biocontext-knowledge-queries

BioContext Knowledge Queries

Use this skill when the user wants to look up gene/protein annotations, query pathway databases, find cell type markers, search biomedical literature, or explore drug-disease associations. BioContext provides programmatic access to 49 biomedical databases through a unified Python API.

This is a knowledge integration layer — use it to annotate analysis results (e.g., annotate DEG lists with protein function, find pathways for gene clusters, validate marker genes against PanglaoDB).

Available Functions by Category

Protein & Genomics

Pathways & Functional

Cell Biology

Literature

Drug & Clinical

Ontology

Proteomics

Generic Access

# List all 49 available tools with parameters
ov.biocontext.list_tools()

# Call any tool directly by name
result = ov.biocontext.call_tool("tool_name", param1=value1, ...)

Usage Patterns

Single gene lookup

import omicverse as ov

# Get protein function and domains
info = ov.biocontext.query_uniprot(gene_symbol='TP53', species='9606')

# Get pathway membership
pathways = ov.biocontext.query_reactome(identifier='TP53', species='Homo sapiens')

# Get GO terms
go_terms = ov.biocontext.query_go(gene_name='TP53', size=20)

Annotate a DEG list

# After differential expression: annotate top genes with biological context
deg_genes = ['TP53', 'BRCA1', 'MYC', 'EGFR', 'KRAS']
annotations = {}
for gene in deg_genes:
    annotations[gene] = {
        'uniprot': ov.biocontext.query_uniprot(gene_symbol=gene),
        'pathways': ov.biocontext.query_reactome(identifier=gene),
        'go': ov.biocontext.query_go(gene_name=gene, size=5),
    }

Find cell type markers

# Get known markers for a cell type
markers = ov.biocontext.query_panglaodb(
    species='Hs',           # 'Hs' (human), 'Mm' (mouse), 'Dr' (zebrafish)
    cell_type='T cells',
    organ='Blood',
    min_sensitivity=0.5,
)
# Returns: DataFrame with gene symbols, sensitivity, specificity scores

Drug target exploration

# Find drugs targeting a gene
targets = ov.biocontext.query_opentargets(
    query_string='{ target(ensemblId: "ENSG00000141510") { associatedDiseases { rows { disease { name } score } } } }'
)

# Search clinical trials
trials = ov.biocontext.search_clinical_trials(condition='breast cancer', status='RECRUITING')

Literature search

# Search for papers
results = ov.biocontext.search_literature(
    query='single-cell RNA-seq BRCA1',
    sort_by='RELEVANCE',
    page_size=5,
)

# Get full text of a specific paper
text = ov.biocontext.get_fulltext(pmc_id='PMC1234567')

Species Codes

Different databases use different species identifiers:

Most functions default to human (9606 or homo_sapiens).

Critical API Reference

query_uniprot accepts multiple identifier types

# By gene symbol (most common)
ov.biocontext.query_uniprot(gene_symbol='TP53')

# By UniProt accession
ov.biocontext.query_uniprot(protein_id='P04637')

# By protein name
ov.biocontext.query_uniprot(protein_name='Cellular tumor antigen p53')

query_opentargets uses GraphQL

# OpenTargets requires GraphQL query strings
# See OpenTargets Platform API docs for query syntax
result = ov.biocontext.query_opentargets(
    query_string='{ search(queryString: "BRCA1") { total hits { id name } } }'
)

Troubleshooting

• Empty results for a known gene: Check species parameter. Default is human (9606) — pass species='10090' for mouse genes.
• Timeout on large queries: External API calls have network latency. For batch annotation, add small delays between calls to avoid rate limiting.
• ConnectionError: Requires internet access. BioContext queries external databases in real-time.
• Gene symbol not found: Some databases are case-sensitive. Human genes should be uppercase (TP53), mouse mixed-case (Tp53).
• OpenTargets query fails: GraphQL syntax must be exact. Use ov.biocontext.list_tools() to see available OpenTargets tool variants with example queries.

Examples

• "Look up the protein function and pathways for my top 10 DEGs."
• "Find known T-cell markers from PanglaoDB for my annotation."
• "Search for recent papers about spatial transcriptomics and BRCA1."
• "What drugs target EGFR? Check clinical trials status."

References

• Quick copy/paste commands: reference.md