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How do you model normal/unchanged? #758
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Yes, this is an issue for the call - and one of the largest headaches. Most resources assume that "no phenotype" means "wild type"; but for a huge chunk of the data in MODs, that is simply untrue. In MGI, for example, "no phenotype" or "normal phenotype" means "no phenotype compared to control". The solution to this problem is to get sources to release the "comparator" of the phenotypic effect - when no comparator is given we assume no/rmal means wild. I actually kinda like "wild type" much more than "normal phenotype" - because it makes that explicit! Lets have a good discussion. |
Yes, should be a good discussion. We typically have a note that provides information about which phenotypes were checked and the linked reference should give more info. The parent strain will also be linked in our emerging database. |
I tend to bang on to the effect that there's no such thing as "no phenotype" - every living thing has a phenotype! Anyway, we all know "no phenotype" is just a lazy way of saying "no difference from control (which is usually wild type)", so moving on .... FYPO has a big "normal phenotype" branch (see FYPO:0000257), with a lot of terms that allow us to specify which process, structure, etc. is normal. All the text definitions expliticly say normal = indistinguishable from wild type. It also makes our lives easier that the vast majority of FYPO usage is for S. pombe, and the vast majority of S. pombe experiments use the same strain background as "wild type". We provide instructions for annotators that includes this blurb about "normal":
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@mah11 how to you deal with the 'normal' qualifier in UPHENO? |
The MP also has a branch for normal phenotype (MP:0002873) which has the direct children "no abnormal phenotype detected" (http://purl.obolibrary.org/obo/MP_0002169) and "phenotypic reversion" |
That's probably a question for @matentzn or @dosumis or ?? ... at least, I don't think I have a good answer yet. FYPO logical definitions follow a de-facto pattern that uses a 'normal' qualifier that's analogous to 'abnormal, but 'normal yada' patterns haven't made it into the uPheno collection yet :/ FYPO LDs may end up changing when uPheno does have patterns for normal/wild type/whatever.
Because we think of (and define) 'normal' as "same as wild type" for fission yeast, I don't have a preference either way (beyond the small thing that leaving our term names as "normal" will save some text editing). I wouldn't call a cell "wild type" unless all of its attributes are normal, whereas FYPO has a lot of 'normal X' phenotype terms that are defined as "X is normal (but implicitly, Y or Z may be normal or abnormal)". But for each attribute, "normal thing" still means "this thing is the same as in a completely wild-type cell" (and of course, cell = organism for us).
Me too, but I suspect that if it were easy, we wouldn't still be working on it! |
We have nearly 3,000 annotations to wild type. Just starting to inspect, we also have rescued mutants annotated with 'wild type'. A note like this: "rescues actin incorporation into the cytoskeleton, pseudopod formation, cel motility and morphology, phagocytosis, and chemotaxis defects" This would be a lot of 'normal phenotypes'. |
When researchers investigate developmental and / or cellular phenotypes and find no difference to parental strain, we annotate this as DDPHENO:0000142 wild type.
We have over 4,000 thus annotations and users find them valuable info as they come with distinct references.
Do others annotate when no phenotype has been detected with the methods used in the reference?
If yes, how do others annotate these?
Maybe a topic for a phenobarbitals call, thanks!
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