BioMCP

# BioThings Integration Example Prompts This guide provides example prompts for AI assistants to effectively use the BioThings suite integration in BioMCP. ## Overview of BioThings Suite BioMCP integrates with the complete BioThings suite of APIs: - **MyGene.info** - Gene information and annotations - **MyDisease.info** - Disease ontology and synonyms - **MyVariant.info** - Genetic variant annotations (pre-existing integration, enhanced with BioThings client) - **MyChem.info** - Drug/chemical information and annotations All four services share common infrastructure through the BioThings client module, providing consistent error handling, rate limiting, and response parsing. ## Gene Information Retrieval ### Basic Gene Lookup ``` "What is the TP53 gene?" "Tell me about BRAF" "Get information on the EGFR gene" "What does the BRCA1 gene do?" ``` **Expected tool usage**: `gene_getter("TP53")` → Returns official name, summary, aliases ### Gene by ID ``` "Look up gene with Entrez ID 7157" "What is gene 673?" ``` **Expected tool usage**: `gene_getter("7157")` → Returns TP53 information ### Gene Context for Research ``` "I need to understand the KRAS gene before searching for mutations" "What type of protein does BRAF encode?" "Give me the official name and aliases for MYC" ``` ## Disease Information Retrieval ### Basic Disease Lookup ``` "What is GIST?" "Tell me about melanoma" "Define non-small cell lung cancer" "What is Erdheim-Chester disease?" ``` **Expected tool usage**: `disease_getter("GIST")` → Returns definition, synonyms, ontology IDs ### Disease by Ontology ID ``` "Look up disease MONDO:0018076" "What is DOID:1909?" ``` **Expected tool usage**: `disease_getter("MONDO:0018076")` → Returns disease information ### Disease Synonyms for Research ``` "What are all the names for gastrointestinal stromal tumor?" "Find synonyms for NSCLC" "What other terms are used for melanoma?" ``` ## Variant Information Retrieval (MyVariant.info) MyVariant.info is part of the BioThings suite and provides comprehensive variant annotations. BioMCP has extensive integration with specialized features: ### Basic Variant Lookup ``` "Get information about rs7412" "What is the BRAF V600E variant?" "Look up variant chr7:140453136-140453136" ``` **Expected tool usage**: `variant_getter("rs7412")` → Returns variant annotations with external database links ### Variant Search with Filters ``` "Find pathogenic variants in TP53" "Search for BRCA1 variants with high impact" "Get all loss-of-function variants in KRAS" ``` **Expected tool usage**: `variant_searcher(gene="TP53", significance="pathogenic")` → Returns filtered variant list ### Variant with Cancer Context ``` "What cancer types have BRAF V600E mutations?" "Get TCGA data for TP53 R273H" ``` **Expected tool usage**: Variant tools automatically integrate cBioPortal, TCGA, and 1000 Genomes data when available ## Drug Information Retrieval (MyChem.info) MyChem.info is part of the BioThings suite and provides comprehensive drug/chemical information. ### Basic Drug Lookup ``` "What is imatinib?" "Tell me about aspirin" "Get information on pembrolizumab" "What does metformin do?" ``` **Expected tool usage**: `drug_getter("imatinib")` → Returns drug information with database links ### Drug by ID ``` "Look up DrugBank ID DB00619" "What is CHEMBL941?" "Get details for PubChem CID 5291" ``` **Expected tool usage**: `drug_getter("DB00619")` → Returns drug details by identifier ### Drug Properties and Mechanism ``` "What is the mechanism of action of imatinib?" "Find the chemical formula for aspirin" "What are the trade names for adalimumab?" "How does pembrolizumab work?" ``` **Expected tool usage**: `drug_getter("pembrolizumab")` → Returns mechanism, indications, and properties ## Integrated Research Workflows ### Variant Analysis with Gene Context ``` "Analyze the BRAF V600E mutation - first tell me about the gene, then find pathogenic variants" ``` **Expected tool sequence**: 1. `think(thought="Analyzing BRAF V600E mutation", thoughtNumber=1)` 2. `gene_getter("BRAF")` → Gene context 3. `variant_searcher(gene="BRAF", hgvsp="V600E", significance="pathogenic")` → Variant details ### Clinical Trial Search with Disease Expansion ``` "Find clinical trials for GIST patients" "Search for trials treating gastrointestinal stromal tumors" ``` **Expected tool usage**: - `trial_searcher(conditions=["GIST"], expand_synonyms=True)` - Automatically searches for: GIST OR "gastrointestinal stromal tumor" OR "GI stromal tumor" ### Comprehensive Gene-Disease Research ``` "I'm researching EGFR mutations in lung cancer. Start with the gene, then the disease, then find relevant trials" ``` **Expected tool sequence**: 1. `think(thought="Researching EGFR in lung cancer", thoughtNumber=1)` 2. `gene_getter("EGFR")` → Gene