Mole (unit vs skin blemish)

[zoependlington]

During the last release, one big issue was the duplicate of "mole", two terms with the same label but completely different definitions:

• UO_0000013 (mole) - "A mole is a substance unit which is equal to the amount of substance of a molecular system which contains as many elementary entities as there are atoms in 0.012 kilogram of carbon 12."
• UBERON_1000010 (mole) - A benign tumor on the skin, usually with darker pigment.

Currently the UBERON term is on the exclude list and is not in EFO. However, it is worth looking into as to whether we need the anatomy term in EFO.

We do currently have a disease term for:

• nevus (EFO_0000625) which has the synonym of mole of skin and skin mole - "Nevus (or naevus, plural nevi or naevi, from nævus, Latin for \"birthmark\") is the medical term for sharply circumscribed[1] and chronic lesions of the skin or mucosa. These lesions are commonly named birthmarks or beauty marks. Nevi are benign by definition. However, 25% of malignant melanomas (a skin cancer) arise from pre-existing nevi.[2] Using the term nevus and nevi loosely, most physicians and dermatologists are actually referring to a variant of nevus called the \"melanocytic nevus\", which are composed of melanocytes. Histologically, melanocytic nevi are distinguished from lentigines (also a type of benign pigmented macule) by the presence of nests of melanocytes, which lentigines (plural form of lentigo) lack."

[paolaroncaglia]

@zoependlington Wrt the skin term, my understanding, from prior knowledge and from a quick look at the Wikipedia entries for nevus and mole, is that 'mole' is a colloquial synonym for 'melanocytic nevus' (sure, the most common type of nevi), that the EFO term is the correct broad parent for all types of nevi including moles, and that the UBERON term may need revising. We should move mole-containing synonyms of EFO 'nevus' to EFO 'melanocytic nevus'. We could double-check this using a non-Wikipedia and non-UBERON reference. In fact, MONDO has 'mole' and 'mole of skin' as exact synonyms of 'melanocytic nevus'. Mondo doesn't have 'nevus'; their 'melanocytic nevus' is a subclass of melanocytic skin neoplasm benign neoplasm of skin

[paolaroncaglia]

Following up on this. Skin moles derive from "irregular" growth of cells, and as such, even when benign, I wouldn't consider them in scope for an anatomy ontology, but rather for a phenotype or disease one. So, I would keep UBERON_1000010 (mole) in the "exclude" list for EFO, as it is now. Suggestions on fixing mole- and nevi-related synonyms follow. "Mole" is used to refer to both 'nevus' and 'melanocytic nevus'. So, to be conservative, I'd suggest to link "mole" to the broader term 'nevus':

• [ ] Re. EFO:0000625 'nevus', I suggest to leave its existing synonyms as are, and add "mole" as related synonym (related, because it's a potentially ambiguous term, as in mole unit, or the mole animal);
• [ ] Re. EFO:0009675 'melanocytic nevus', I suggest to remove the following synonyms as they are (or will be) already present on its parent term 'nevus' above: "nevus", "mole" and "mole of skin". Check if they come from EFO or Mondo.
• [ ] MONDO:0005073 'melanocytic nevus' xrefs to EFO:0000625 'nevus' => ask them to change to EFO:0009675 'melanocytic nevus' Also,
• [ ] Check children of EFO:0000625 'nevus', there seems to be an Orphanet-derived issue... if the links are incorrect, do they come from/need to be fixed in EFO or Mondo? Or both?