cmungall
commented
7 years ago It always helps to look at defs. The DO class has no def here, but properties of parent defs are inferred.
- NCIT:C7113 ! Endometrioid Tumor *** [DEF: "A benign, borderline, or malignant epithelial tumor of the female reproductive system characterized by the presence of glands and/or cysts lined by neoplastic cells that resemble endometrial cells."]
The NCIT class is explicitly malignancy-neutral
is_a DOID:162 ! cancer [DEF: "A disease of cellular proliferation >>>>>that is malignant<<<< and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis."]
is_a DOID:0050686 ! organ system cancer [DEF: "A cancer that is classified based on the organ it starts in."]
is_a DOID:193 ! reproductive organ cancer [DEF: "An organ system cancer that is manifested in the reproductive organs."]
is_a DOID:120 ! female reproductive organ cancer [DEF: "A reproductive organ cancer that is manifested in the female genitals. This includes organs such as the ovaries, fallopian tubes, uterus, cervix, vagina and vulva."]
is_a DOID:3001 ! female reproductive endometrioid cancerthe DOID is malignant
what is confusing is that the DO has confusing EXACT syns that should be BROAD based on implicit malignancy-neutralness
id: DOID:3001
name: female reproductive endometrioid cancer
namespace: disease_ontology
synonym: "endometrioid neoplasm" EXACT [NCI2004_11_17:C7113]
synonym: "endometrioid tumor (morphologic abnormality)" EXACT [SNOMEDCT_2005_07_31:253013001]
synonym: "female reproductive endometrioid neoplasm" RELATED []
xref: NCI:C7113
xref: SNOMEDCT_US_2016_03_01:253013001
xref: UMLS_CUI:C0474809
is_a: DOID:120 ! female reproductive organ cancer
There are many examples of DO terms mapped to NCIT, where they use 'cancer' in the label and NCIT uses 'neoplasm'. I think these mappings are incorrect. An example is below.
More examples are in this spreadsheet.
Not sure if NCIT tumor terms should be mapped to DO cancer terms. An example is below.