Ideas for improvements

[mmslindner]

Thanks for creating that great tool, it's really insightful to follow the evolution of the taxonomy.

There are two edge cases that are currently not captured yet in the time machine:

1. Deprecated taxon ids. For example, BK polyomavirus (tid: 10629) has been deprecated a while ago, but this information is not shown anywhere. A plus would be if you could link to taxa that are supposed to replace those deprecated taxa (Betapolyomavirus hominis (tid: 1891762) for BK polyomavirus)
2. Show synonyms. Sometimes, species are represented by different taxon ids with synonymous names. One such example is Emmonsia parva and Blastomyces parvus. Sometimes, one of the synonyms is getting deprecated after a while (see above).

So far, I have only used the web interface. Maybe some of that is already available when working with the code directly?

[audy]

Hi @mmslindner thanks for the suggestions. For 1, these are recorded in the sqlite database but they're not displayed in the web interface. Actually, they are displayed, but only because there's a bug. I think adding this would be straightforward 👍

Show synonyms

I'll look into this. I left this out of the MVP because I thought it could turn into a can of worms (i.e. what if synonyms change between versions?). However, I think it would be useful at the very least to redirect to the current scientific name for a given synonym.

[mmslindner]

Thank you! Indeed, synonyms can be messy... Also, finding out which is the current "correct" scientific name would require including other resources like ICTV