Interactions

1. proteinSequence

Processes and adds protein sequence information to a ComponentDefinition object

Args:

• rowobj: an object that holds a row of data in a spreadsheet

should include:

• obj (ComponentDefinition): The SBOL object to which the sequence is linked
• col_cell_dict (dict): Dictionary where keys are column names and values are cell contents.

Process:

• iterates through the columns in ‘rowobj.col_cell_dict’
• if the value is a URL, it is appended to the ‘sequence’ attribute of the SBOL object
• if the value is a string of valid amino acid characters, it is cleaned (whitespace and * removed) and added as an SBOL Sequence object with appropriate encoding
• adds the Sequence object to the SBOL document and links it to the SBOL ComponentDefinition

2. encodesFor

Generates an SBOL ModuleDefinition for a DNA sequence that encodes a protein.

Args:

• rowobj: an object that holds a row of data in a spreadsheet

should include:

• obj_uri (str): URI of the DNA sequence
• col_cell_dict (dict): Dictionary where keys are column names and values are cell contents.
• “Encodes for" column in col_cell_dict, specifying the protein URI this DNA sequence encodes for

Process:

• extracts DNA component URI and protein component URI
• creates an SBOL ModuleDefinition with two functional components: DNA and protein
• adds an interaction of type 'genetic production' where the DNA acts as a template and the protein is the product
• ModuleDefinition and all associated entities (functional components, interactions, participations) are added to the SBOL document.

3. ** repressor**

Generates an SBOL ModuleDefinition for a DNA sequence and its repressor protein(s).

Args:

• rowobj: an object that holds a row of data in a spreadsheet

should include:

• obj_uri (str): URI of the DNA sequence
• col_cell_dict (dict): Dictionary where keys are column names and values are cell contents

Process:

• extracts DNA component URI and protein component URI
• iterates through the list of protein URIs from the appropriate column (which represents repressors)
• adds an interaction of type 'inhibition' where the DNA is inhibited by the repressor protein
• ModuleDefinition and all associated entities (functional components, interactions, participations) are added to the SBOL document

4. activator

Generates an SBOL ModuleDefinition for a DNA sequence and its activator protein(s).

Args:

• rowobj: an object that holds a row of data in a spreadsheet

should include:

• obj_uri (str): URI of the DNA sequence
• col_cell_dict (dict): Dictionary where keys are column names and values are cell contents

Process:

• extracts DNA component URI and protein component URI
• iterates through the list of protein URIs from the appropriate column (which represents activators)
• adds an interaction of type “stimulation” where the DNA is stimulated by the activator protein
• ModuleDefinition and all associated entities (functional components, interactions, participations) are added to the SBOL document

5. complexComponent

Generates an SBOL ModuleDefinition for the formation of a complex involving a protein and/or another molecule

Args:

• rowobj: an object that holds a row of data in a spreadsheet

should include:

• obj_uri (str): URI of the DNA sequence
• col_cell_dict (dict): Dictionary where keys are column names and values are cell contents

Process:

• extracts DNA component URI from ‘rowobj.obj_uri’
• iterates through the columns to identify the protein and molecule URIs
• creates an SBOL ModuleDefinition with functional components for the product, protein, and molecule
• adds an interaction of type 'non-covalent binding' where the protein and molecule react to form the product
• ModuleDefinition and all associated entities (functional components, interactions, participations) are added to the SBOL document