WBbt:0005780, wrong 'is_a' relationship

[ANiknejad]

Hi Wormbase team,

I would like to draw your attention to this error:

[Term] id: WBbt:0005780 name: non-striated muscle is_a: WBbt:0003675 ! muscle cell => a muscle is not a cell

Kind regards,

Anne Niknejad bgee.org curator UNIL University of Lausanne

[raymond91125]

In C. elegnas (perhaps most nematodes), muscles are generally individualized as cells rather than tissues. See WormAtlas https://www.wormatlas.org/glossary/sglossary.htm#striatedmuscle. I hope this does not cause problems for you.

[chris-grove]

@raymond91125 I think we could address this issue by formally changing the name of the term "non-striated muscle" to "non-striated muscle cell" and define it as such (a cell). Likewise this could be done for all of the descendant terms.

[raymond91125]

Sure. The names without "cell" are in-line with WormAtlas usage thus should be kept in synonyms.

[matentzn]

I would generally strongly advice against this - now our species specific anatomy classes are being used outside our own mods, we should never migrate a term to mean something else just because the labels look similar. Unless muscle cell and muscle really mean the same, it would be better if you created new terms instead of renaming existing ones..

[chris-grove]

@matentzn The issue here is that in C. elegans, because it' such a small animal, it's pretty much true that each 'muscle' in the worm is an individual muscle cell, so they are essentially synonymous, although I would very much prefer to be explicit and label it as such ("a cell"). Here's a screenshot of the term and some of its descendants:

So "non-striated muscle" is a subclass of "muscle cell" essentially because the meaning is already "non-striated muscle cell" bit it isn't obvious the way the labels are constructed. I'm not suggesting changing the meaning of any existing term. I'm only suggesting that the labels are updated to properly reflect the actual meaning.