Merge pull request #247 from opencb/TASK-1111

TASK-1111 Add Pharmagenomics data to CellBase
opencb · Jul 12, 2023 · d7e9c96 · d7e9c96
2 parents 924664d + 7aae905
commit d7e9c96
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Showing 23 changed files with 2,398 additions and 0 deletions.
diff --git a/biodata-models/src/main/avro/variantAnnotation.avdl b/biodata-models/src/main/avro/variantAnnotation.avdl
@@ -185,6 +185,35 @@ protocol VariantAnnotations {
         union { null, array<string> } bibliography;
     }
 
+    record PharmacogenomicsAlleles {
+        union { null, string } allele;
+        union { null, string } annotation;
+        union { null, string } description;
+    }
+
+    record PharmacogenomicsClinicalAnnotation {
+        union { null, string } variantId;
+        union { null, array<string> } geneNames;
+        union { null, array<string> } phenotypes;
+        union { null, array<string> } phenotypeTypes;
+        union { null, string } confidence;
+        union { null, string } score;
+        union { null, string } url;
+        union { null, string } summary;
+        union { null, array<string> } pubmed;
+        union { null, array<PharmacogenomicsAlleles> } alleles;
+    }
+
+    record Pharmacogenomics {
+        union { null, string } id;
+        union { null, string } name;
+        union { null, string } source;
+        union { null, array<string> } types;
+        union { null, string } smiles;
+        union { null, string } inChI;
+        union { null, array<PharmacogenomicsClinicalAnnotation> } annotations;
+    }
+
     record GeneCancerAssociation {
         union { null, string } id;
         union { null, string } source;
@@ -299,6 +328,7 @@ protocol VariantAnnotations {
         union { null, array<GeneMirnaTarget> } geneMirnaTargets;
         union { null, array<GeneCancerAssociation> } geneCancerAssociations;
         union { null, array<EvidenceEntry> } traitAssociation;
+        union { null, array<Pharmacogenomics> } pharmacogenomics;
         union { null, array<GwasAssociation> } gwas;
         union { null, array<CancerHotspotVariantAnnotation> } cancerHotspots;
         union { null, array<Score> } functionalScore;

diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/pharma/PharmaChemical.java b/biodata-models/src/main/java/org/opencb/biodata/models/pharma/PharmaChemical.java
@@ -0,0 +1,191 @@
+package org.opencb.biodata.models.pharma;
+
+import org.opencb.biodata.models.core.Xref;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class PharmaChemical {
+    private String id;
+    private String source;
+    private String name;
+    private List<String> genericNames;
+    private List<String> tradeNames;
+    private List<String> tradeMixtures;
+    private List<String> types;
+    private List<Xref> xrefs;
+    private String smiles;
+    private String inChI;
+    private List<PharmaVariantAnnotation> variants;
+    private List<PharmaGeneAnnotation> genes;
+
+    private Map<String, Object> attributes;
+
+    public PharmaChemical() {
+        this.genericNames = new ArrayList<>();
+        this.tradeNames = new ArrayList<>();
+        this.tradeMixtures = new ArrayList<>();
+        this.types = new ArrayList<>();
+        this.xrefs = new ArrayList<>();
+        this.variants = new ArrayList<>();
+        this.genes = new ArrayList<>();
+        this.attributes = new HashMap<>();
+    }
+
+    public PharmaChemical(String id, String source, String name, List<String> genericNames, List<String> tradeNames,
+                          List<String> tradeMixtures, List<String> types, List<Xref> xrefs, String smiles, String inChI,
+                          List<PharmaVariantAnnotation> variants, List<PharmaGeneAnnotation> genes, Map<String, Object> attributes) {
+        this.id = id;
+        this.source = source;
+        this.name = name;
+        this.genericNames = genericNames;
+        this.tradeNames = tradeNames;
+        this.tradeMixtures = tradeMixtures;
+        this.types = types;
+        this.xrefs = xrefs;
+        this.smiles = smiles;
+        this.inChI = inChI;
+        this.variants = variants;
+        this.genes = genes;
+        this.attributes = attributes;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("PharmaChemical{");
+        sb.append("id='").append(id).append('\'');
+        sb.append(", source='").append(source).append('\'');
+        sb.append(", name='").append(name).append('\'');
+        sb.append(", genericNames=").append(genericNames);
+        sb.append(", tradeNames=").append(tradeNames);
+        sb.append(", tradeMixtures=").append(tradeMixtures);
+        sb.append(", types=").append(types);
+        sb.append(", xrefs=").append(xrefs);
+        sb.append(", smiles='").append(smiles).append('\'');
+        sb.append(", inChI='").append(inChI).append('\'');
+        sb.append(", variants=").append(variants);
+        sb.append(", genes=").append(genes);
+        sb.append(", attributes=").append(attributes);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getId() {
+        return id;
+    }
+
+    public PharmaChemical setId(String id) {
+        this.id = id;
+        return this;
+    }
+
+    public String getSource() {
+        return source;
+    }
+
+    public PharmaChemical setSource(String source) {
+        this.source = source;
+        return this;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public PharmaChemical setName(String name) {
+        this.name = name;
+        return this;
+    }
+
+    public List<String> getGenericNames() {
+        return genericNames;
+    }
+
+    public PharmaChemical setGenericNames(List<String> genericNames) {
+        this.genericNames = genericNames;
+        return this;
+    }
+
+    public List<String> getTradeNames() {
+        return tradeNames;
+    }
+
+    public PharmaChemical setTradeNames(List<String> tradeNames) {
+        this.tradeNames = tradeNames;
+        return this;
+    }
+
+    public List<String> getTradeMixtures() {
+        return tradeMixtures;
+    }
+
+    public PharmaChemical setTradeMixtures(List<String> tradeMixtures) {
+        this.tradeMixtures = tradeMixtures;
+        return this;
+    }
+
+    public List<String> getTypes() {
+        return types;
+    }
+
+    public PharmaChemical setTypes(List<String> types) {
+        this.types = types;
+        return this;
+    }
+
+    public List<Xref> getXrefs() {
+        return xrefs;
+    }
+
+    public PharmaChemical setXrefs(List<Xref> xrefs) {
+        this.xrefs = xrefs;
+        return this;
+    }
+
+    public String getSmiles() {
+        return smiles;
+    }
+
+    public PharmaChemical setSmiles(String smiles) {
+        this.smiles = smiles;
+        return this;
+    }
+
+    public String getInChI() {
+        return inChI;
+    }
+
+    public PharmaChemical setInChI(String inChI) {
+        this.inChI = inChI;
+        return this;
+    }
+
+    public List<PharmaVariantAnnotation> getVariants() {
+        return variants;
+    }
+
+    public PharmaChemical setVariants(List<PharmaVariantAnnotation> variants) {
+        this.variants = variants;
+        return this;
+    }
+
+    public List<PharmaGeneAnnotation> getGenes() {
+        return genes;
+    }
+
+    public PharmaChemical setGenes(List<PharmaGeneAnnotation> genes) {
+        this.genes = genes;
+        return this;
+    }
+
+    public Map<String, Object> getAttributes() {
+        return attributes;
+    }
+
+    public PharmaChemical setAttributes(Map<String, Object> attributes) {
+        this.attributes = attributes;
+        return this;
+    }
+}
diff --git a/biodata-models/src/main/java/org/opencb/biodata/models/pharma/PharmaClinicalAllele.java b/biodata-models/src/main/java/org/opencb/biodata/models/pharma/PharmaClinicalAllele.java
@@ -0,0 +1,70 @@
+package org.opencb.biodata.models.pharma;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class PharmaClinicalAllele {
+    private String allele;
+    private String annotation;
+    private String description;
+
+    private Map<String, Object> attributes;
+
+    public PharmaClinicalAllele() {
+        this.attributes = new HashMap<>();
+    }
+
+    public PharmaClinicalAllele(String allele, String annotation, String description, Map<String, Object> attributes) {
+        this.allele = allele;
+        this.annotation = annotation;
+        this.description = description;
+        this.attributes = attributes;
+    }
+
+    @Override
+    public String toString() {
+        final StringBuilder sb = new StringBuilder("PharmaClinicalAllele{");
+        sb.append("allele='").append(allele).append('\'');
+        sb.append(", annotation='").append(annotation).append('\'');
+        sb.append(", description='").append(description).append('\'');
+        sb.append(", attributes=").append(attributes);
+        sb.append('}');
+        return sb.toString();
+    }
+
+    public String getAllele() {
+        return allele;
+    }
+
+    public PharmaClinicalAllele setAllele(String allele) {
+        this.allele = allele;
+        return this;
+    }
+
+    public String getAnnotation() {
+        return annotation;
+    }
+
+    public PharmaClinicalAllele setAnnotation(String annotation) {
+        this.annotation = annotation;
+        return this;
+    }
+
+    public String getDescription() {
+        return description;
+    }
+
+    public PharmaClinicalAllele setDescription(String description) {
+        this.description = description;
+        return this;
+    }
+
+    public Map<String, Object> getAttributes() {
+        return attributes;
+    }
+
+    public PharmaClinicalAllele setAttributes(Map<String, Object> attributes) {
+        this.attributes = attributes;
+        return this;
+    }
+}