6.6 KiB
6.6 KiB
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 |
|---|---|---|---|---|---|---|---|---|---|
| Immunotherapy Response Prediction - Tools Reference | import | https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-immunotherapy-response-prediction/TOOLS_REFERENCE.md | e2520a96 | 2026-06-26 | prompt | accepted | upstream | false |
Immunotherapy Response Prediction - Tools Reference
Tools Used by Phase
Phase 1: Input Standardization & Cancer Context
| Tool | Parameters | Response | Purpose |
|---|---|---|---|
OpenTargets_get_disease_id_description_by_name |
diseaseName |
{data: {search: {hits: [{id, name, description}]}}} |
Resolve cancer to EFO ID |
MyGene_query_genes |
query |
{hits: [{_id, symbol, name, ensembl: {gene}}]} |
Resolve gene to Ensembl/Entrez IDs |
ensembl_lookup_gene |
gene_id, species='homo_sapiens' |
{data: {id, display_name, description, biotype}} |
Gene details |
Phase 2: TMB Analysis
| Tool | Parameters | Response | Purpose |
|---|---|---|---|
fda_pharmacogenomic_biomarkers |
drug_name, biomarker, limit |
{count, shown, results: [{Drug, Biomarker, TherapeuticArea, LabelingSection}]} |
FDA TMB-H approvals |
Phase 3: Neoantigen Analysis
| Tool | Parameters | Response | Purpose |
|---|---|---|---|
UniProt_get_function_by_accession |
accession |
List of strings | Protein function for neoantigen assessment |
iedb_search_epitopes |
organism_name, source_antigen_name |
{status, data, count} |
Known epitopes |
EnsemblVEP_annotate_rsid |
variant_id |
VEP annotation with SIFT/PolyPhen | Variant impact |
Phase 4: MSI/MMR Status
| Tool | Parameters | Response | Purpose |
|---|---|---|---|
fda_pharmacogenomic_biomarkers |
biomarker='Microsatellite Instability', limit |
FDA MSI-H approvals | MSI-H drug approvals |
Phase 5: PD-L1 Expression
| Tool | Parameters | Response | Purpose |
|---|---|---|---|
HPA_get_cancer_prognostics_by_gene |
gene_name='CD274' |
Cancer prognostic data | PD-L1 prognostic context |
HPA_get_rna_expression_by_source |
gene_name, source_type, source_name (ALL 3 required) |
Expression data | Baseline expression |
Phase 6: Immune Microenvironment
| Tool | Parameters | Response | Purpose |
|---|---|---|---|
HPA_get_cancer_prognostics_by_gene |
gene_name |
Cancer prognostics | Immune gene prognostics |
enrichr_gene_enrichment_analysis |
gene_list (array), libs (array, REQUIRED) |
Enrichment results | Immune pathway analysis |
Phase 7: Mutation-Based Predictors
| Tool | Parameters | Response | Purpose |
|---|---|---|---|
cBioPortal_get_mutations |
study_id, gene_list (string!) |
{data: [{proteinChange, mutationType, studyId, ...}]} |
Mutation prevalence |
Phase 8: Clinical Evidence & ICI Options
| Tool | Parameters | Response | Purpose |
|---|---|---|---|
FDA_get_indications_by_drug_name |
drug_name, limit |
{meta, results} |
FDA-approved indications |
FDA_get_mechanism_of_action_by_drug_name |
drug_name, limit |
{meta, results} |
Drug mechanism |
FDA_get_clinical_studies_info_by_drug_name |
drug_name, limit |
{meta, results} |
Clinical study data |
