Curie Validator
Documentation
- class pandasaurus.curie_validator.CurieValidator[source]
CurieValidator is responsible for validating CURIE prefixes and CURIEs of slim terms. It also suggests replacements for obsoleted slim terms.
- static construct_term_list(seed_list) List[Term][source]
Returns list of Term objects after running validate_curie_list and find_obsolete_terms methods.
- Parameters:
seed_list – A list of seed terms where each term is a CURIE string
- Returns:
List of Term objects
- abstract static find_obsolete_term_replacement(curie_list: Dict[str, str]) Dict[str, str][source]
Suggests terms for each obsoleted terms in the curie_list.
- Parameters:
curie_list – List of CURIEs
- Returns:
List of suggested term
- static find_obsolete_terms(curie_list: List[str]) Dict[source]
Returns obsoleted terms in the curie_list and label and IRI for of the term that is replaced the obsoleted terms.
- Parameters:
curie_list – List of CURIEs
Examples
An example output that shows 1 obsoleted CURIE:{‘CL:0011107’: {‘term’: ‘CL:0011107’, ‘label’: ‘obsolete Muller cell’, depr_status’: ‘true’,‘new_term’: ‘CL:0000636’, new_term_label’: ‘Mueller cell’}- Returns:
True or False status of the term for each term
- static get_validation_report(term_list: List[Term])[source]
Returns validation report which includes invalid and obsoleted terms.
- Parameters:
term_list – A list of seed terms where each term is a Term object
- static validate_curie_list(curie_list: List[str]) Dict[str, bool][source]
Reports whether the CURIEs are valid or not.
- Parameters:
curie_list – List of CURIEs
Examples
An example output that shows 2 valid and 1 invalid CURIEs:{‘CL:0002681’: {‘label’: ‘kidney cortical cell’, ‘valid’: True},‘CL:0002518’: {‘label’: ‘kidney epithelial cell’, ‘valid’: True},‘CL:1234567’: {‘label’: None, ‘valid’: False}}- Returns:
True or False status of the CURIE validation for each term