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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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| 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.
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.