API Reference

Complete API reference for the biodbs package.

Modules

biodbs.fetch

Data fetching from biological databases.

Fetcher Classes

• UniProt_Fetcher - Fetch protein data from UniProt REST API
• PubChem_Fetcher - Fetch chemical data from PubChem PUG REST/View APIs
• Ensembl_Fetcher - Fetch genomic data from Ensembl REST API
• BioMart_Fetcher - Query Ensembl BioMart for gene annotations
• KEGG_Fetcher - Fetch pathway and gene data from KEGG API
• ChEMBL_Fetcher - Fetch bioactivity data from ChEMBL API
• QuickGO_Fetcher - Fetch GO annotations from QuickGO API
• HPA_Fetcher - Fetch protein expression from Human Protein Atlas
• NCBI_Fetcher - Fetch gene data from NCBI Entrez
• FDA_Fetcher - Fetch drug/device data from openFDA
• Reactome_Fetcher - Fetch pathway data from Reactome
• DO_Fetcher - Fetch disease terms from Disease Ontology
• EnrichR_Fetcher - Perform gene set enrichment via EnrichR
• HGNC_Fetcher - Fetch gene nomenclature from HGNC
• ClinVar_Fetcher - Fetch clinical variant data from ClinVar

Key Functions

• uniprot_get_entry - Get a UniProt entry by accession
• uniprot_search - Search UniProtKB with query
• pubchem_get_compound - Get compound by CID
• ensembl_lookup - Lookup entity by Ensembl ID
• kegg_get - Get KEGG entry by ID
• kegg_link - Get cross-references between databases
• hgnc_fetch_by_symbol - Fetch gene by approved symbol
• hgnc_search_symbol - Wildcard search on gene symbols
• clinvar_search_gene - Search and fetch variants for a gene
• clinvar_fetch_by_id - Fetch variant summaries by variation UID

Full Fetch API Reference

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biodbs.translate

ID translation between biological databases.

Enums

• GeneIDType - Universal gene ID type aliases (resolved per backend)
• TranslationDatabase - Available translation backends

Gene Translation

• translate_gene_ids - Translate gene IDs between databases
• translate_gene_ids_kegg - Translate gene IDs using KEGG API

Protein Translation

• translate_protein_ids - Translate protein IDs via UniProt ID mapping
• translate_gene_to_uniprot - Map gene symbols to UniProt accessions
• translate_uniprot_to_gene - Map UniProt accessions to gene symbols
• translate_uniprot_to_pdb - Map UniProt accessions to PDB IDs
• translate_uniprot_to_ensembl - Map UniProt accessions to Ensembl gene IDs

Chemical Translation

• translate_chemical_ids - Translate chemical IDs via PubChem
• translate_chembl_to_pubchem - Map ChEMBL IDs to PubChem CIDs
• translate_pubchem_to_chembl - Map PubChem CIDs to ChEMBL IDs

Full Translate API Reference

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biodbs.analysis

Statistical analysis and enrichment functions.

Classes

• ORAResult - Container for over-representation analysis results
• ORATermResult - Single term result from ORA
• Pathway - Represents a biological pathway with gene sets

Enums

• Species - Supported species for ORA
• GOAspect - Gene Ontology aspects (BP, MF, CC)
• CorrectionMethod - Multiple testing correction methods
• TranslationDatabase - Backends for automatic ID translation in ORA
• PathwayDatabase - Pathway database sources

ORA Functions

• ora - Generic ORA against any gene sets or GMT file
• ora_kegg - ORA against KEGG pathways
• ora_go - ORA against Gene Ontology terms
• ora_reactome - ORA against Reactome pathways (API)
• ora_reactome_local - ORA against Reactome pathways (local)
• ora_enrichr - ORA via EnrichR web service

GMT Functions

• load_gmt - Load a GMT file into Pathway objects
• save_gmt - Write Pathway objects to a GMT file
• fetch_gmt - Fetch gene sets from KEGG or EnrichR as GMT

Utility Functions

• hypergeometric_test - Compute hypergeometric p-value
• multiple_test_correction - Apply multiple testing correction

Full Analysis API Reference

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biodbs.graph

Knowledge graph building and analysis.

Classes

• KnowledgeGraph - Container for nodes and edges with graph operations
• Node - Represents a biological entity
• Edge - Represents a relationship between nodes

Enums

• NodeType - Types of nodes (GENE, PROTEIN, DISEASE, etc.)
• EdgeType - Types of edges (IS_A, PART_OF, etc.)
• DataSource - Data sources (DISEASE_ONTOLOGY, GENE_ONTOLOGY, etc.)

Builder Functions

• build_graph - Build graph from nodes and edges
• build_disease_graph - Build graph from Disease Ontology data
• build_go_graph - Build graph from QuickGO data
• build_reactome_graph - Build graph from Reactome data
• build_kegg_graph - Build graph from KEGG data
• merge_graphs - Merge multiple graphs

Export Functions

• to_networkx - Export to NetworkX DiGraph
• to_json_ld - Export to JSON-LD for KG-RAG
• to_rdf - Export to RDF format
• to_neo4j_csv - Export to Neo4j CSV format
• to_cypher - Generate Cypher queries

Utility Functions

• find_shortest_path - Find shortest path between nodes
• find_all_paths - Find all paths between nodes
• get_neighborhood - Get nodes within N hops
• find_hub_nodes - Find highly connected nodes
• get_graph_statistics - Get graph statistics

Full Graph API Reference