ols_lookup module
- ols_lookup.calculate_overlap(str1, str2)[source]
Calculate the overlap between two strings.
Parameters: str1 (str): The first string. str2 (str): The second string.
Returns: float: The overlap between the two strings.
- ols_lookup.fetch_searchStr_info(searchStr, type='class,individual', ontology_name=None)[source]
Fetch searchStr information from the EBI OLS4 API.
Parameters: searchStr (str): The search string. type (str): The type of search. Default is ‘class,individual’. ontology_name (str): The name of the ontology. Default is None.
Returns: dict: The JSON response from the API.
- ols_lookup.find_best_match(part, labels)[source]
Find the best match for a given part in a list of labels.
Parameters: part (str): The part to match. labels (list): A list of labels.
Returns: str: The best match.
- ols_lookup.generate_substrings(input_string)[source]
Generate all possible substrings from a given string.
Parameters: input_string (str): The input string.
Returns: list: A list of substrings.
- ols_lookup.get_matching_entries(searchStr, type=None, ontology_name=None)[source]
Get matching entries for a given searchStr.
Parameters: searchStr (str): The search string. type (str): The type of search. Default is None. ontology_name (str): The name of the ontology. Default is None.
Returns: tuple: A tuple containing a list of labels and a list of entries.
- ols_lookup.main(input_string, output_format, type=None, ontology_name=None)[source]
Main function to handle the input and output.
Parameters: input_string (str): The input string. output_format (str): The output format. type (str): The type of search. Default is None. ontology_name (str): The name of the ontology. Default is None.