analytical-grounding

Analytical Grounding

Use this skill for source-declared records that ground an analytical statement, without asking Genomi to choose the interpretation.

Use When

• The input is a controlled pathway or gene-set name/id and the agent needs its canonical member genes.
• The input is a controlled cell type and the agent needs marker-gene records.
• The input is a genomic interval and the agent needs overlaps against declared GENCODE or ENCODE annotation files.

Operations

• 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.

Boundaries

• These are retrieval verbs over declared source coverage.
• Do not use them as experimental protocol recommendations, workflow templates, or free-text biological interpretation.
• Treat 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.
• Preserve source priors. A pathway member, marker gene, interval overlap, or druggable-target membership row is evidence context, not a selected answer.

Examples

• 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"}