biocontext_kb.core.stringdb

biocontext_kb.core.stringdb#

Functions#

get_string_id(protein_symbol[, species, return_field, ...])

Map protein identifiers (gene names, synonyms, UniProt IDs) to STRING database IDs. Using STRING IDs improves reliability.

get_string_interactions(protein_symbol, species[, ...])

Retrieve protein-protein interactions for a given protein with scores above threshold. Always provide species parameter.

get_string_network_image(protein_symbol, species[, ...])

Generate protein-protein interaction network image from STRING database. Always provide species parameter.

get_string_similarity_scores(protein_symbol, ...[, ...])

Retrieve protein homology similarity scores from STRING database based on Smith-Waterman bit scores. Only scores above 50 reported.

Package Contents#

biocontext_kb.core.stringdb.get_string_id(protein_symbol, species='', return_field='stringId', limit=1)#

Map protein identifiers (gene names, synonyms, UniProt IDs) to STRING database IDs. Using STRING IDs improves reliability.

Returns:

STRING ID string (e.g., ‘9606.ENSP00000269305’) or dict with error message.

Return type:

str or dict

Parameters:

  • protein_symbol (Annotated[str, Field(description="Protein name or identifier (e.g., 'TP53')")])

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

  • return_field (Annotated[str, Field(description="Field to return: 'stringId' or 'preferredName'")])

  • limit (Annotated[int, Field(description='Maximum number of matches to return')])

biocontext_kb.core.stringdb.get_string_interactions(protein_symbol, species, min_score=700)#

Retrieve protein-protein interactions for a given protein with scores above threshold. Always provide species parameter.

Returns:

Protein interactions array with stringId_A, stringId_B, preferredName_A/B, score, evidence channels or error message.

Return type:

list or dict

Parameters:

  • protein_symbol (Annotated[str, Field(description="Protein name to search for (e.g., 'TP53')")])

  • species (Annotated[str, Field(description="Species taxonomy ID (e.g., '10090' for mouse)")])

  • min_score (Annotated[int, Field(description='Minimum combined score threshold (0-1000)', ge=0, le=1000)])

biocontext_kb.core.stringdb.get_string_network_image(protein_symbol, species, flavor='confidence', min_score=700)#

Generate protein-protein interaction network image from STRING database. Always provide species parameter.

Returns:

Network visualization as PNG image object or error message.

Return type:

Image or dict

Parameters:

  • protein_symbol (Annotated[str, Field(description="Protein name to search for (e.g., 'TP53')")])

  • species (Annotated[str, Field(description="Species taxonomy ID (e.g., '10090' for mouse)")])

  • flavor (Annotated[str, Field(description="Network flavor (e.g., 'confidence', 'evidence', 'actions')")])

  • min_score (Annotated[int, Field(description='Minimum combined score threshold (0-1000)', ge=0, le=1000)])

biocontext_kb.core.stringdb.get_string_similarity_scores(protein_symbol, protein_symbol_comparison, species='')#

Retrieve protein homology similarity scores from STRING database based on Smith-Waterman bit scores. Only scores above 50 reported.

Returns:

Similarity scores array with stringId_A, stringId_B, bitscore or error message.

Return type:

list or dict

Parameters:

  • protein_symbol (Annotated[str, Field(description="First protein symbol (e.g., 'TP53')")])

  • protein_symbol_comparison (Annotated[str, Field(description="Second protein symbol (e.g., 'MKI67')")])

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

Contents