Current Genomi capability catalog, entry operations, and what each capability is for.

Capabilities are focused evidence domains. The host agent chooses a capability from the user's intent, reads the matching skill, and calls the smallest useful operation.

Catalog

Capability	Start when	Entry operations
Active Genome Index	The user supplies a genome source or asks about selected AGI evidence	`active_genome_index.summarize`
Analytical grounding	The task needs pathway members, cell-type markers, or interval features	`pathway.retrieve_members`, `cell_type.retrieve_markers`, `region.retrieve_features`
Ancestry	The user asks for population context, PCA projection, or reference-panel similarity	`ancestry.list_reference_panels`, `ancestry.estimate_population_context`
ClinVar	Exact ClinVar/sample matching or candidate triage is needed	`clinvar.scan_candidates`
Decode dashboard	The user runs the all-at-once dashboard flow	`decode.render_dashboard`
Functional genomics	CRISPR, RNAi, dependency, viability, resistance, or perturbation evidence	`functional_genomics.compare_gene_perturbation`
gnomAD	Public population allele frequency for a specific variant	`gnomad.fetch_population_frequency`
GWAS Catalog	GWAS association evidence for variants or genes	`gwas.compare_variant_associations`, `gwas.compare_gene_associations`
Journal	Investigation notes, evidence links, reviewed source memory	`journal.append_entry`, `journal.search_entries`, `research.build_target_packet`, `research.list_sources`
Nutrigenomics	Single-marker nutrient metabolism, food tolerance, or declared diet-response domains	`nutrigenomics.list_domains`, `nutrigenomics.retrieve_domain_markers`
Pharmacogenomics	Drug response, PGx alleles, labels, guidelines, or PharmCAT	`pharmacogenomics.review_medication`
Phenotype and disease	Phenotypes, disease topics, risk topics, or candidate genes	`phenotype.compare_disease_evidence`, `phenotype.compare_gene_hpo_evidence`, `phenotype.compare_drug_target_evidence`
Polygenic scores	PGS Catalog scores or applying a published scoring file to a genome	`prs.search_scores`, `prs.calculate_score`
Sequence	ORFs, translation, restriction sites, Kozak context, primer checks, reference matching	`sequence.analyze`
Variant evidence	rsID, variant, gene, condition, or public source-backed claims	`variant.resolve`

Operation list

Active Genome Index

active_genome_index.classify_callset_qc
active_genome_index.classify_genotype_support
active_genome_index.classify_region_callability
active_genome_index.summarize

Analytical grounding

cell_type.retrieve_markers
pathway.retrieve_members
region.retrieve_features

Ancestry

ancestry.build_source_context
ancestry.check_sample_overlap
ancestry.estimate_population_context
ancestry.list_reference_panels
ancestry.project_pca

ClinVar

clinvar.match_variants
clinvar.scan_candidates

Decode

decode.render_dashboard

Functional genomics

functional_genomics.compare_gene_perturbation
functional_genomics.import_perturbation_table
functional_genomics.query_geo
functional_genomics.retrieve_perturbation_records

gnomAD

gnomad.fetch_population_frequency

GWAS Catalog

gwas.compare_gene_associations
gwas.compare_variant_associations

Journal and reviewed research

journal.append_entry
journal.export_memory
journal.search_entries
journal.summarize
research.build_target_packet
research.list_sources
research.query
research.record
research.search

Nutrigenomics

nutrigenomics.build_source_context
nutrigenomics.list_domains
nutrigenomics.retrieve_domain_markers
nutrigenomics.retrieve_variant_records

Pharmacogenomics

pharmacogenomics.check_pharmcat
pharmacogenomics.describe_gene_requirements
pharmacogenomics.fetch_clinpgx
pharmacogenomics.fetch_fda_labels
pharmacogenomics.fetch_pgxdb
pharmacogenomics.import_pharmcat_artifacts
pharmacogenomics.preflight_pharmcat
pharmacogenomics.prepare_outside_call_tsv
pharmacogenomics.review_medication
pharmacogenomics.run_pharmcat
pharmacogenomics.validate_outside_call_tsv

Phenotype and disease

phenotype.compare_disease_evidence
phenotype.compare_drug_target_evidence
phenotype.compare_gene_hpo_evidence
phenotype.normalize_terms
phenotype.plan_risk_investigation
phenotype.retrieve_disease_drug_targets
phenotype.retrieve_gene_disease_associations
phenotype.retrieve_trait_gene_records

Polygenic scores

prs.build_source_context
prs.calculate_score
prs.check_score_overlap
prs.fetch_score_metadata
prs.import_scoring_file
prs.list_imported_scores
prs.search_scores

Sequence

sequence.analyze
sequence.check_primers
sequence.classify_kozak
sequence.find_orfs
sequence.find_restriction_sites
sequence.match_reference
sequence.translate

Variant evidence

variant.gather_allele_context
variant.gather_gene_context
variant.resolve

Capability boundaries

Use public-only tools for public questions.
Use AGI-backed tools only after current-session source approval, AGI approval, or default-user selection grants access.
Keep source families separate when priors differ. For example, GWAS association evidence, ClinVar clinical assertions, HPO disease annotations, and pharmacogenomic labels answer different questions.
Confidence is synthesized at answer time from evidence quality, coverage, conflicts, source trust, and missing evidence. It is not a static tool field.

Capabilities

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