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Hypermedia API for NCBO's ontology-related projects
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Inconsistent data returned by the /classes endpoint #65

Open mdorf opened 4 years ago

mdorf commented 4 years ago

This does not happen with every ontology. But while running the new server_data_comparator script, I've discovered the following behavior:

https://stagedata.bioontology.org/ontologies/PDQ/classes?no_links=true&no_context=true&display=prefLabel,synonym,definition,submission&pagesize=30

If you look for the class: "http://purl.bioontology.org/ontology/PDQ/CDR0000660818, you will discover the following output (note that "definition" is missing):

{
    "prefLabel": "perindopril erbumine",
    "synonym": [
        "Coversyl"
    ],
    "definition": [ ],
    "submission": "https://stagedata.bioontology.org/ontologies/PDQ/submissions/17",
    "@id": "http://purl.bioontology.org/ontology/PDQ/CDR0000660818",
    "@type": "http://www.w3.org/2002/07/owl#Class"
}

If you then change the order of the fields in the display parameter, the results come back with different fields populated. "definition" is now present, while "prefLabel" is null.

https://stagedata.bioontology.org/ontologies/PDQ/classes?no_links=true&no_context=true&display=synonym,definition,prefLabel,submission&pagesize=30

{
    "synonym": [
        "Coversyl"
    ],
    "definition": [
        "The tert-butylamine salt of perindopril, the ethyl ester of a non-sulfhydryl angiotensin converting enzyme (ACE) inhibitor with antihypertensive activity. Upon hydrolysis, perindopril erbumine is converted to its active form perindoprilat, inhibiting ACE and the conversion of angiotensin I to angiotensin II; consequently, angiotensin II-mediated vasoconstriction and angiotensin II-stimulated aldosterone secretion from the adrenal cortex are inhibited and diuresis and natriuresis ensue. Check for \"https://www.cancer.gov/about-cancer/treatment/clinical-trials/intervention/C47666\" active clinical trials using this agent. (\"http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C47666\" NCI Thesaurus)"
    ],
    "prefLabel": null,
    "submission": "https://stagedata.bioontology.org/ontologies/PDQ/submissions/17",
    "@id": "http://purl.bioontology.org/ontology/PDQ/CDR0000660818",
    "@type": "http://www.w3.org/2002/07/owl#Class"
}

This class contains both the prefLabel and definition, which is evident by running this call:

https://data.bioontology.org/ontologies/PDQ/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FPDQ%2FCDR0000660818?no_links=true&no_context=true&display=prefLabel,synonym,definition,submission

{
    "prefLabel": "perindopril erbumine",
    "synonym": [
        "Coversyl"
    ],
    "definition": [
        "The tert-butylamine salt of perindopril, the ethyl ester of a non-sulfhydryl angiotensin converting enzyme (ACE) inhibitor with antihypertensive activity. Upon hydrolysis, perindopril erbumine is converted to its active form perindoprilat, inhibiting ACE and the conversion of angiotensin I to angiotensin II; consequently, angiotensin II-mediated vasoconstriction and angiotensin II-stimulated aldosterone secretion from the adrenal cortex are inhibited and diuresis and natriuresis ensue. Check for \"https://www.cancer.gov/about-cancer/treatment/clinical-trials/intervention/C47666\" active clinical trials using this agent. (\"http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI%20Thesaurus&code=C47666\" NCI Thesaurus)"
    ],
    "submission": "http://data.bioontology.org/ontologies/PDQ/submissions/17",
    "@id": "http://purl.bioontology.org/ontology/PDQ/CDR0000660818",
    "@type": "http://www.w3.org/2002/07/owl#Class"
}

So, the order of the display parameters appears to affect the results, which should not be the case. This does not appear to be an issue across the board.

mdorf commented 4 years ago

Here is another example with SNOMED (Term with ID: http://purl.bioontology.org/ontology/SNOMEDCT/773397000)

https://data.bioontology.org/ontologies/SNOMEDCT/classes?no_links=true&no_context=true&display=prefLabel,synonym,definition,submission&pagesize=30

Produces:

{
    "prefLabel": "Non-hypoproteinemic hypertrophic gastropathy",
    "synonym": [
        "Hypertrophic gastropathy without hypoproteinemia"
    ],
    "definition": [ ],
    "submission": "http://data.bioontology.org/ontologies/SNOMEDCT/submissions/20",
    "@id": "http://purl.bioontology.org/ontology/SNOMEDCT/773397000",
    "@type": "http://www.w3.org/2002/07/owl#Class"
}

Where as:

https://data.bioontology.org/ontologies/SNOMEDCT/classes?no_links=true&no_context=true&display=synonym,definition,submission&pagesize=30

Produces:

{
    "synonym": [
        "Hypertrophic gastropathy without hypoproteinemia"
    ],
    "definition": [
        "A rare gastroesophageal disease characterized by diffusely enlarged gastric folds, excessive mucus secretion, normal serum protein and gastric TGF-alpha levels. Patients typically present anemia, abdominal pain not related to eating or bowel habits and absence of peripheral edema."
    ],
    "submission": "http://data.bioontology.org/ontologies/SNOMEDCT/submissions/20",
    "@id": "http://purl.bioontology.org/ontology/SNOMEDCT/773397000",
    "@type": "http://www.w3.org/2002/07/owl#Class"
}

The "definition" is absent in the first case and present in the second. The term itself contains both a prefLabel and definition:

https://data.bioontology.org/ontologies/SNOMEDCT/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FSNOMEDCT%2F773397000?no_links=true&no_context=true&display=prefLabel,synonym,definition,submission&pagesize=30

{
    "prefLabel": "Non-hypoproteinemic hypertrophic gastropathy",
    "synonym": [
        "Hypertrophic gastropathy without hypoproteinemia"
    ],
    "definition": [
        "A rare gastroesophageal disease characterized by diffusely enlarged gastric folds, excessive mucus secretion, normal serum protein and gastric TGF-alpha levels. Patients typically present anemia, abdominal pain not related to eating or bowel habits and absence of peripheral edema."
    ],
    "submission": "http://data.bioontology.org/ontologies/SNOMEDCT/submissions/20",
    "@id": "http://purl.bioontology.org/ontology/SNOMEDCT/773397000",
    "@type": "http://www.w3.org/2002/07/owl#Class"
}