pato
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pato-ontology
ectopic in PATO
see MP ticket https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2930
Summary of the issue is that ectopic should not be a synonym of mislocalised (PATO:0000628) there are subtle yet important differences. Suggest adding a term for ectopic.
I think it should be a subclass of mislocalised. Being mislocalized is necessary but not sufficient: See cyclopia & any other general shift in pattern (e.g. dorsalization of a fly larva or of a wing). I think the context is important - if the whole patterning of a structure shifts, developmental biologists wouldn't typically use the term 'ectopic' - but they would if something forms in the context in which it's not normally found. e.g. a macrochaeta (large bristle) forming in an eye or an ommatidium forming on a leg.
Homeotic transformations might sometimes be a grey area. FlyBase has a 'ectopic' as a qualifier used in phenotype curation. Might be helpful to review those. l can try to pull together a report of examples.
We may also want to ask Chris Grove to add some worm examples. I'll email him to ask.
@sbello @dosumis I've gathered all the definitions of worm phenotype terms referring to 'ectopic', and I have some issues with the current definitions (I intend to change the definitions or create other terms). I also looked up the term 'ectopic' in NCBO Bioportal (most refer to PATO term 'mislocalised'), in the literature (a little bit on earliest references in PubMed ~1890-1910), and dictionary references as well as a Google etymology search result:
https://docs.google.com/spreadsheets/d/1izCT_wm-Y_EtO_dFpUqTPImlFD3bpx2RncX4w9uZ2pw/edit?usp=sharing
I think it seems pretty clear that 'ectopic' means 'out of place' or 'in an abnormal position or place' or 'displaced'. Earliest references in the biomedical literature appear to be to 'ectopic gestation'/'ectopic pregnancy' and a little later to 'ectopic beats' as in heartbeats occurring at abnormal points in the heart. I would be wary of implying or suggesting that it means something more specific unless there has been a clear declaration of a new use of the word in the biomedical literature somewhere at some point. The term 'mislocalised'/'mislocalized' has many instances in NCBO BioPortal as well, all seemingly stemming from the PATO term.
