Use Case Gallery
Twelve more workflows, one batch endpoint.
Each entry below is a complete use case: audience, what you send, and a prompt sketch ready to adapt. The infrastructure is identical to the four main guides: a list of items, a prompt template, and a streaming batch request.
Genomics & Genetics
Rare disease phenotype-to-gene matching
Given candidate genes from exome sequencing, ask whether each has published associations with the phenotype in question. Genes with convergent evidence across human genetics and model organisms rise to the top; zero-literature genes are explicitly flagged.
Does {item} have published associations with [HPO terms]?
Return: gene, human phenotype evidence, mouse KO phenotype, OMIM entry, PMIDs.Pharmacogenomics - drug-gene interaction triage
For a 120-gene pharmacogenomics panel, retrieve which drug classes interact with each gene, the clinical consequence (efficacy or toxicity), and whether PharmGKB or CPIC guidelines exist.
For the pharmacogene {item}, what drug classes interact with it?
Return: gene, interacting drugs, clinical effect (efficacy/toxicity), guideline level, PMIDs.Copy number variant gene content annotation
For each gene within a CNV, retrieve haploinsufficiency context, dominant disease associations, and any published CNV cases at that locus.
Is {item} known to be dosage-sensitive or haploinsufficient?
Return: gene, dominant disease, CNV literature, DECIPHER/ClinGen evidence, PMIDs.Cancer Biology
Oncogene / tumor suppressor classification
Classify each gene from a cancer DEG list as oncogene, tumor suppressor, passenger, or unknown, with the strongest supporting evidence in the cancer type of interest.
In the context of [cancer type], is {item} an oncogene, tumor suppressor, or unknown?
Return: gene, classification, strongest evidence sentence, cancer type specificity, PMIDs.Tumor microenvironment marker annotation
For marker genes from a single-cell TME dataset, retrieve which cell type each marks, whether it is a checkpoint or immunosuppressive factor, and whether it has been explored as a therapeutic target.
Is {item} a known marker of immune or stromal cell subsets in the tumor microenvironment?
Is it a checkpoint or immunosuppressive target?
Return: gene, cell type, immune function, therapeutic relevance, PMIDs.Cancer driver vs. passenger gene triage
For recurrently mutated genes from somatic mutation analysis, retrieve functional evidence - pathway membership, hotspot context, mouse model data - and score each gene's likelihood of being a driver.
In [cancer type], is {item} a likely driver gene based on published functional evidence?
Return: gene, driver evidence, pathway, hotspot context, PMIDs, driver probability: High/Med/Low.Neuroscience & Complex Disease
Alzheimer's / Parkinson's candidate gene scoring
For each candidate gene from GWAS or multi-omics, retrieve expression in the relevant brain cell type, known role in protein aggregation or clearance, and functional validation in disease models.
Does {item} have published evidence for a role in Alzheimer's or Parkinson's disease?
Return: gene, cell-type expression, aggregation/clearance role, disease model evidence, PMIDs.Autoimmune GWAS locus functional annotation
For fine-mapped loci from an autoimmune GWAS, retrieve immune cell expression, known role in JAK-STAT / NF-kB / TCR/BCR signaling, and any human genetic evidence beyond the GWAS signal.
Does {item} have evidence for a functional role in T cell, B cell, or macrophage biology relevant to autoimmune disease?
Return: gene, immune cell expression, signaling pathway, autoimmune evidence, PMIDs.Psychiatric disorder polygenic risk gene interpretation
For top-ranked genes from a PRS model, retrieve synaptic function, neurodevelopmental role, and enrichment in brain eQTL datasets to support mechanistic hypothesis generation.
What is the published functional role of {item} in brain development or synaptic biology?
Is it associated with schizophrenia, bipolar disorder, or ASD in genetic studies?
Return: gene, brain function, psychiatric genetic evidence, eQTL context, PMIDs.Experimental Follow-up
Proteomics hit functional annotation
For proteins that change in abundance under a perturbation, retrieve known function in the biological context, key interaction partners, and whether any published study has validated it in a similar model.
What is the known function of {item} in [biological process or cell type]?
Does it have known interaction partners relevant to [pathway]?
Return: protein, function, key interactors, relevant experimental evidence, PMIDs.Biomarker candidate clinical evidence validation
For circulating biomarker candidates, retrieve whether each has been measured in patient blood/serum before, disease association evidence, and any published sensitivity/specificity estimates.
Has {item} been studied as a circulating biomarker for [disease]?
Return: gene/protein, biomarker evidence, specimen type, clinical association, PMIDs.Cross-tissue expression specificity check
For a list of candidates, retrieve published evidence on expression pattern across tissues and cell types. Highly ubiquitous genes are deprioritized; tissue-restricted ones advance.
Based on published literature, is {item} expressed broadly across human tissues or restricted to specific cell types? Flag if ubiquitous.
Return: gene, expression pattern, most specific cell type, PMIDs.