// Alliance of Genome Resources entity types
export const ENTITY_TYPES = [
"gene",
"allele",
"disease",
"phenotype",
"expression",
"orthology",
"interaction",
"variant",
"transgenic_allele",
"construct",
"affected_genomic_model",
"go_term",
"do_term",
"publication",
] as const;
export type EntityType = (typeof ENTITY_TYPES)[number];
// Supported model organisms in AGR
export const SPECIES = [
"Homo sapiens",
"Mus musculus",
"Rattus norvegicus",
"Danio rerio",
"Drosophila melanogaster",
"Caenorhabditis elegans",
"Saccharomyces cerevisiae",
"Xenopus laevis",
"Xenopus tropicalis",
] as const;
export type Species = (typeof SPECIES)[number];
// Species short names for search filters
export const SPECIES_MAP: Record<string, Species> = {
human: "Homo sapiens",
mouse: "Mus musculus",
rat: "Rattus norvegicus",
zebrafish: "Danio rerio",
fly: "Drosophila melanogaster",
worm: "Caenorhabditis elegans",
yeast: "Saccharomyces cerevisiae",
frog: "Xenopus laevis",
xenopus: "Xenopus tropicalis",
};
// Gene ID prefixes by data source
export const GENE_ID_PREFIXES = [
"HGNC", // Human
"MGI", // Mouse
"RGD", // Rat
"ZFIN", // Zebrafish
"FB", // FlyBase (Drosophila)
"WB", // WormBase (C. elegans)
"SGD", // Yeast
"Xenbase", // Xenopus
] as const;
// Search result types
export interface SearchResult {
id: string;
symbol?: string;
name: string;
species?: string;
category: string;
description?: string;
highlights?: Record<string, string[]>;
}
export interface SearchResponse {
query: string;
results: SearchResult[];
total: number;
aggregations?: Record<string, unknown>;
}
// Gene types
export interface GeneBasicInfo {
id: string;
symbol: string;
name: string;
species: {
name: string;
commonNames?: string;
taxonId: string;
};
soTermName?: string;
geneSynopsis?: string;
geneSynopsisUrl?: string;
automatedGeneSynopsis?: string;
}
export interface GeneLocation {
chromosome: string;
start: number;
end: number;
strand?: string;
assembly?: string;
}
export interface CrossReference {
id: string;
displayName?: string;
globalCrossRefId?: string;
pages?: string[];
url?: string;
}
export interface GeneData extends GeneBasicInfo {
genomeLocations?: GeneLocation[];
crossReferences?: CrossReference[];
synonyms?: string[];
}
// Disease types
export interface DiseaseAnnotation {
id: string;
name: string;
doId?: string;
associationType?: string;
evidence?: string[];
publications?: PublicationRef[];
}
export interface DiseaseResponse {
results: DiseaseAnnotation[];
total: number;
}
// Expression types
export interface ExpressionAnnotation {
id: string;
assay?: string;
anatomicalStructure?: {
id: string;
name: string;
};
stage?: {
id: string;
name: string;
};
publications?: PublicationRef[];
}
export interface ExpressionResponse {
results: ExpressionAnnotation[];
total: number;
}
// Ortholog types
export interface Ortholog {
gene: {
id: string;
symbol: string;
species: {
name: string;
};
};
homologyType?: string;
methodCount?: number;
best?: boolean;
bestReverse?: boolean;
}
export interface OrthologyResponse {
results: Ortholog[];
total: number;
}
// Phenotype types
export interface PhenotypeAnnotation {
id: string;
phenotype: string;
phenotypeStatement?: string;
primaryAnnotatedEntities?: Array<{
id: string;
name: string;
type: string;
}>;
publications?: PublicationRef[];
}
export interface PhenotypeResponse {
results: PhenotypeAnnotation[];
total: number;
}
// Interaction types
export interface Interaction {
interactorAGeneId: string;
interactorASymbol: string;
interactorBGeneId: string;
interactorBSymbol: string;
interactionType?: string;
detectionMethod?: string;
publications?: PublicationRef[];
}
export interface InteractionResponse {
results: Interaction[];
total: number;
}
// Allele/Variant types
export interface Allele {
id: string;
symbol: string;
name?: string;
synonyms?: string[];
alleleType?: string;
gene?: {
id: string;
symbol: string;
};
species?: {
name: string;
};
}
export interface AlleleResponse {
results: Allele[];
total: number;
}
// Publication types
export interface PublicationRef {
id: string;
pubMedId?: string;
citation?: string;
}
// AllianceMine query types
export interface AllianceMineResult {
type: string;
id: number;
relevance: number;
fields: Record<string, unknown>;
}
export interface AllianceMineResponse {
results: AllianceMineResult[];
totalHits: number;
facets?: Record<string, unknown>;
}
// API Error type
export interface APIError {
status: number;
message: string;
details?: string;
}
