datasource: Funguild?

[zachary-foster]

I was recently working with a python script for looking up attributes of fungal species called funguild.

https://github.com/UMNFuN/FUNGuild

This python script expects a table with a column named "taxonomy" formatted in the UNITE taxonomy format (e.g. k__Fungi.p__Basidiomycota.c__Agaricomycetes.o__Agaricales.f__Strophariaceae.g__Psilocybe.s__Psilocybe_semilanceata). It calls the following API:

http://www.stbates.org/funguild_db.php

and returns info like:

> head(funguild_matrix[, 108:116])
               Taxon Taxon.Level Trophic.Mode                Guild Growth.Morphology     Trait Confidence.Ranking Notes                                                               Citation.Source
1          Psilocybe          13   Saprotroph Undefined Saprotroph         Agaricoid Poisonous           Probable  NULL                                  Tedersoo L, et al. 2014. Science 346:1256688
2    Ophiosphaerella          13   Saprotroph Undefined Saprotroph              NULL      NULL           Probable  NULL                                  Tedersoo L, et al. 2014. Science 346:1256688
3       Pringsheimia          13   Saprotroph Undefined Saprotroph              NULL      NULL           Probable  NULL                                  Tedersoo L, et al. 2014. Science 346:1256688
4           Hypocrea          13   Pathotroph         Mycoparasite              NULL      NULL    Highly Probable  NULL Tedersoo L, et al. 2014. Science 346:1256688; Samuels G. 2007, self published
5          Conlarium          13   Saprotroph Undefined Saprotroph              NULL      NULL           Probable  NULL                                  Tedersoo L, et al. 2014. Science 346:1256688
6 Sclerostagonospora          13   Saprotroph Undefined Saprotroph              NULL      NULL           Probable  NULL                                  Tedersoo L, et al. 2014. Science 346:1256688

The python script works ok, but I dont like how it needs a whole table in a specific format when it just uses one column.

Would this be something traits could/should implement? An R solution would be welcome! Thanks

[sckott]

Thanks @zachary-foster

Sounds good to me - you want someone else to do the R bit or did you want to? - happy to help

[zachary-foster]

Cool. I would not mind doing it, but I will not have time for a while probably and, since I got the python script to work for my immediate needs, it is not a priority for me right now. I was mostly just posting this as a record of the idea in case anyone else wanted to do it or if I had time to do it in the future.

[sckott]

Cool, thanks.

If anyone wants to do this go for it - I may do at some point if no one else does.

[wcornwell]

If you do get around to fungi, we'll have a growing set of fungal trait data here: https://github.com/traitecoevo/fungaltraits

should be eventually linked to unite, index fungorum, and funguild if everything goes as planned.

[sckott]

thx @wcornwell ! just submitted a new ver of this pkg to CRAN - will try to get to funguild soon

[maelle]

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