{
  "schemaVersion": "1.0.0",
  "projectVersion": "1.0.0",
  "policy": "Una capacidad debe pertenecer a un módulo, declarar madurez, evidencia y limitaciones.",
  "modules": [
    {
      "schemaVersion": "1.0.0",
      "id": "sequence-analysis",
      "titleEs": "Análisis molecular de secuencias",
      "descriptionEs": "Normalización, composición, transcripción, traducción, ORF y uso de codones.",
      "version": "1.0.0",
      "maturity": "validated",
      "package": "@human-genome-labs/genetics-core",
      "entrypoint": "packages/genetics-core/src/index.ts",
      "capabilities": [
        "sequence.summary",
        "sequence.translation",
        "sequence.orf",
        "sequence.codon_usage"
      ],
      "evidenceLevel": "computational_prediction",
      "clinicalUse": false,
      "inputs": [
        "FASTA",
        "DNA",
        "RNA"
      ],
      "outputs": [
        "ScientificResult",
        "JSON",
        "protein-sequence"
      ],
      "limitations": [
        "Una ORF o traducción computacional no demuestra expresión ni función."
      ],
      "sourceIds": [
        "ncbi-genetic-codes"
      ],
      "owners": [
        "core-maintainers"
      ],
      "roadmap": [
        "soporte de códigos genéticos adicionales",
        "pruebas de propiedades"
      ]
    },
    {
      "schemaVersion": "1.0.0",
      "id": "variant-analysis",
      "titleEs": "Efecto molecular de variantes",
      "descriptionEs": "Aplicación de variantes simples y comparación exploratoria sobre CDS aisladas.",
      "version": "1.0.0",
      "maturity": "validated",
      "package": "@human-genome-labs/genetics-core",
      "entrypoint": "packages/genetics-core/src/index.ts",
      "capabilities": [
        "variant.apply",
        "variant.coding_effect",
        "variant.allele_fraction"
      ],
      "evidenceLevel": "computational_prediction",
      "clinicalUse": false,
      "inputs": [
        "DNA",
        "VCF-like variant",
        "read counts"
      ],
      "outputs": [
        "ScientificResult",
        "molecular-effect"
      ],
      "limitations": [
        "No anota transcritos reales ni clasifica variantes clínicamente."
      ],
      "sourceIds": [
        "igvf",
        "igvf"
      ],
      "owners": [
        "core-maintainers"
      ],
      "roadmap": [
        "normalización de variantes",
        "integración con anotaciones GFF3"
      ]
    },
    {
      "schemaVersion": "1.0.0",
      "id": "noncanonical-structures",
      "titleEs": "Estructuras no canónicas",
      "descriptionEs": "Detección de motivos candidatos y modelado de evidencia para G4, tríplex y otras conformaciones.",
      "version": "1.0.0",
      "maturity": "experimental",
      "package": "@human-genome-labs/genetics-core",
      "entrypoint": "packages/genetics-core/src/index.ts",
      "capabilities": [
        "structure.g4_candidate"
      ],
      "evidenceLevel": "computational_prediction",
      "clinicalUse": false,
      "inputs": [
        "DNA"
      ],
      "outputs": [
        "candidate-regions"
      ],
      "limitations": [
        "Un motivo de secuencia no demuestra formación estructural in vivo."
      ],
      "sourceIds": [
        "g4-review"
      ],
      "owners": [
        "research-maintainers"
      ],
      "roadmap": [
        "métodos alternativos",
        "benchmarks con conjuntos publicados"
      ]
    },
    {
      "schemaVersion": "1.0.0",
      "id": "somatic-observation",
      "titleEs": "Observaciones de mosaicismo somático",
      "descriptionEs": "Resumen estadístico de fracciones alélicas y trazabilidad de supuestos.",
      "version": "1.0.0",
      "maturity": "experimental",
      "package": "@human-genome-labs/genetics-core",
      "entrypoint": "packages/genetics-core/src/index.ts",
      "capabilities": [
        "somatic.allele_fraction"
      ],
      "evidenceLevel": "observed",
      "clinicalUse": false,
      "inputs": [
        "read-counts"
      ],
      "outputs": [
        "frequency-estimate",
        "confidence-interval"
      ],
      "limitations": [
        "La fracción de lecturas no equivale directamente a la fracción celular."
      ],
      "sourceIds": [
        "smaht"
      ],
      "owners": [
        "research-maintainers"
      ],
      "roadmap": [
        "modelos beta-binomiales",
        "filtros de calidad"
      ]
    },
    {
      "schemaVersion": "1.0.0",
      "id": "pangenome",
      "titleEs": "Representación de pangenomas",
      "descriptionEs": "Contrato conceptual para referencias en grafo, haplotipos y rutas.",
      "version": "1.0.0",
      "maturity": "concept",
      "capabilities": [
        "pangenome.metadata"
      ],
      "evidenceLevel": "unknown",
      "clinicalUse": false,
      "inputs": [
        "graph-reference",
        "haplotypes"
      ],
      "outputs": [
        "paths",
        "graph-intervals"
      ],
      "limitations": [
        "No incluye todavía un motor de grafos ni alineamiento."
