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SED-ML / KiSAO

Ontology of algorithms for analyzing biological models, their parameters, and their outputs
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Some KISAO terms do not match KISAO pattern #97

Closed matthiaskoenig closed 3 years ago

matthiaskoenig commented 3 years ago

The following terms have incorrect ids (the trailing _ is incorrect):

http://www.biomodels.net/kisao/KISAO#_KISAO_0000800
http://www.biomodels.net/kisao/KISAO#_KISAO_0000801
http://www.biomodels.net/kisao/KISAO#_KISAO_0000802
http://www.biomodels.net/kisao/KISAO#_KISAO_0000803
http://www.biomodels.net/kisao/KISAO#_KISAO_0000804
http://www.biomodels.net/kisao/KISAO#_KISAO_0000805
http://www.biomodels.net/kisao/KISAO#_KISAO_0000806
http://www.biomodels.net/kisao/KISAO#_KISAO_0000807
http://www.biomodels.net/kisao/KISAO#_KISAO_0000808
http://www.biomodels.net/kisao/KISAO#_KISAO_0000809
http://www.biomodels.net/kisao/KISAO#_KISAO_0000810
http://www.biomodels.net/kisao/KISAO#_KISAO_0000811
http://www.biomodels.net/kisao/KISAO#_KISAO_0000812
http://www.biomodels.net/kisao/KISAO#_KISAO_0000813
http://www.biomodels.net/kisao/KISAO#_KISAO_0000814
http://www.biomodels.net/kisao/KISAO#_KISAO_0000815

Code example:

for term_id in kisao._ontology:
    if "KISAO#_KISAO_" in term_id:
        # logger.warning(f"Incorrect kisao id: {term_id}")
        print(term_id)
        continue
    try:
        kisao_id = kisao_ontology.get_normalized_id(term_id.split('#')[1], dialect=IdDialect.kisao)
    except (KeyError, ValueError) as err:
        print(f"Missing entries: {term_id}")
        print(err)
jonrkarr commented 3 years ago

These are the terms @luciansmith created. These ids need to be corrected.

jonrkarr commented 3 years ago

These ids also should have been added sequentially, starting from the greatest existing id.

jonrkarr commented 3 years ago

Corrected in 2.21.