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mgijax / mammalian-phenotype-ontology

Standard terms for annotating mammalian phenotypic data
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review placement of organ tumor terms #4035

Open sbello opened 5 days ago

sbello commented 5 days ago

Some incidence in specific tissue tumor terms are under both neoplasia and the tissue morphology branches while others are only under neoplasia. We should review these and make sure they are consistent.

Example

sbello commented 3 days ago

What is the 'reticulum' in the term 'decreased reticular tumor incidence' MP:0020197 definition is: less than the expected number of neoplams in the reticulum, usually in the form of a distinct mass, in a specific population in a given time period Looking in Uberon I find UBERON:0007361 'ruminant reticulum' that has NCIT xref 'reticulum' but this seems wrong as there is a child term 'decreased mononuclear phagocyte tumor incidence' There is also stellate reticulum - part of the developing tooth UBERON:0006950 and eye trabecular network (reticulum in synonyms) but these also make no sense with the child term
There is also an increased incidence term with the same issues There are no annotations in RGD using either term Term was entered by @nicolevasilevsky back in 2014 so I'm guessing Nicole has no memory of these either. Searching pubmed for 'reticular tumor' (no quotes) turns up papers about Fibroblastic reticular-cell tumor CL has reticular cell maybe this is what it is? But I don't see mononuclear phagocyte as a decedent of reticular cell so the placement still doesn't make sense

Do we want to put blood cell specific terms under the cell morphology? Not so sure about this, it makes more sense for organs and tissues but not really for the cells.

sbello commented 3 days ago

removed the eq from increased lip tumor incidence - this was using lipoma which is just wrong

several other eqs are using the MP term 'neoplasm' - should these go as well?

sbello commented 3 days ago

increased mouth tumor incidence is under alimentary system tumor incidence but mouth morphology is under facial morphology and not under alimentary system, why?

sbello commented 3 days ago

why is facial tumor incidence under integument system incidence?