biocontext_kb.core.uniprot

biocontext_kb.core.uniprot#

Functions#

get_uniprot_id_by_protein_symbol(protein_symbol[, species])

Retrieve UniProt accession ID from protein name and species. Returns the primary accession or None if not found.

get_uniprot_protein_info([protein_id, protein_name, ...])

Retrieve protein information from UniProt database. Provide at least one of protein_id, protein_name, or gene_symbol.

Package Contents#

biocontext_kb.core.uniprot.get_uniprot_id_by_protein_symbol(protein_symbol, species='9606')#

Retrieve UniProt accession ID from protein name and species. Returns the primary accession or None if not found.

Returns:

UniProt accession ID string (e.g., ‘P04637’) or None if not found.

Return type:

str or None

Parameters:

  • protein_symbol (Annotated[str, Field(description="Gene or protein name to search for (e.g., 'SYNPO')")])

  • species (Annotated[str, Field(description="Organism taxonomy ID (e.g., '9606' for human)")])

biocontext_kb.core.uniprot.get_uniprot_protein_info(protein_id=None, protein_name=None, gene_symbol=None, species=None, include_references=False)#

Retrieve protein information from UniProt database. Provide at least one of protein_id, protein_name, or gene_symbol.

Returns:

Protein information with accession, proteinDescription, genes, organism, sequence, functions, keywords, references or error message.

Return type:

dict

Parameters:

  • protein_id (Annotated[Optional[str], Field(description="Protein accession number (e.g., 'P04637')")])

  • protein_name (Annotated[Optional[str], Field(description="Protein name to search for (e.g., 'P53')")])

  • gene_symbol (Annotated[Optional[str], Field(description="Gene symbol to search for (e.g., 'TP53')")])

  • species (Annotated[Optional[str], Field(description="Taxonomy ID (e.g., '10090') or species name")])

  • include_references (Annotated[bool, Field(description='Include references and cross-references in response')])

Contents