APCalign-app

APCalign-app is a Shiny interface to the R package APCalign. This app aligns and updates Australian plant taxon name strings. using taxonomic information from the Australian Plant Census (APC) and Australian Plant Name Index (APNI).

Supplying your taxon names

Taxon names can be typed directly into the name input box, making sure the names are seperated by commas. This method is suited to alignments and updates for a small number of taxa

For larger alignments and updates, we recommend uploading a .csv and selecting the column which contains your taxon names

Supplying additional identifiers

In cases where there are multiple records for a genus or family alignment e.g. Eucalyptus sp., you can nominate an additional identifier from another column in your data that is linked to your taxon name e.g. collection site or collector name. This information is retained under `suggested_name` and clarifies that the records are not identical taxon concepts. The identifier feature is only available via the "Upload" method

Handling of taxonomic splits

Taxonomic splits refers to instances where a single taxon concept is subsequently split into multiple taxon concepts. For such taxa, when the aligned_name is the 'old' taxon concept name, it is impossible to know which of the currently accepted taxon concepts the name represents.

APCalign-app offers three alternative approaches to handle these instances:

  • Most likely species which gives you the accepted_name of the original taxon_concept; alternative names are documented in suggested_name
  • Collapse to higher taxon which declares that for split names, there is no way to be certain about which accepted_name is appropriate and therefore updates the aligned_name to the genus level; no accepted_name is returned, suggested_name documents the possible species-level names
  • Display all which gives you all the currently accepted names that were split from the original taxon_concept

Frequently Asked Questions

1. What is the Australian Plant Census (APC) and Australian Plant Name Index (APNI)?

The Australian Plant Census (APC) is national database of accepted taxonomic names for Australian vascular plants. The APC includes information on synonyms, and misapplications of them, as well as established status (native/introduced) and distribution across states and territories.

APCalign-app will first use the APC to align your taxonomic names to ones that exist in the database.

The Australian Plant Index (APNI) is a database containing names of Australian plants and their use in scientific literature. It is primarily used by the botanical community for standardising synonyms. Importantly, APNI does not provide recommendation of taxonomy or nomenclature, this is where the APC comes in.

This app only uses APNI when an alignment cannot be found in the APC

2. How does the app align my names to those in the APC/APNI?

Generally, the app takes the following steps to align names:

  1. Clean the inputted names
  2. Find best alignment with APC/APNI to your input names using 50 matching algorithims with exact and fuzzy matching
  3. Determine the taxon_rank to which the name can be resolved, based on its syntax.
  4. Determine the taxonomic_reference (APC/APNI) of each name-alignment

Learn more about our matching algorithim

3. What if the taxon is not listed in the APC?

The APC is a list of the accepted scientific names for the Australian vascular flora, both native and introduced naturalised taxa, and includes synonyms and misapplications for these names. The APC covers all published scientific plant names used in an Australian context in the taxonomic literature, but excludes taxa known only from cultivation in Australia. A taxon will not be listed in the APC if:

  1. It is a newly described species that has not yet been reviewed for inclusion in the APC
  2. It is a cultivated non-native taxon that is not (yet) designated as naturalised within Australia
  3. It is a name that has not been linked to a taxon concept accepted by the APC. The Australian Plant Names Index (APNI) includes names documented in the literature but not yet linked to an APC taxon concept

4. Where can I find the metadata for the columns in the output data

The metadata for the output columns are summarised in the R package documention

5. Where can I find further information about this app?

APCalign-app is a Shiny interface to the R package APCalign. Learn more about other features at the package website