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Retrieve canonical pathway members, cell-type marker records, and genomic interval feature overlaps from declared analytical sources.
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Based on SOC occupation classification
Use this skill for genetics, genome source, variant, gene, phenotype, disease, screen, pharmacogenomics, and Genomi install/setup maintenance questions.
Build and inspect ClinVar exact-match evidence and candidate inventories. Use for clinical labels, VUS/conflict, carrier context, and drug-response rows.
Activate this skill for "/genomi decode", "decode my genome", "decode my DNA", "show me the dashboard", "the Genomi dashboard", "one-shot rundown", or any all-at-once request that asks Genomi to compose every capability's findings into a single artifact. This is the whole-genome dashboard kicker — it sweeps every relevant Genomi capability in one shot, not a per-target lookup. Composes evidence from every relevant Genomi capability into a single self-contained Genomi Dashboard.html and returns localhost serve metadata. Active genome required.
Answer drug-response, medication, PharmGKB-style, PGxDB, ATC, DrugBank, gene-drug, and variant-drug questions using public PGx evidence plus local sample genotype support when an Active Genome Index is selected.
Plan rare disease, hereditary disease, cancer risk, carrier-relevance, and observed-condition source investigation from public targets or selected active genome evidence.
Answer specific rsID, allele, gene, region, genotype, and absence/callability questions using explicit session context or public evidence.
| name | analytical-grounding |
| description | Retrieve canonical pathway members, cell-type marker records, and genomic interval feature overlaps from declared analytical sources. |
| tools | ["pathway.retrieve_members","cell_type.retrieve_markers","region.retrieve_features"] |
| mutating | false |
Use this skill for source-declared records that ground an analytical statement, without asking Genomi to choose the interpretation.
pathway.retrieve_members: retrieve Reactome, KEGG human pathway, or
supplied or installed MSigDB Hallmark GMT member genes. Use a source for
free-text pathway names unless the identifier prefix makes the source clear.cell_type.retrieve_markers: retrieve HPA single-cell marker
records, installed CellMarker/PanglaoDB tables, or supplied marker tables.region.retrieve_features: retrieve interval overlaps from
supplied or installed GENCODE GTF and/or ENCODE cCRE BED files for
GRCh37/GRCh38. Supply assembly; without it the tool reports unsupported
assembly instead of guessing a genome build.coverage_status literally:
data_returned: declared source records were returned.in_scope_empty: the input was in declared scope, and no records matched.out_of_scope_for_input: the source, assembly, identifier, or required
source file is outside declared coverage.pathway.retrieve_members with {"pathway_id_or_name":"R-HSA-70635"}pathway.retrieve_members with {"pathway_id_or_name":"hsa00010"}cell_type.retrieve_markers with {"cell_type_id_or_name":"hepatocytes","source":"hpa"}cell_type.retrieve_markers with {"cell_type_id_or_name":"Hepatocyte","source":"cellmarker"}region.retrieve_features with {"region":"1:1000-1250","assembly":"GRCh38"}The installer can cache gencode-grch38, gencode-grch37,
encode-ccre-grch38, panglaodb-markers, and cellmarker-human under
GENOMI_HOME. MSigDB Hallmark requires a user-supplied official GMT export.
A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.
Retrieve canonical marker genes for a controlled cell-type source entity.
Use when: Returns source-declared marker genes for HPA single-cell records or supplied CellMarker, PanglaoDB, or ENCODE marker tables.
Why necessary: Cell-type identity questions need marker records, not disease genetics or GWAS evidence.
Result semantics: Returns marker records only; it does not annotate clusters, assign cell identities, rank cell types, or interpret cell states. Free-text cluster IDs and hypothetical cell-state labels are out of scope.
Retrieve canonical member genes for a controlled pathway or gene-set source entity.
Use when: Returns source-declared member genes for Reactome pathways, KEGG human pathways, or supplied MSigDB Hallmark GMT gene sets.
Why necessary: Pathway membership is a grounding fact and should be retrieved separately from disease or variant claims.
Result semantics: Returns pathway membership records only; it does not infer pathway activity, choose genes, or summarize pathway biology. Free-text pathway names should include source unless the identifier prefix implies a declared source.
Retrieve genomic-region feature annotations from supplied or installed GENCODE and ENCODE annotation files.
Use when: The user or an upstream tool supplies a genomic interval and the agent needs transcript or regulatory-feature overlaps for an explicit GRCh37 or GRCh38 assembly.
Why necessary: Genomic coordinates need gene and regulatory feature context before they can be biologically discussed.
Result semantics: Returns source-declared interval overlaps for the assembly shown in query. Empty results mean no overlap in declared files, not biological absence outside declared coverage.