In ropenscilabs/taxa: Classes for Storing and Manipulating Taxonomic Data

Goals of the taxa package

Encode taxonomic information from divserse sources

Taxonomic data can come from many different sources including:

• Sequence data annotations
• Occurance data annotations
• Taxonomy databases
• Museum records
• Species checklists
• Herbarium records

Each of these might encode taxonomic data in different ways. Sometimes the taxonomic data itself is the focus and sometimes it is only one of many ways to annotate the data. Therefore taxa needs to be intuitve enough so that users not interested in the intirciaes of taxonomy can ignore them, while sill allowing for more adavnce usages when needed.

Combine taxonomic data from multiple sources

Combining taxonomic data is difficult since there any many conflicting taxonomies, so taxa needs to support conflicting taxonomies. Often users will have conflicting taxonomic data when combining sources, but they will want to combine it in such a way that a consensus taxonomy can be reached. Therefore, tools will be needed to identify and resolve conflicts

Filtering taxonomic data

Hierarchical data is difficult to filter, so taxa needs special filtering functions. These need to operate fast enough to work on datasets with 10,000 taxa or more.

Manipulating taxonomic data

There should be tools to modify taxonomies, including:

• Add taxa
• Remove taxa
• Combine taxa as synonyms
• Spilt taxa with synonyms into different taxa
• Change/add ranks, names, authorities, etc

Exploring taxonomic data

The taxa pacakge will need ways to explore taxonomic hierarchies interactivly. Plotting taxonomic data is complex so is best left to other packages, but text-based tree exploration should be supported. Combined with effective filtering techniques, this should be sufficient.

ropenscilabs/taxa documentation built on Feb. 23, 2024, 6:31 p.m.