      ],
      "sourceIds": [
        "hprc-draft"
      ],
      "owners": [
        "research-maintainers"
      ],
      "roadmap": [
        "RFC de coordenadas en grafo",
        "adaptadores GFA/GBZ"
      ]
    },
    {
      "schemaVersion": "1.0.0",
      "id": "file-formats",
      "titleEs": "Interoperabilidad de formatos",
      "descriptionEs": "Lectores transparentes para FASTA, GFF3 y VCF con conversión explícita de coordenadas.",
      "version": "1.0.0",
      "maturity": "validated",
      "package": "@human-genome-labs/file-formats",
      "entrypoint": "packages/file-formats/src/index.ts",
      "capabilities": [
        "format.fasta",
        "format.gff3",
        "format.vcf"
      ],
      "evidenceLevel": "observed",
      "clinicalUse": false,
      "inputs": [
        "FASTA",
        "GFF3",
        "VCF"
      ],
      "outputs": [
        "typed-records",
        "ScientificResult"
      ],
      "limitations": [
        "Cobertura inicial sin BCF, BGZF, tabix ni extensiones completas."
      ],
      "sourceIds": [],
      "owners": [
        "core-maintainers"
      ],
      "roadmap": [
        "serialización GFF3/VCF",
        "índices y archivos comprimidos"
      ]
    },
    {
      "schemaVersion": "1.0.0",
      "id": "organism-profiles",
      "titleEs": "Perfiles de organismo",
      "descriptionEs": "Contexto configurable de polímero, hebras, topología, compartimento y código genético.",
      "version": "1.0.0",
      "maturity": "validated",
      "package": "@human-genome-labs/organism-profiles",
      "entrypoint": "packages/organism-profiles/src/index.ts",
      "capabilities": [
        "profile.organism_context"
      ],
      "evidenceLevel": "observed",
      "clinicalUse": false,
      "inputs": [
        "profile-id"
      ],
      "outputs": [
        "organism-context"
      ],
      "limitations": [
        "Los perfiles genéricos deben especializarse antes de análisis reales."
      ],
      "sourceIds": [],
      "owners": [
        "core-maintainers"
      ],
      "roadmap": [
        "perfiles taxonómicos versionados",
        "validación contra catálogos externos"
      ]
    }
  ],
  "capabilities": [
    {
      "id": "sequence.summary",
      "titleEs": "Resumen de secuencia",
      "descriptionEs": "Composición, GC, símbolos ambiguos y entropía.",
      "moduleId": "sequence-analysis",
      "maturity": "validated",
      "evidenceLevel": "computational_prediction",
      "inputs": [
        "DNA"
      ],
      "outputs": [
        "sequence-summary"
      ],
      "interfaces": [
        "library",
        "cli",
        "web"
      ],
      "limitations": [
        "Las bases ambiguas requieren interpretación probabilística."
      ]
    },
    {
      "id": "sequence.translation",
      "titleEs": "Traducción de secuencia",
      "descriptionEs": "Traducción por hebra, marco y código genético.",
      "moduleId": "sequence-analysis",
      "maturity": "validated",
      "evidenceLevel": "computational_prediction",
      "inputs": [
        "DNA"
      ],
      "outputs": [
        "protein-sequence"
      ],
      "interfaces": [
        "library",
        "cli",
        "web",
        "game"
      ],
      "limitations": [
        "No demuestra expresión proteica."
      ]
    },
    {
      "id": "sequence.orf",
      "titleEs": "Detección de ORF",
      "descriptionEs": "Busca marcos abiertos de lectura completos o incompletos.",
      "moduleId": "sequence-analysis",
      "maturity": "validated",
      "evidenceLevel": "computational_prediction",
      "inputs": [
        "DNA"
      ],
      "outputs": [
        "genomic-intervals",
        "protein-sequence"
      ],
      "interfaces": [
        "library",
        "cli",
        "web"
      ],
      "limitations": [
        "Los ORF dependen del código y parámetros seleccionados."
      ]
    },
    {
      "id": "sequence.codon_usage",
      "titleEs": "Uso de codones",
      "descriptionEs": "Frecuencias de codones por marco.",
      "moduleId": "sequence-analysis",
      "maturity": "validated",
      "evidenceLevel": "computational_prediction",
      "inputs": [
        "DNA"
      ],
      "outputs": [
        "frequency-table"
      ],
      "interfaces": [
        "library",
        "cli"
      ],
      "limitations": [
        "No corrige sesgos de muestreo ni expresión."
      ]
    },
    {
      "id": "variant.apply",
      "titleEs": "Aplicación de variante",
      "descriptionEs": "Aplica sustituciones e indels simples con verificación de REF.",
      "moduleId": "variant-analysis",
      "maturity": "validated",
      "evidenceLevel": "computational_prediction",
      "inputs": [
        "DNA",
        "variant"
      ],
      "outputs": [
        "alternate-sequence"
      ],
      "interfaces": [
        "library",
        "cli"
      ],
      "limitations": [
        "No normaliza ni alinea variantes complejas."
