drug-discovery-prompts/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-spatial-omics-analysis/tool-reference.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
Spatial Omics: Tool Parameter & Response Reference		import	https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-spatial-omics-analysis/tool-reference.md	e2520a96	2026-06-26	prompt	accepted	upstream	false

Spatial Omics: Tool Parameter & Response Reference

Critical parameter names and response formats. Referenced from SKILL.md.

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Verified Parameter Names

Tool	Parameter	CORRECT	Common MISTAKE	Notes
MyGene_query_genes	query	query	q	Filter results by symbol field
STRING_functional_enrichment	identifiers	protein_ids (array)	identifiers	Also needs species=9606
STRING_get_interaction_partners	identifiers	protein_ids (array)	identifiers	limit, confidence_score optional
ReactomeAnalysis_pathway_enrichment	genes	identifiers (string)	Array	SPACE-SEPARATED string, NOT array
HPA_get_subcellular_location	gene	gene_name	ensembl_id	Uses gene symbol
HPA_get_cancer_prognostics_by_gene	gene	ensembl_id	gene_name	Uses Ensembl ID, NOT symbol
HPA_get_rna_expression_by_source	params	gene_name, source_type, source_name	-	ALL 3 required
HPA_get_rna_expression_in_specific_tissues	gene	ensembl_id	gene_name	Uses Ensembl ID
HPA_get_comprehensive_gene_details_by_ensembl_id	all params	ALL 5 required	Missing booleans	Set booleans to False except expression
OpenTargets_get_target_tractability_by_ensemblID	target	ensemblId	ensemblID	camelCase
OpenTargets_get_associated_drugs_by_target_ensemblID	target	ensemblId, size	-	Both REQUIRED
OpenTargets_get_associated_targets_by_disease_efoId	disease	efoId	diseaseId	Returns nested response
DGIdb_get_gene_druggability	genes	genes (array)	gene_name	Array of strings
DGIdb_get_drug_gene_interactions	genes	genes (array)	gene_name	Array of strings
ClinicalTrials_search_studies	action	action='search_studies'	Missing action	action is REQUIRED
ensembl_lookup_gene	species	species='homo_sapiens'	No species	REQUIRED parameter
GTEx tools	gencode	gencode_id (array)	gene_id	Requires versioned GENCODE ID

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Response Format Reference

Tool	Response Format	Key Fields
STRING_functional_enrichment	{status, data: [{category, term, description, p_value, fdr, inputGenes}]}	Filter by FDR < 0.05
ReactomeAnalysis_pathway_enrichment	{data: {pathways: [{pathway_id, name, p_value, fdr, entities_found, entities_total}]}}	Top 20 returned
STRING_get_interaction_partners	{status, data: [{preferredName_A, preferredName_B, score}]}	Score > 0.7 for high confidence
MyGene_query_genes	{hits: [{_id, symbol, name, ensembl: {gene}, entrezgene}]}	Filter by exact symbol match
HPA_get_subcellular_location	{gene_name, main_locations: [], additional_locations: [], location_summary}	Direct dict response
OpenTargets_get_target_tractability_by_ensemblID	{data: {target: {id, tractability: [{label, modality, value}]}}}	Check value=true
DGIdb_get_gene_druggability	{data: {genes: {nodes: [{name, geneCategories: [{name}]}]}}}	GraphQL response
PubMed_search_articles	Plain list of [{pmid, title, authors, journal, pub_date}]	No data wrapper
ClinicalTrials_search_studies	{total_count, studies: [{nctId, title, status, conditions}]}	total_count can be None

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Fallback Strategies

Pathway Enrichment

• Primary: STRING_functional_enrichment (most comprehensive, one call)
• Fallback: ReactomeAnalysis_pathway_enrichment (Reactome-specific)
• Default: Individual gene GO annotations (GO_get_annotations_for_gene)

Tissue Expression

• Primary: HPA_get_rna_expression_by_source
• Fallback: HPA_get_comprehensive_gene_details_by_ensembl_id
• Default: Note "tissue expression data unavailable"

Disease Association

• Primary: OpenTargets_get_associated_targets_by_disease_efoId
• Fallback: OpenTargets_target_disease_evidence (per gene)
• Default: Skip disease section if no disease context

Drug Information

• Primary: OpenTargets_get_associated_drugs_by_target_ensemblID
• Fallback: DGIdb_get_drug_gene_interactions
• Default: Note "no approved drugs identified"

Literature

• Primary: PubMed_search_articles
• Fallback: openalex_literature_search
• Default: Note "no spatial-specific literature found"

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Limitations & Known Issues

Database-Specific

• Enrichment: enrichr_gene_enrichment_analysis returns connectivity graph (107MB), NOT standard enrichment. Use STRING_functional_enrichment instead
• GTEx: SOAP-style tools requiring operation parameter; needs versioned GENCODE IDs (e.g., ENSG00000141510.16)
• HPA: Some tools use gene_name, others use ensembl_id - check parameter reference
• OpenTargets: Disease IDs use underscore format (MONDO_0007254), not colon
• cBioPortal_get_cancer_studies: BROKEN - has literal {limit} in URL causing 400 error

Conceptual

• No raw spatial data processing: Analyzes gene LISTS, not raw spatial matrices
• No spatial statistics: Cannot perform Moran's I, spatial autocorrelation, or variogram analysis
• No image analysis: Cannot process H&E or fluorescence images
• No deconvolution: Use BayesSpace, cell2location, RCTD externally
• Ligand-receptor inference: Based on gene co-expression + known pairs, not spatial proximity statistics (use CellChat, NicheNet, COMMOT externally)

Technical

• Large gene lists: >200 genes may slow STRING queries; batch or sample
• Response format variability: Always check both dict and list response types
• Rate limits: STRING and OpenTargets may throttle frequent requests