Naming Conventions Automated Check

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Naming Conventions Automated Check

Discussion on this check can be found here.

Requirements

  1. Each label must be unique.
  2. Each entity must not have more than one label.
  3. Each entity should have a label using rdfs:label.

Fixes

Uniqueness

Update at least one label to distinguish between the two terms. Add the original label to a oboInOwl:hasExactSynonym (alternatively, narrow, related, or broad) or IAO:0000118 (alternative term) annotation.

If the terms are exactly the same:

  1. Obsolete one of them by adding the owl:deprecated annotation property with a boolean value of true
  2. Add obsolete to the beginning of this term’s label
  3. Add a IAO:0100001 (term replaced by) annotation to this term pointing to the other, non-deprecated term.
    • Make sure this is an IRI annotation by selecting “IRI Editor” when adding the annotation in Protégé

Multiple Labels

Determine which label most accurately describes the term. Change the other label(s) to oboInOwl:hasExactSynonym (alternatively, narrow, related, or broad) or IAO:0000118 (alternative term).

Missing Labels

Add an rdfs:label annotation to each term that is missing a label. For adding labels in bulk, check out ROBOT template.

Implementation

ROBOT report is run over the ontology. A count of violations for each of the following checks is retrieved from the report object: duplicate label, multiple labels, and missing label. If there are any of these violations, it is an error.

import dash_utils
from dash_utils import format_msg


def has_valid_labels(report):
   """Check fp 12 - naming conventions.

   If the ontology passes all ROBOT report label checks, return PASS.

   Args:
       report (Report): complete ROBOT report

   Return:
       PASS, INFO, or ERROR with optional help message
   """
   if report is None:
       return {'status': 'INFO',
               'comment': 'ROBOT Report could not be generated'}

   # all error level
   duplicates = report.getViolationCount('duplicate_label')
   missing = report.getViolationCount('missing_label')
   multiples = report.getViolationCount('multiple_labels')

   if duplicates > 0 and multiples > 0 and missing > 0:
       # all three violations
       return {'status': 'ERROR',
               'comment': ' '.join([duplicate_msg.format(duplicates),
                                    multiple_msg.format(multiples),
                                    missing_msg.format(missing),
                                    help_msg])}
   elif duplicates > 0 and multiples > 0:
       # duplicate and multiple labels
       return {'status': 'ERROR',
               'comment': ' '.join([duplicate_msg.format(duplicates),
                                    multiple_msg.format(multiples),
                                    help_msg])}
   elif duplicates > 0 and missing > 0:
       # duplicate and missing labels
       return {'status': 'ERROR',
               'comment': ' '.join([duplicate_msg.format(duplicates),
                                    missing_msg.format(missing),
                                    help_msg])}
   elif multiples > 0 and missing > 0:
       # multiple and missing labels
       return {'status': 'ERROR',
               'comment': ' '.join([multiple_msg.format(multiples),
                                    missing_msg.format(missing),
                                    help_msg])}
   elif duplicates > 0:
       # just duplicate labels
       return {'status': 'ERROR',
               'comment': ' '.join([duplicate_msg.format(duplicates),
                                    help_msg])}
   elif multiples > 0:
       # just multiple labels
       return {'status': 'ERROR',
               'comment': ' '.join([multiple_msg.format(multiples),
                                    help_msg])}
   elif missing > 0:
       # just missing labels
       return {'status': 'ERROR',
               'comment': ' '.join([missing_msg.format(missing),
                                    help_msg])}
   else:
       # no label violations present
       return {'status': 'PASS'}


# violation messages
duplicate_msg = '{0} duplicate labels.'
multiple_msg = '{0} multiple labels.'
missing_msg = '{0} missing labels.'
help_msg = 'See ROBOT Report for details.'