`term_callback` should check for obsolete ChEBI classes

[sfluegel05]

Test Case Failing for term_callback

A test case for term_callback is failing because it is not correctly ignoring/skipping obsolete ChEBI terms. As a result, the test cases for _extract_class_hierarchy and _graph_to_raw_dataset are also failing as output of term_callback are used by them.

Current Behavior:

• Right now, this failure does not seem to affect the current pre-processing pipeline with Real data, because obsolete ChEBI terms typically do not have SMILES strings.
• The _graph_to_raw_dataset method filters out data instances:
  • without SMILES strings:
  • without relationship to other instances

    data = data[~data["SMILES"].isnull()]
    data = data[data.iloc[:, self._LABELS_START_IDX:].any(axis=1)]

    So, even though obsolete terms are not specifically filtered, their lack of SMILES strings ensures they are excluded from the dataset.

Potential Future Issue:

• In future versions of ChEBI, if any obsolete terms do have SMILES strings and maintain relationships with non-obsolete terms, it could become a problem.
• Since the current filtering is based solely on non-null SMILES strings and relationships to other terms, there’s no explicit logic to filter obsolete terms.

Example of a Problematic Obsolete Term:

[Term]
id: CHEBI:77533
name: Compound G
is_a: CHEBI:99999
property_value: http://purl.obolibrary.org/obo/chebi/smiles "C1=C1Br" xsd:string
is_obsolete: true

If terms like this exist in future releases, the current approach could lead to errors because obsolete terms with SMILES strings might slip through the filters.

Proposed Solution: We can update the term_callback logic to explicitly ignore obsolete terms by checking for the is_obsolete clause:

if isinstance(clause, fastobo.term.IsObsoleteClause):
    if clause.obsolete:
        # If the term document contains an "obsolete: true" clause, skip this term.
        return False

This solution would ensure that obsolete terms are skipped before they are processed, preventing potential future issues with the dataset.

Originally posted by @aditya0by0 in https://github.com/ChEB-AI/python-chebai/issues/48#issuecomment-2332645174