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Logical definition of "ovarian granulosa cell tumor" is redundant #8268
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Thanks @matentzn - that was my general impression from the qc error log. Did you come across why this happened now as a result of running the refresh imports? @sabrinatoro or @nicolevasilevsky are either of you able to take the curator role on this to resolve this issue? |
It is either due to changes in CL classification (one that made granulosa cell part of the ovaries) or because the role chain |
no, I can't, sorry |
A quick fix is to remove the logical definition of ovarian granulosa cell tumor, but someone should probably google the following: Are all granulosa cell tumors are by definition "ovarian"? |
From a few references I've seen:
|
here's the issue id: MONDO:0006036
name: granulosa cell tumor
def: "A slow-growing, malignant tumor, characterize by the presence of granulosa-like cells and Call-Exner bodies, that is almost always found in the ovary. In rare cases, it has also been found in the testicle. There are two types of granulosa cell tumor that can be distinguished under the microscope: the adult and the juvenile. The testicular juvenile granulosa cell tumors are perhaps the most common congenital testicular neoplasms." [NCIT:C3070]
intersection_of: MONDO:0005070 ! neoplasm
intersection_of: disease_has_location CL:0000501 ! granulosa cell we need better DPs for neoplasm->CL |
I agree with everything said here. In addition:
PR has been updated; waiting for QC checks to run. |
Sure, I added an issue referencing back to this for more details. |
#8262(closed)#8264 caused the following failure as pointed out by @twhetzel:DISJOINT-SIB-OF ovarian granulosa cell tumor SubClassOf Nothing
Axiom Impact
Axioms used 1 times
The problem is a bit opaque as it is caught by an ancient check which has long since been superceded by
robot reason --allow-equivalent-classes none
(the test injects hypothetical siblings and makes sure they can theoretically exist, thereby ensuring a child is not the same as its parent).Here is the issue:
granulosa cell tumor
is defined as a granulosa cell tumor EquivalentTo neoplasm and (disease has location some granulosa cell) and ovarian granulosa cell tumor is defined as a granulosa cell tumor and (disease has location some ovary). Unfortunately, through a chain of inference in CL, granulosa cell is considered a part of theovaries
. So saying that ovarian granulosa cell tumor is has (disease has location some ovary) is redundant, therefore the two classes are considered the same.This is a great catch by QC. My assumption is that either the fact that granulosa cell is considered a part of the
ovaries
is wrong, or ovarian granulosa cell tumor is logically underspecified!The text was updated successfully, but these errors were encountered: