122 lines
6.6 KiB
Markdown
122 lines
6.6 KiB
Markdown
---
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title: "Immunotherapy Response Prediction - Tools 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-immunotherapy-response-prediction/TOOLS_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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# Immunotherapy Response Prediction - Tools Reference
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## Tools Used by Phase
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### Phase 1: Input Standardization & Cancer Context
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| Tool | Parameters | Response | Purpose |
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|------|-----------|----------|---------|
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| `OpenTargets_get_disease_id_description_by_name` | `diseaseName` | `{data: {search: {hits: [{id, name, description}]}}}` | Resolve cancer to EFO ID |
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| `MyGene_query_genes` | `query` | `{hits: [{_id, symbol, name, ensembl: {gene}}]}` | Resolve gene to Ensembl/Entrez IDs |
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| `ensembl_lookup_gene` | `gene_id`, `species='homo_sapiens'` | `{data: {id, display_name, description, biotype}}` | Gene details |
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### Phase 2: TMB Analysis
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| Tool | Parameters | Response | Purpose |
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|------|-----------|----------|---------|
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| `fda_pharmacogenomic_biomarkers` | `drug_name`, `biomarker`, `limit` | `{count, shown, results: [{Drug, Biomarker, TherapeuticArea, LabelingSection}]}` | FDA TMB-H approvals |
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### Phase 3: Neoantigen Analysis
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| Tool | Parameters | Response | Purpose |
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|------|-----------|----------|---------|
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| `UniProt_get_function_by_accession` | `accession` | List of strings | Protein function for neoantigen assessment |
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| `iedb_search_epitopes` | `organism_name`, `source_antigen_name` | `{status, data, count}` | Known epitopes |
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| `EnsemblVEP_annotate_rsid` | `variant_id` | VEP annotation with SIFT/PolyPhen | Variant impact |
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### Phase 4: MSI/MMR Status
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| Tool | Parameters | Response | Purpose |
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|------|-----------|----------|---------|
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| `fda_pharmacogenomic_biomarkers` | `biomarker='Microsatellite Instability'`, `limit` | FDA MSI-H approvals | MSI-H drug approvals |
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### Phase 5: PD-L1 Expression
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| Tool | Parameters | Response | Purpose |
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|------|-----------|----------|---------|
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| `HPA_get_cancer_prognostics_by_gene` | `gene_name='CD274'` | Cancer prognostic data | PD-L1 prognostic context |
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| `HPA_get_rna_expression_by_source` | `gene_name`, `source_type`, `source_name` (ALL 3 required) | Expression data | Baseline expression |
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### Phase 6: Immune Microenvironment
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| Tool | Parameters | Response | Purpose |
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|------|-----------|----------|---------|
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| `HPA_get_cancer_prognostics_by_gene` | `gene_name` | Cancer prognostics | Immune gene prognostics |
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| `enrichr_gene_enrichment_analysis` | `gene_list` (array), `libs` (array, REQUIRED) | Enrichment results | Immune pathway analysis |
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### Phase 7: Mutation-Based Predictors
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| Tool | Parameters | Response | Purpose |
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|------|-----------|----------|---------|
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| `cBioPortal_get_mutations` | `study_id`, `gene_list` (string!) | `{data: [{proteinChange, mutationType, studyId, ...}]}` | Mutation prevalence |
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### Phase 8: Clinical Evidence & ICI Options
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| Tool | Parameters | Response | Purpose |
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|------|-----------|----------|---------|
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| `FDA_get_indications_by_drug_name` | `drug_name`, `limit` | `{meta, results}` | FDA-approved indications |
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| `FDA_get_mechanism_of_action_by_drug_name` | `drug_name`, `limit` | `{meta, results}` | Drug mechanism |
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| `FDA_get_clinical_studies_info_by_drug_name` | `drug_name`, `limit` | `{meta, results}` | Clinical study data |
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| `OpenTargets_get_drug_mechanisms_of_action_by_chemblId` | `chemblId` | `{data: {drug: {mechanismsOfAction: {rows}}}}` | Drug MOA |
