Trait databases: Metadata submission repo

• Overview
• Description
• Get started
• Contributing
• Citation
• Acknowledgments
• References

Overview

This repository is a bank centralizing metadata files describing various published trait databases.

Its content (folder metadata/) is used by the R package traitdatabases to download, import, clean, and homogenize trait data.

Description

The metadata file describes all information needed to document and process the trait database. It is structured in four sections:

• status: the status of the metadata file
• dataset: general metadata of the dataset
• taxonomy: information about taxonomic columns
• traits: description of the trait data

Section status

Tag name	Description	Example
status	The status of the metadata file. Should be one of: - draft - incomplete (some metadata need to be added) - complete (all metadata has been filled in)	draft

Section dataset

Tag name	Description	Example
id	The dataset identifier1. It's up to you to choose this identifier. Can be the name of the database, the first author and year, etc.	hodgson_2023
title	The dataset title. Typically the title of the (data) paper.	"A functional trait database of arable weeds from Eurasia and North Africa"
description	A short description of the dataset	"The functional traits of […] for 928 arable weed species."
license	The dataset license.	CC BY-SA 4.0
bibtex	The name of the dataset citation file in a BibTex format (optional)	hodgson_2023.bib
doi	The Digital Object Identifier (DOI) of the dataset description	10.5287/ora-pp4y9nkoz
url	The URL of the dataset description (paper)	https://ora.ox.ac.uk/objects/uuid:abafafd9-e8a2-4e84-a339-0a11bf2858ae
taxon	The taxonomic group (mammals, birds, etc.)	plants
taxonomic_level	The taxonomic resolution (individuals, species, genus, etc.)	species
type	One of: - static (a file that can be downloaded) - api (access data through a query)	static
file_url	The full URL to download the static file. NB. Equal to .na if type: api	https://ora.ox.ac.uk/objects/uuid:abafafd9-e8a2-4e84-a339-0a11bf2858ae/files/s8p58pf68w
file_name	The name of the static file (with file extension). NB. Equal to .na if type: api	Functional+trait+database+of+arable+ weeds+from+Eurasia+and+ North+Africa.xlsx
file_extension	The file extension of the static file. NB. Equal to .na if type: api	.xlsx
manual_download	Does the data file need to be manually downloaded? One of: - yes: only for specific cases like data hosted by Wiley Online Library - no: data file can be downloaded through command line (most cases) - .na: if type: api	no
sheet	The sheet number that contains data (only for xslx file) NB. Equal to .na for non Excel file or if type: api	1
long_format	Are the trait data in long format?. One of: - yes: data are in long format - no: data are in wide format (most cases) - .na: if type: api	no
skip_rows	The number of header rows to remove (if any)	.na
col_separator	The character used to separate columns (for txt or csv files)	.na
na_value	The characters used for missing values (if any)	NA
comment	Any relevant comment (if any)	.na

Section taxonomy

Tag name	Description	Example
genus	The column name of the genus (when species and genus names are separated)	.na
species	The column name of the species (when species and genus names are separated)	.na
binomial	The column name of the binomial name	Species

Section traits

Tag name	Description	Example
variable	The column name of the trait (as in the data file)	SLA
name	The full name of the trait	Specific leaf area
category	The category of the trait[^2]	Leaf morphology
type	The type of the trait. One of: - quantitative - categoric	quantitative
units	The "original" unit of the trait (for quantitative trait only)	mm2.mg-1

In the case of categorical traits, all categories should be listed with two fileds: value and description. This information describes each level of the categorical trait. For instance:

- variable: VEGPROP      
  name: Vegetative propagation of perennials
  category: reproduction
  type: categorical      
  units: .na 
  levels: 
  - value: 1            
    description: yes
  - value: 0 
    description: no 

Get started

Follow this 6-step procedure to submit a metadata file for a new trait dataset.

Before proceeding, make sure that the dataset you want to add is not already in traitdatabases-metadata.

Also, have a look at the example from the Hodgson et al. 2023 to understand which information is expected in each field.

1. Fork this repository

Click on the Fork icon on the top right of this repository.

click on ‘Create fork’

2. Install the traitdatabases package

## Install < remotes > package (if not already installed) ----
if (!requireNamespace(c("remotes", "here"), quietly = TRUE)) {
  install.packages(c("remotes", "here"))
}

## Install < traitdatabases > from GitHub ----
remotes::install_github("frbcesab/traitdatabases")

3. Create a new metadata file

Choose the name of your dataset. Then, use the function td_create_metadata_file as follow:

traitdatabases::td_create_metadata_file(
  name = "hodgson_2023", # name of your dataset
  path = here::here("metadata")
)

4. Complete the metadata

Depending on the format, open a text editor or excel to fill in the metadata.

It is recommended to add a bibtex file with the citation information of the trait database in the same folder as the metadata file.

5. Check and commit changes

Double check that everything is complete, without errors. Finally, update the status of the metadata file (‘complete’, or ‘incomplete’), stage the new files and commit the changes.

6. Make a pull request

This will contribute directly to the growth of the metadata on trait databases. Your pull request will be reviewed in the shortest delay.
Thank you for your contribution :)

Contributing

All types of contributions are encouraged and valued. For more information, check out our Contributor Guidelines.

Please note that the traitdatabases-metadata project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Citation

Please cite traitdatabases as:

Casajus N, Coux C & Frelat R (2025) traitdatabases: An R package to compile trait databases. R package version 0.0.0.9000. https://github.com/frbcesab/traitdatabases/

Acknowledgments

Coming soon…

References

Coming soon…

Footnotes

1. The dataset identifier should be short and should only contain letters, numbers and the symbol _. ↩