ValWood
commented
12 months ago from
original comment https://github.com/pombase/website/issues/2053#issuecomment-1625501150
How should the phenotypes look? Some alleles have multiple associated phenotypes.
I think that's going to be a bit tricky, specially for famous alleles, like cdc25-22 and so, which will have many many phenotypes. If there is an ontologic way to restrict to the high order terms that would be the best, I think (some kind of slim, but not sure that's possible).
However, I am not sure variant -> phenotype is the most meaningful link. Probably the user would like to see which alleles give a certain phenotype, rather than what a particular sequence modification does when hovering over it. This does not seem possible/easy on the gene page. However, if we are still thinking of a separate view like the one in the PDB, in which the sequence opens in a different window and you also have the structure, then we could have a scrollable list of all phenotypes like in the gene page, where the user can pick some and only the alleles that give those phenotypes can be displayed. In the same way, it could be that when you click on a particular modification, a list with all phenotypes associated with the modification is rendered below the graph (clearly this cannot be a tooltip when mouseover).
I thought what would be really nice instead of a phenotype list is to have some ontology tree with only the FYPO terms of that gene so you can also pick high-order terms, but then I had a look at the cut phenotype tree in OLS and realised that it would look atrocious (https://www.ebi.ac.uk/ols4/ontologies/fypo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FFYPO_0000229). That tree is for one term only! Admitedly, perhaps one of the most connected, and famous phenotypes in pombe, but still...
@manulera
@ValWood This would be very useful. I wonder if it could operate like the filters so you would check specific phenotypes and modifications and the display would reduce to show only those.