      ]
    },
    {
      "id": "variant.coding_effect",
      "titleEs": "Efecto codificante exploratorio",
      "descriptionEs": "Compara traducción de referencia y alternativa.",
      "moduleId": "variant-analysis",
      "maturity": "validated",
      "evidenceLevel": "computational_prediction",
      "inputs": [
        "CDS",
        "variant"
      ],
      "outputs": [
        "molecular-effect"
      ],
      "interfaces": [
        "library",
        "cli",
        "web"
      ],
      "limitations": [
        "No es interpretación clínica."
      ]
    },
    {
      "id": "variant.allele_fraction",
      "titleEs": "Fracción alélica observada",
      "descriptionEs": "Calcula proporción e intervalo Wilson.",
      "moduleId": "variant-analysis",
      "maturity": "validated",
      "evidenceLevel": "observed",
      "inputs": [
        "read-counts"
      ],
      "outputs": [
        "frequency-estimate"
      ],
      "interfaces": [
        "library",
        "cli",
        "web"
      ],
      "limitations": [
        "No estima directamente fracción celular."
      ]
    },
    {
      "id": "structure.g4_candidate",
      "titleEs": "Candidatos G-cuádruplex",
      "descriptionEs": "Detecta patrones de cuatro tractos G.",
      "moduleId": "noncanonical-structures",
      "maturity": "experimental",
      "evidenceLevel": "computational_prediction",
      "inputs": [
        "DNA"
      ],
      "outputs": [
        "candidate-regions"
      ],
      "interfaces": [
        "library",
        "cli",
        "web"
      ],
      "limitations": [
        "Motivo no equivale a estructura formada."
      ]
    },
    {
      "id": "somatic.allele_fraction",
      "titleEs": "Observación somática",
      "descriptionEs": "Contrato experimental para observaciones de mosaicismo.",
      "moduleId": "somatic-observation",
      "maturity": "experimental",
      "evidenceLevel": "observed",
      "inputs": [
        "read-counts"
      ],
      "outputs": [
        "frequency-estimate"
      ],
      "interfaces": [
        "library",
        "cli"
      ],
      "limitations": [
        "Requiere modelar pureza, ploidía y errores."
      ]
    },
    {
      "id": "pangenome.metadata",
      "titleEs": "Metadatos de pangenoma",
      "descriptionEs": "Representa conceptos de caminos, haplotipos y grafos.",
      "moduleId": "pangenome",
      "maturity": "concept",
      "evidenceLevel": "unknown",
      "inputs": [
        "graph-reference"
      ],
      "outputs": [
        "graph-metadata"
      ],
      "interfaces": [
        "library"
      ],
      "limitations": [
        "No existe motor de análisis implementado."
      ]
    },
    {
      "id": "format.fasta",
      "titleEs": "Lectura y escritura FASTA",
      "descriptionEs": "Parsea secuencias sin imponer un organismo.",
      "moduleId": "file-formats",
      "maturity": "validated",
      "evidenceLevel": "observed",
      "inputs": [
        "FASTA"
      ],
      "outputs": [
        "sequence-records"
      ],
      "interfaces": [
        "library",
        "cli"
      ],
      "limitations": [
        "No indexa archivos grandes."
      ]
    },
    {
      "id": "format.gff3",
      "titleEs": "Lectura GFF3",
      "descriptionEs": "Parsea características y convierte coordenadas.",
      "moduleId": "file-formats",
      "maturity": "validated",
      "evidenceLevel": "observed",
      "inputs": [
        "GFF3"
      ],
      "outputs": [
        "genomic-features"
      ],
      "interfaces": [
        "library",
        "cli"
      ],
      "limitations": [
        "No implementa todas las extensiones de proveedores."
      ]
    },
    {
      "id": "format.vcf",
      "titleEs": "Lectura VCF",
      "descriptionEs": "Parsea variantes, INFO, FORMAT y muestras.",
      "moduleId": "file-formats",
      "maturity": "validated",
      "evidenceLevel": "observed",
      "inputs": [
        "VCF"
      ],
      "outputs": [
        "variant-records"
      ],
      "interfaces": [
        "library",
        "cli"
      ],
      "limitations": [
        "No normaliza variantes ni soporta BCF."
      ]
    },
    {
      "id": "profile.organism_context",
      "titleEs": "Contexto de organismo",
      "descriptionEs": "Selecciona polímero, hebras, topología y código genético.",
      "moduleId": "organism-profiles",
      "maturity": "validated",
      "evidenceLevel": "observed",
      "inputs": [
        "profile-id"
      ],
      "outputs": [
        "organism-context"
      ],
      "interfaces": [
        "library",
        "cli",
        "web"
      ],
      "limitations": [
        "La selección del perfil no reemplaza metadatos de muestra."
      ]
    }
  ]
}