information 3. `disease_getter("lung cancer")` → Disease context and synonyms 4. `trial_searcher(conditions=["lung cancer"], interventions=["EGFR inhibitor"])` → Trials with synonym expansion ### Multi-Gene Analysis ``` "Compare TP53, BRAF, and KRAS genes" "Tell me about the RAS family genes: KRAS, NRAS, HRAS" ``` **Expected tool usage**: Multiple `gene_getter()` calls for each gene ## Advanced Use Cases ### Gene Alias Resolution ``` "What is the official name for the p53 gene?" "Is TRP53 the same as TP53?" ``` **Expected tool usage**: `gene_getter("p53")` → Will resolve to TP53 ### Disease Name Disambiguation ``` "Is GIST the same as gastrointestinal stromal tumor?" "What's the MONDO ID for melanoma?" ``` **Expected tool usage**: `disease_getter("GIST")` → Shows all synonyms and IDs ### Trial Search Without Synonym Expansion ``` "Find trials specifically mentioning 'GIST' not other names" ``` **Expected tool usage**: `trial_searcher(conditions=["GIST"], expand_synonyms=False)` ### Integrated Literature and Gene Search ``` "Find recent papers about TP53 mutations - first tell me about the gene" ``` **Expected tool sequence**: 1. `gene_getter("TP53")` → Gene context 2. `article_searcher(genes=["TP53"], keywords=["mutation"])` → Literature ### Drug-Target Research ``` "I'm researching imatinib for CML treatment. Get drug info, then find trials" "What targets does pembrolizumab hit? Then find related articles" ``` **Expected tool sequence**: 1. `think(thought="Researching imatinib for CML", thoughtNumber=1)` 2. `drug_getter("imatinib")` → Drug information and mechanism 3. `trial_searcher(interventions=["imatinib"], conditions=["chronic myeloid leukemia"])` ## Tips for AI Assistants 1. **Always use think() first** for complex biomedical queries 2. **Gene context helps interpretation**: Get gene info before analyzing variants 3. **Disease synonyms improve search**: Use expand_synonyms=True (default) for comprehensive results 4. **Drug mechanisms matter**: Get drug info before searching trials to understand targets 5. **Real-time data**: All BioThings data is fetched live, ensuring current information 6. **Combine tools**: Gene + disease + variant + drug tools work together for comprehensive analysis ## Common Patterns ### Pattern 1: Gene → Variant → Clinical Impact ``` gene_getter("BRAF") → variant_searcher(gene="BRAF", significance="pathogenic") → article_searcher(genes=["BRAF"], diseases=["melanoma"]) ``` ### Pattern 2: Disease → Trials → Locations ``` disease_getter("NSCLC") → trial_searcher(conditions=["NSCLC"], expand_synonyms=True) → trial_locations_getter(nct_id="NCT...") ``` ### Pattern 3: Multi-Gene Pathway Analysis ``` gene_getter("EGFR") → gene_getter("KRAS") → gene_getter("BRAF") → article_searcher(genes=["EGFR", "KRAS", "BRAF"], keywords=["pathway"]) ``` ## Unified Search with BioThings Domains BioMCP's unified search now supports gene, drug, and disease domains alongside articles, trials, and variants: ### Domain-Specific Search ``` "Search for BRAF in the gene domain" "Find imatinib in drugs" "Look up melanoma in diseases" ``` **Expected tool usage**: - `search(domain="gene", keywords=["BRAF"])` - `search(domain="drug", keywords=["imatinib"])` - `search(domain="disease", keywords=["melanoma"])` ### Unified Query Language with BioThings ``` "genes.symbol:BRAF AND genes.type:protein-coding" "drugs.tradename:gleevec" "diseases.name:melanoma OR diseases.synonym:malignant melanoma" ``` **Expected tool usage**: Query parser automatically routes to appropriate domains ### Cross-Domain Gene Searches ``` "gene:BRAF" # Searches articles, variants, genes, and trials "Search everything about TP53" ``` **Expected behavior**: - Gene queries trigger searches across multiple domains - Results include gene info, variants, articles, and related trials ### Cross-Domain Disease Searches ``` "disease:melanoma" # Searches articles, trials, and diseases "Find all information about NSCLC" ``` **Expected behavior**: - Disease queries search articles, trials, and disease databases - Disease synonyms are automatically expanded in trial searches ### Combined Domain Queries ``` "gene:BRAF AND disease:melanoma" "drugs.indication:leukemia AND trials.phase:3" "genes.symbol:EGFR AND articles.year:>2023" ``` ### Unified Fetch ``` "Fetch BRAF from gene domain" "Get imatinib details from drugs" "Retrieve melanoma information from diseases" ``` **Expected tool usage**: - `fetch(id="BRAF", domain="gene")` - `fetch(id="imatinib", domain="drug")` - `fetch(id="melanoma", domain="disease")` ## Error Handling If a gene/disease is not found: - Check for typos or alternative names - Try searching with partial names - Use official symbols for genes (e.g., "TP53" not "p53 gene") - For diseases, try both common and medical names