Add synonym type information to synonyms.tsv

[jar398]

Dear all,

I noticed that the file "synonyms.tsv" (downloaded from http://files.opentreeoflife.org/ott/)
includes both common names and scientific names in the same file but
each of the rows in the file is not labelled whether it is a common name or a scientific name.
Is there any way to find out more information about this?
Thank you very much in advance.

Best regards,
Krittameth T.

[jar398]

Jonathan A Rees [email protected]
to opentreeoflife
... The synonyms file ought to have not just the type information (e.g. common name) but the source (NCBI, GBIF, etc.). It's not a huge project but it does require changing the internal representations in the taxonomy generator.

One question I have is whether we should have the common names in there at all. Often the same common name is a 'synonym' for dozens of species and this kind of screws up our alignment code. Also common names never occur as OTU labels in studies, and study OTUs is the main raison d'etre for OTT. What do you think, remove the common names?

[jar398]

This is implemented. Now we need a way to access this information from taxomachine. Issue: OpenTreeOfLife/taxomachine#142