alrichardbollans / mining_trait_data

Collection of methods for extracting and compiling plant trait data

Python packages for gathering plant trait data

Disclaimer

WARNING: The information contained herein is provided as a public service with the understanding that authors make no warranties, either expressed or implied, concerning the accuracy, completeness, reliability, or suitability of the information.

In particular, concerning lists of poisonous/toxic plants --- just because a plant is not on the list DOES NOT mean that it is not dangerous/poisonous/toxic. Similarly, concerning lists of non_poisonous plants --- just because a plant is on the list DOES NOT mean that it is not dangerous/poisonous/toxic.

Installation

pip install git+https://github.com/alrichardbollans/[email protected]

Sources

See cite.txt file in each package for lists of sources.

Name resolution

Names from different datasets are matched using the wcvpy package (https://github.com/alrichardbollans/wcvpy)

Metabolite Methods

Note that methods related to metabolite data have been moved to: https://github.com/alrichardbollans/phytochempy

mining_trait_data's Issues

Include complete datasets here

i.e. those not restricted taxonomically or geographically (e.g. poison vars)

Pykew install

For powo searches, the installation of pykew currently needs modifying as per the commit here: RBGKew/pykew@5363379

However, the relevant functions should be made to work with the existing version of pykew

Moving portals to POWO

May need to update various methods related to WCVP/WCSP and POWO following:
https://powo.science.kew.org/upcoming-changes

Spatial autocorrelation

Add methods to clean_plant_occurrences to thin occurrence datasets by e.g. keeping only one record per 10 x10 arcmin grid cell to limit spatial autocorrelation (as in Pengjuan Zu et al., ‘Pollen Sterols Are Associated with Phylogeny and Environment but Not with Pollinator Guilds’, New Phytologist 230, no. 3 (May 2021): 1169–84, https://doi.org/10.1111/nph.17227.)

Citations

Improve citation guidelines for each package

More data sources

Many of the given feature also appear in the relatively comprehensive Dr. Duke's Phytochemical and Ethnobotanical Databases, so would be helpful to incorporate this.

Source filters

Allowing filtering by source, and better documentation of validity of sources

Catch empty dataframes in cleaning

Currently when empty dataframes without the 'Accepted_Name' column are passed to compile_hits an error is raised. However, these dataframes should just be ignored. Moreover, when an empty list of dataframes is passed to this method an error is raised. it would be better in this instance if an empty csv is output with the usual headings

Unnecessary imports on module loading

The modules are set up to import everything necessary for all the methods in the module to run. However, this means that every usage of the module requires all the libraries even if only a variable is required. For example, getting the poison data ends up requiring an install of pykew from powo_searches, which is totally unnecessary. Fix this by only importing libraries within the functions where they are required.

Add source breakdown

Add a breakdown of sources, primarily number of hits (restricted by family)

Metabolite vars

Improve usability of metabolite searches by simplifying processes.

Add full occurrence pipeline

Using pygbif, add pipeline for downloading gbif occurrences and cleaning them.

Methods raising errors with no data

Some methods will end up raising an error when doing name matching in cases where no data is found e.g. when search_powo returns no hits it will try to do name matching on a nonexistent column.