/fungaltraits

A dynamic database of fungal trait measurements

Primary LanguageROtherNOASSERTION

fungaltraits aka funfun: a dynamic functional trait database for the world's fungi

DOIBuild Status

How to cite the DB?

Please cite this database as:

Flores-Moreno, Habacuc, Treseder, Kathleen, K., , Cornwell, William, K., Maynard, Daniel S., Milo, Amy, M., Abarenkov, Kessy, Afkhami, Michelle, E., Aguilar-Trigueros, Carlos, A., Bates, Scott, Bhatnagar, Jennifer, M., Busby, Posy, E., Christian, Natalie, Crowther, Thomas W., Floudas, Dimitri, Gazis, Romina, Hibbett, David, Kennedy, Peter, F., Lindner, Daniel, L., Nilsson, R. Henrik, Powell, Jeff, Schildhauer, Mark, Schilling, Jonathan, Zanne, Amy, E. 2019. fungaltraits aka funfun: a dynamic functional trait database for the world's fungi. Dataset: https://github.com/traitecoevo/fungaltraits. DOI

Table of content

How to use this package

Install the package

install.packages("devtools")
devtools::install_github("ropenscilabs/datastorr")
devtools::install_github("traitecoevo/fungaltraits")
library(fungaltraits)

Access the fungal traits database

fungal_traits()

This will download the data, and load it into R, and you're ready to do analyses. The meta-data associated with the data is in the zip file that can be downloaded here.

If you use this package in a published paper, please note the version number. This will allow others to reproduce your work later. There is a Zenodo DOI associated with each release, insuring that it will be stable in the future.

The current doi is DOI

That's it, really. Below is information about the data sources, how to contribute data and the versioned data distribution system (which we think is really cool), feel free to check it out, but you don't need to read the rest of this to use the package.

Collaboration with FUNGuild

funfun leverages the ecological guilds present in the FUNGuild dataset. Currently funfun collates the most common fungal guild at the genus level and matches it to each observation. As the end user wants different resolution a separate query to FUNGuild can be run.

Submission guidelines

Thank you for contributing to Funfun (a fungal functional trait database). Below you will find a simple set of instructions to contribute to this DB. For assistance or enquiries please contact funtothefun@gmail.com. Before submitting keep in mind that this a living, open access DB, which we think is pretty cool (i.e. it will update as taxonomy changes, more data get added, and errors are corrected, all this while preserving previous versions; free on all restrictions on access).

Essential information

It is essential that in your submission at least include the information below (if you prefer to fill-in some templates follow this link):

  • Submission: Once that you have fill in the essential information detailed below submit your data to funtothefun@gmail.com

  • Data file: It must include a column with a scientific name (genus, genus and species epithet) for each entry (row), and a column for each other variable included. See an example here.

  • Units for each variable included in your data file: International system units are preferred. (i.e. g, kg, bp, etc) OR you can fill in the dataMatchColumns.csv file, see here .

  • Essential metadata: Provide here a descriptor of your study, to whatever detail you are willing, that will help end users when examining your data in the future. This often includes such information as “experiment_type” whether the data was collected in the lab, field, data compilation; “tissue_type” (did you measure sporocarps, mycelium, fruiting bodies?). Don’t really know what to include? See this file for some inspiration.

  • Reference for your study OR .bib file: Not published yet? Not a problem! Grab this template and fill in as much information as you can! We will update this information as studies get published. Just let us know.

  • Contact information: Please give us a name, email address and physical address for the main contact person in your study.

Note that comma-separated files (.csv) are the preferred format for these files.

Data sources

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  • Kojta, Anna K., Grażyna Jarzynska, and Jerzy Falandysz. "Mineral composition and heavy metal accumulation capacity of Bay Bolete (Xerocomus badius) fruiting bodies collected near a former gold and copper mining area." Journal of Geochemical Exploration 121 (2012): 76-82.

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  • Wang, Xue-Mei, et al. "Content and bioaccumulation of nine mineral elements in ten mushroom species of the genus Boletus." Journal of analytical methods in chemistry 2015 (2015).

  • Wang, Xue-Mei, et al. "Variations in element levels accumulated in different parts of Boletus edulis collected from Central Yunnan Province, China." Journal of Chemistry 2015 (2015a).

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  • Zeng, X., et al. "Antioxidant capacity and mineral contents of edible wild Australian mushrooms." Revista de Agaroquimica y Tecnologia de Alimentos 18.4 (2012): 367-379.

  • Zhang, Dan, et al. "TraceeElements in Leccinum scabrum mushrooms and topsoils from Klodzka Dale in Sudety Mountains, Poland." Journal of Mountain Science 10.4 (2013): 621-627.

Funfun DB governance:

Endophytes:

Genes and Chemistry:

Guilds:

Mycorrhizae:

Pathogens:

Saprobes:

Taxonomy:

Database:

Notes for making a release using this living dataset design

This is for database maintainers

  • Update the DESCRIPTION file to increase the version number. Once we are past version 1.0.0, we will use semantic versioning so be aware of when to change what number.
  • Rebuild funtothefun.csv and funtothefun.zip making whatever improvements/fixes are necessary
  • Commit data and code changes and DESCRIPTION and push to GitHub
  • With R in the package directory, run
fungaltraits:::fungal_traits_release("<description>")

where "<description>" is a brief description of new features of the release.