @@ -126,7 +125,6 @@ public Transcript(String id, String name, String biotype, String status, String
this.strand = strand;
this.version = version;
this.source = source;
this.supportLevel = supportLevel;
this.genomicCodingStart = codingRegionStart;
this.genomicCodingEnd = codingRegionEnd;
this.cdnaCodingStart = cdnaCodingStart;
Expand Down Expand Up @@ -170,7 +168,6 @@ public String toString() {
sb.append(", description='").append(description).append('\'');
sb.append(", version=").append(version);
sb.append(", source='").append(source).append('\'');
sb.append(", supportLevel='").append(supportLevel).append('\'');
sb.append(", exons=").append(exons);
sb.append(", xrefs=").append(xrefs);
sb.append(", tfbs=").append(tfbs);
Expand Down Expand Up @@ -270,15 +267,6 @@ public Transcript setSource(String source) {
return this;
}

public String getSupportLevel() {
return supportLevel;
}

public Transcript setSupportLevel(String supportLevel) {
this.supportLevel = supportLevel;
return this;
}

public int getGenomicCodingStart() {
return genomicCodingStart;
}
Expand Down Expand Up @@ -429,7 +417,6 @@ public boolean equals(Object o) {
Objects.equals(getProteinSequence(), that.getProteinSequence()) &&
Objects.equals(getDescription(), that.getDescription()) &&
Objects.equals(getSource(), that.getSource()) &&
Objects.equals(getSupportLevel(), that.getSupportLevel()) &&
Objects.equals(getExons(), that.getExons()) &&
Objects.equals(getXrefs(), that.getXrefs()) &&
Objects.equals(getTfbs(), that.getTfbs()) &&
Expand All @@ -439,6 +426,6 @@ public boolean equals(Object o) {

@Override
public int hashCode() {
return Objects.hash(getId(), getName(), getChromosome(), getStart(), getEnd(), getStrand(), getBiotype(), getStatus(), getGenomicCodingStart(), getGenomicCodingEnd(), getCdnaCodingStart(), getCdnaCodingEnd(), getCdsLength(), getcDnaSequence(), getProteinId(), getProteinSequence(), getDescription(), getVersion(), getSource(), getSupportLevel(), getExons(), getXrefs(), getTfbs(), getAnnotationFlags(), getAnnotation());
return Objects.hash(getId(), getName(), getChromosome(), getStart(), getEnd(), getStrand(), getBiotype(), getStatus(), getGenomicCodingStart(), getGenomicCodingEnd(), getCdnaCodingStart(), getCdnaCodingEnd(), getCdsLength(), getcDnaSequence(), getProteinId(), getProteinSequence(), getDescription(), getVersion(), getSource(), getExons(), getXrefs(), getTfbs(), getAnnotationFlags(), getAnnotation());
}
}
2 changes: 1 addition & 1 deletion biodata-models/src/main/java/org/opencb/biodata/models/core/TranscriptAnnotation.java
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Expand Up @@ -20,7 +20,7 @@
package org.opencb.biodata.models.core;

import java.util.List;

import org.opencb.biodata.models.variant.avro.Constraint;

public class TranscriptAnnotation {

Expand Down