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| `OpenTargets_get_associated_drugs_by_disease_efoId` | `efoId`, `size` | `{data: {disease: {knownDrugs: {count, rows}}}}` | Drugs for cancer |
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| `OpenTargets_get_approved_indications_by_drug_chemblId` | `chemblId` | Approved indications | Drug approvals |
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| `drugbank_get_drug_basic_info_by_drug_name_or_id` | `query`, `case_sensitive`, `exact_match`, `limit` (ALL 4) | Drug info | Drug details |
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| `drugbank_get_targets_by_drug_name_or_drugbank_id` | `query`, `case_sensitive`, `exact_match`, `limit` (ALL 4) | Drug targets | ICI targets |
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| `drugbank_get_pharmacology_by_drug_name_or_drugbank_id` | `query`, `case_sensitive`, `exact_match`, `limit` (ALL 4) | Pharmacology | Drug pharmacology |
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| `search_clinical_trials` | `condition`, `intervention`, `query_term`, `pageSize` | `{total_count, studies}` | Active ICI trials |
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| `PubMed_search_articles` | `query`, `limit` | `{status, data, metadata}` | Literature evidence |
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### Phase 9: Resistance Risk Assessment
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| Tool | Parameters | Response | Purpose |
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|------|-----------|----------|---------|
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| `civic_search_evidence_items` | `therapy_name`, `disease_name` | `{data: {evidenceItems: {nodes}}}` | Resistance evidence |
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| `gnomad_get_gene_constraints` | `gene_symbol` | Gene constraint metrics | Gene essentiality |
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## Key ICI Drug Reference
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| Drug | ChEMBL ID | DrugBank ID | Target |
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|------|-----------|-------------|--------|
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| Pembrolizumab | CHEMBL3137343 | DB09037 | PD-1 (PDCD1) |
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| Nivolumab | CHEMBL2108738 | DB09035 | PD-1 (PDCD1) |
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| Atezolizumab | CHEMBL3707227 | DB11595 | PD-L1 (CD274) |
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| Durvalumab | CHEMBL3301587 | DB11714 | PD-L1 (CD274) |
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| Ipilimumab | CHEMBL1789844 | DB06186 | CTLA-4 |
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| Avelumab | CHEMBL3833373 | DB11945 | PD-L1 (CD274) |
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| Cemiplimab | CHEMBL4297723 | DB14716 | PD-1 (PDCD1) |
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## Key Gene IDs
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| Gene | Ensembl ID | Entrez ID | UniProt | Role |
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|------|-----------|-----------|---------|------|
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| PDCD1 (PD-1) | ENSG00000188389 | 5133 | Q15116 | ICI target |
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| CD274 (PD-L1) | ENSG00000120217 | 29126 | Q9NZQ7 | ICI target |
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| CTLA4 | ENSG00000163599 | 1493 | P16410 | ICI target |
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| BRAF | ENSG00000157764 | 673 | P15056 | Driver mutation |
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| STK11 | ENSG00000118046 | 6794 | Q15831 | Resistance |
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| PTEN | ENSG00000284792 | 5728 | P60484 | Resistance |
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| JAK1 | ENSG00000162434 | 3716 | P23458 | Resistance |
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| JAK2 | ENSG00000096968 | 3717 | O60674 | Resistance |
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| B2M | ENSG00000166710 | 567 | P61769 | Resistance |
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| KEAP1 | ENSG00000079999 | 9817 | Q14145 | Resistance |
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| POLE | ENSG00000177084 | 5426 | Q07864 | Sensitivity |
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| MLH1 | ENSG00000076242 | 4292 | P40692 | MMR |
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| MSH2 | ENSG00000095002 | 4436 | P43246 | MMR |
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| MSH6 | ENSG00000116062 | 2956 | P52701 | MMR |
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| PMS2 | ENSG00000122512 | 5395 | P54278 | MMR |
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## Common Parameter Mistakes
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| Wrong | Correct | Tool |
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|-------|---------|------|
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| `q` | `query` | `MyGene_query_genes` |
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| `rsid` | `variant_id` | `EnsemblVEP_annotate_rsid` |
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| `gene_list=['BRAF']` | `gene_list='BRAF'` | `cBioPortal_get_mutations` |
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| 3 params | ALL 4 params required | All `drugbank_*` tools |
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| no `species` | `species='homo_sapiens'` | `ensembl_lookup_gene` |
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| `genericName` | `drugName` | `OpenTargets_get_drug_id_description_by_name` |
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