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obophenotype / human-phenotype-ontology

Ontology for the description of human clinical features
http://obophenotype.github.io/human-phenotype-ontology/
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"Neoplasm by anatomical site" shouldn't be the parent of "Abnormality of the digestive system" #9938

Closed birkanozer closed 11 months ago

birkanozer commented 1 year ago

HPO term [Term] id: HP:0034930 name: Digestive system neoplasm def: "A tumor (abnormal growth of tissue) of the digestive system." [] is_a: HP:0025031 ! Abnormality of the digestive system property_value: http://purl.org/dc/elements/1.1/date "2023-07-09T14:37:49Z" xsd:dateTime property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-0736-9199

[Term] id: HP:0025031 name: Abnormality of the digestive system comment: Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus. is_a: HP:0011793 ! Neoplasm by anatomical site property_value: http://purl.org/dc/elements/1.1/date "2016-08-27T13:44:32Z" xsd:dateTime property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-0736-9199

Bug description On the July 2023 version, a new HPO term of "Digestive system neoplasm" added to the ontology. The immediate parent of this HPO term is "Abnormality of the digestive system". As you can see on above the immediate parent of the "Abnormality of the digestive system" is "Neoplasm by anatomical site". If we follow the tree to the leaf nodes of the "Abnormality of the digestive system", we find this section below:

Abnormality of the digestive system Abnormality of digestive system physiology Abdominal symptom Abnormal bowel sounds Nausea and vomiting Constipation Abdominal pain Protein avoidance Diarrhea ...

Since "Neoplasm by anatomical site" is the sole parent of the "Abnormality of the digestive system", all the terms in the tree above are listed as a subset of "Neoplasm". Sure, we can see this symptoms in neoplasms, but the neoplasms are neither most common nor only reason of this symptoms. I think, "Digestive system neoplasm" should have 2 parents, "Abnormality of the digestive system" and "Neoplasm by anatomical site", and the relations of the "Abnormality of the digestive system" should revert back the June 2023 version of the ontology.

LCCarmody commented 1 year ago

Hi, I noticed this too...but checking out the HP-edit file and OLS, it appears to be fixed. Could you check if this is still an issue for you?

birkanozer commented 11 months ago

Yes it looks like the problem has been fixed.

LCCarmody commented 11 months ago

Great! Thanks for reporting. Closing.