feat: integration of new gene-wise conditions (#385) (#386)

protos/annonars/genes/base.proto

@@ -928,6 +928,124 @@ message PanelAppRecord {
  Panel panel = 10;
 }
 
+// Record from the integrated conditions computation.
+message ConditionsRecord {
+ // A gene-disease association entry.
+ message GeneDiseaseAssociationEntry {
+ // Enumeration for sources.
+ enum GeneDiseaseAssociationSource {
+ // nil
+ GENE_DISEASE_ASSOCIATION_SOURCE_UNKNOWN = 0;
+ // OMIM
+ GENE_DISEASE_ASSOCIATION_SOURCE_OMIM = 1;
+ // Orphanet
+ GENE_DISEASE_ASSOCIATION_SOURCE_ORPHANET = 2;
+ // PanelApp
+ GENE_DISEASE_ASSOCIATION_SOURCE_PANELAPP = 3;
+ }
+
+ // Enumeration for confidence levels.
+ enum ConfidenceLevel {
+ // nil
+ CONFIDENCE_LEVEL_UNKNOWN = 0;
+ // High confidence.
+ CONFIDENCE_LEVEL_HIGH = 1;
+ // Medium confidence.
+ CONFIDENCE_LEVEL_MEDIUM = 2;
+ // Low confidence.
+ CONFIDENCE_LEVEL_LOW = 3;
+ }
+
+ // The gene-disease association source.
+ GeneDiseaseAssociationSource source = 1;
+ // The gene-disease association confidence level.
+ ConfidenceLevel confidence = 2;
+ }
+
+ // A labeled disorder.
+ message LabeledDisorder {
+ // The disorder ID.
+ string term_id = 1;
+ // The disorder name.
+ optional string title = 2;
+ }
+
+ // A gene-disease association.
+ message GeneDiseaseAssociation {
+ // The HGNC ID.
+ string hgnc_id = 1;
+ // The gene-disease association entries.
+ repeated LabeledDisorder labeled_disorders = 2;
+ // Overall disease name.
+ optional string disease_name = 3;
+ // Disease definition.
+ optional string disease_definition = 4;
+ // The gene-disease association sources.
+ repeated GeneDiseaseAssociationEntry.GeneDiseaseAssociationSource sources = 5;
+ // Overall disease-gene association confidence level.
+ GeneDiseaseAssociationEntry.ConfidenceLevel confidence = 6;
+ }
+
+ // A panel from PanelApp.
+ message PanelappPanel {
+ // PanelApp panel ID.
+ int32 id = 1;
+ // PanelApp panel name.
+ string name = 2;
+ // PanelApp panel version.
+ string version = 3;
+ }
+
+ // An association of a gene by HGNC with a panel from PanelApp.
+ message PanelappAssociation {
+ // Enumeration for PanelApp confidence level.
+ enum PanelappConfidence {
+ // nil
+ PANELAPP_CONFIDENCE_UNKNOWN = 0;
+ // PanelApp green confidence.
+ PANELAPP_CONFIDENCE_GREEN = 1;
+ // PanelApp amber confidence.
+ PANELAPP_CONFIDENCE_AMBER = 2;
+ // PanelApp red confidence.
+ PANELAPP_CONFIDENCE_RED = 3;
+ // PanelApp none confidence (when removed after expert review).
+ PANELAPP_CONFIDENCE_NONE = 4;
+ }
+
+ // Enumeration for entity type.
+ enum PanelappEntityType {
+ // nil
+ PANELAPP_ENTITY_TYPE_UNKNOWN = 0;
+ // PanelApp gene entity type.
+ PANELAPP_ENTITY_TYPE_GENE = 1;
+ // PanelApp region entity type.
+ PANELAPP_ENTITY_TYPE_REGION = 2;
+ // PanelApp short tandem repeat entity type.
+ PANELAPP_ENTITY_TYPE_STR = 3;
+ }
+
+ // The HGNC ID.
+ string hgnc_id = 1;
+ // The PanelApp confidence level.
+ PanelappConfidence confidence_level = 2;
+ // The PanelApp entity type.
+ PanelappEntityType entity_type = 3;
+ // The PanelApp entity name.
+ optional string mode_of_inheritance = 4;
+ // The PanelApp publications.
+ repeated string phenotypes = 5;
+ // The PanelApp panel.
+ PanelappPanel panel = 6;
+ }
+
+ // The HGNC ID.
+ string hgnc_id = 1;
+ // The gene-disease associations.
+ repeated GeneDiseaseAssociation disease_associations = 2;
+ // The PanelApp associations.
+ repeated PanelappAssociation panelapp_associations = 3;
+}
+
 // Entry in the genes RocksDB database.
 message Record {
  // Information from the ACMG secondary finding list.
@@ -958,4 +1076,6 @@ message Record {
  DecipherHiRecord decipher_hi = 13;
  // GenomicsEngland PanelApp gene information.
  repeated PanelAppRecord panelapp = 14;
+ // Conditions record.
+ ConditionsRecord conditions = 15;
 }