109 lines
6.0 KiB
Markdown
109 lines
6.0 KiB
Markdown
---
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title: "Spatial Omics: Tool Parameter & Response Reference"
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task: ""
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lineage_type: import
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upstream_source: https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-spatial-omics-analysis/tool-reference.md
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upstream_sha: e2520a96
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imported_at: 2026-06-26
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prompt_class: prompt
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upstream_changes: accepted
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author: upstream
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validated: false
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---
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# Spatial Omics: Tool Parameter & Response Reference
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Critical parameter names and response formats. Referenced from SKILL.md.
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---
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## Verified Parameter Names
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| Tool | Parameter | CORRECT | Common MISTAKE | Notes |
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|------|-----------|---------|----------------|-------|
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| `MyGene_query_genes` | query | `query` | `q` | Filter results by `symbol` field |
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| `STRING_functional_enrichment` | identifiers | `protein_ids` (array) | `identifiers` | Also needs `species=9606` |
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| `STRING_get_interaction_partners` | identifiers | `protein_ids` (array) | `identifiers` | `limit`, `confidence_score` optional |
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| `ReactomeAnalysis_pathway_enrichment` | genes | `identifiers` (string) | Array | SPACE-SEPARATED string, NOT array |
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| `HPA_get_subcellular_location` | gene | `gene_name` | `ensembl_id` | Uses gene symbol |
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| `HPA_get_cancer_prognostics_by_gene` | gene | `ensembl_id` | `gene_name` | Uses Ensembl ID, NOT symbol |
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| `HPA_get_rna_expression_by_source` | params | `gene_name`, `source_type`, `source_name` | - | ALL 3 required |
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| `HPA_get_rna_expression_in_specific_tissues` | gene | `ensembl_id` | `gene_name` | Uses Ensembl ID |
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| `HPA_get_comprehensive_gene_details_by_ensembl_id` | all params | ALL 5 required | Missing booleans | Set booleans to False except expression |
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| `OpenTargets_get_target_tractability_by_ensemblID` | target | `ensemblId` | `ensemblID` | camelCase |
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| `OpenTargets_get_associated_drugs_by_target_ensemblID` | target | `ensemblId`, `size` | - | Both REQUIRED |
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| `OpenTargets_get_associated_targets_by_disease_efoId` | disease | `efoId` | `diseaseId` | Returns nested response |
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| `DGIdb_get_gene_druggability` | genes | `genes` (array) | `gene_name` | Array of strings |
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| `DGIdb_get_drug_gene_interactions` | genes | `genes` (array) | `gene_name` | Array of strings |
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| `ClinicalTrials_search_studies` | action | `action='search_studies'` | Missing action | `action` is REQUIRED |
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| `ensembl_lookup_gene` | species | `species='homo_sapiens'` | No species | REQUIRED parameter |
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| GTEx tools | gencode | `gencode_id` (array) | `gene_id` | Requires versioned GENCODE ID |
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---
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## Response Format Reference
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| Tool | Response Format | Key Fields |
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|------|----------------|------------|
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| `STRING_functional_enrichment` | `{status, data: [{category, term, description, p_value, fdr, inputGenes}]}` | Filter by FDR < 0.05 |
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| `ReactomeAnalysis_pathway_enrichment` | `{data: {pathways: [{pathway_id, name, p_value, fdr, entities_found, entities_total}]}}` | Top 20 returned |
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| `STRING_get_interaction_partners` | `{status, data: [{preferredName_A, preferredName_B, score}]}` | Score > 0.7 for high confidence |
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| `MyGene_query_genes` | `{hits: [{_id, symbol, name, ensembl: {gene}, entrezgene}]}` | Filter by exact symbol match |
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| `HPA_get_subcellular_location` | `{gene_name, main_locations: [], additional_locations: [], location_summary}` | Direct dict response |
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| `OpenTargets_get_target_tractability_by_ensemblID` | `{data: {target: {id, tractability: [{label, modality, value}]}}}` | Check value=true |
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| `DGIdb_get_gene_druggability` | `{data: {genes: {nodes: [{name, geneCategories: [{name}]}]}}}` | GraphQL response |
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| `PubMed_search_articles` | Plain list of `[{pmid, title, authors, journal, pub_date}]` | No data wrapper |
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| `ClinicalTrials_search_studies` | `{total_count, studies: [{nctId, title, status, conditions}]}` | total_count can be None |
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---
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## Fallback Strategies
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### Pathway Enrichment
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- **Primary**: STRING_functional_enrichment (most comprehensive, one call)
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- **Fallback**: ReactomeAnalysis_pathway_enrichment (Reactome-specific)
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- **Default**: Individual gene GO annotations (GO_get_annotations_for_gene)
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### Tissue Expression
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- **Primary**: HPA_get_rna_expression_by_source
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- **Fallback**: HPA_get_comprehensive_gene_details_by_ensembl_id
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- **Default**: Note "tissue expression data unavailable"
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### Disease Association
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- **Primary**: OpenTargets_get_associated_targets_by_disease_efoId
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- **Fallback**: OpenTargets_target_disease_evidence (per gene)
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- **Default**: Skip disease section if no disease context
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### Drug Information
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- **Primary**: OpenTargets_get_associated_drugs_by_target_ensemblID
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- **Fallback**: DGIdb_get_drug_gene_interactions
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- **Default**: Note "no approved drugs identified"
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### Literature
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- **Primary**: PubMed_search_articles
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- **Fallback**: openalex_literature_search
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- **Default**: Note "no spatial-specific literature found"
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---
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## Limitations & Known Issues
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### Database-Specific
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- **Enrichment**: `enrichr_gene_enrichment_analysis` returns connectivity graph (107MB), NOT standard enrichment. Use `STRING_functional_enrichment` instead
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- **GTEx**: SOAP-style tools requiring `operation` parameter; needs versioned GENCODE IDs (e.g., `ENSG00000141510.16`)
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- **HPA**: Some tools use `gene_name`, others use `ensembl_id` - check parameter reference
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- **OpenTargets**: Disease IDs use underscore format (`MONDO_0007254`), not colon
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- **cBioPortal_get_cancer_studies**: BROKEN - has literal `{limit}` in URL causing 400 error
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### Conceptual
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- **No raw spatial data processing**: Analyzes gene LISTS, not raw spatial matrices
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- **No spatial statistics**: Cannot perform Moran's I, spatial autocorrelation, or variogram analysis
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- **No image analysis**: Cannot process H&E or fluorescence images
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- **No deconvolution**: Use BayesSpace, cell2location, RCTD externally
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- **Ligand-receptor inference**: Based on gene co-expression + known pairs, not spatial proximity statistics (use CellChat, NicheNet, COMMOT externally)
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### Technical
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- **Large gene lists**: >200 genes may slow STRING queries; batch or sample
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- **Response format variability**: Always check both dict and list response types
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- **Rate limits**: STRING and OpenTargets may throttle frequent requests
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