OpenTargets_get_drug_mechanisms_of_action_by_chemblId |
chemblId |
{data: {drug: {mechanismsOfAction: {rows}}}} |
Drug MOA |
OpenTargets_get_associated_drugs_by_disease_efoId |
efoId, size |
{data: {disease: {knownDrugs: {count, rows}}}} |
Drugs for cancer |
OpenTargets_get_approved_indications_by_drug_chemblId |
chemblId |
Approved indications | Drug approvals |
drugbank_get_drug_basic_info_by_drug_name_or_id |
query, case_sensitive, exact_match, limit (ALL 4) |
Drug info | Drug details |
drugbank_get_targets_by_drug_name_or_drugbank_id |
query, case_sensitive, exact_match, limit (ALL 4) |
Drug targets | ICI targets |
drugbank_get_pharmacology_by_drug_name_or_drugbank_id |
query, case_sensitive, exact_match, limit (ALL 4) |
Pharmacology | Drug pharmacology |
search_clinical_trials |
condition, intervention, query_term, pageSize |
{total_count, studies} |
Active ICI trials |
PubMed_search_articles |
query, limit |
{status, data, metadata} |
Literature evidence |
Phase 9: Resistance Risk Assessment
| Tool | Parameters | Response | Purpose |
|---|---|---|---|
civic_search_evidence_items |
therapy_name, disease_name |
{data: {evidenceItems: {nodes}}} |
Resistance evidence |
gnomad_get_gene_constraints |
gene_symbol |
Gene constraint metrics | Gene essentiality |
Key ICI Drug Reference
| Drug | ChEMBL ID | DrugBank ID | Target |
|---|---|---|---|
| Pembrolizumab | CHEMBL3137343 | DB09037 | PD-1 (PDCD1) |
| Nivolumab | CHEMBL2108738 | DB09035 | PD-1 (PDCD1) |
| Atezolizumab | CHEMBL3707227 | DB11595 | PD-L1 (CD274) |
| Durvalumab | CHEMBL3301587 | DB11714 | PD-L1 (CD274) |
| Ipilimumab | CHEMBL1789844 | DB06186 | CTLA-4 |
| Avelumab | CHEMBL3833373 | DB11945 | PD-L1 (CD274) |
| Cemiplimab | CHEMBL4297723 | DB14716 | PD-1 (PDCD1) |
Key Gene IDs
| Gene | Ensembl ID | Entrez ID | UniProt | Role |
|---|---|---|---|---|
| PDCD1 (PD-1) | ENSG00000188389 | 5133 | Q15116 | ICI target |
| CD274 (PD-L1) | ENSG00000120217 | 29126 | Q9NZQ7 | ICI target |
| CTLA4 | ENSG00000163599 | 1493 | P16410 | ICI target |
| BRAF | ENSG00000157764 | 673 | P15056 | Driver mutation |
| STK11 | ENSG00000118046 | 6794 | Q15831 | Resistance |
| PTEN | ENSG00000284792 | 5728 | P60484 | Resistance |
| JAK1 | ENSG00000162434 | 3716 | P23458 | Resistance |
| JAK2 | ENSG00000096968 | 3717 | O60674 | Resistance |
| B2M | ENSG00000166710 | 567 | P61769 | Resistance |
| KEAP1 | ENSG00000079999 | 9817 | Q14145 | Resistance |
| POLE | ENSG00000177084 | 5426 | Q07864 | Sensitivity |
| MLH1 | ENSG00000076242 | 4292 | P40692 | MMR |
| MSH2 | ENSG00000095002 | 4436 | P43246 | MMR |
| MSH6 | ENSG00000116062 | 2956 | P52701 | MMR |
| PMS2 | ENSG00000122512 | 5395 | P54278 | MMR |
Common Parameter Mistakes
| Wrong | Correct | Tool |
|---|---|---|
q |
query |
MyGene_query_genes |
rsid |
variant_id |
EnsemblVEP_annotate_rsid |
gene_list=['BRAF'] |
gene_list='BRAF' |
cBioPortal_get_mutations |
| 3 params | ALL 4 params required | All drugbank_* tools |
no species |
species='homo_sapiens' |
ensembl_lookup_gene |
genericName |
drugName |
OpenTargets_get_drug_id_description_by_name |