TaxRefine: OpenRefine utilities for taxon name validation
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README.md

taxrefine

OpenRefine utilities for taxon name validation.

What TaxRefine does

TaxRefine summarizes search results from the GBIF API to try to pick the best supported interpretation of a particular name from across the hundreds of checklists assembled by GBIF.

TaxRefine is a wrapper around GBIF's Search Names. It searches for names on the GBIF Nub using the /species/match API query; if it finds no matches, it uses the /species/search to look for the exact name on other checklists.

Once it finds a match, it finds the list of related names on GBIF (using the /species/{int}/related API query). It then goes through all these related names and groups them on the basis of four criteria:

  1. Scientific name
  2. Accepted name
  3. Authority
  4. Kingdom

It returns them sorted by the number of checklists matched in each group. For each group, it also generates a summary of possible values (this might still be a little buggy).

Tasks we might want to do

We hope to meet the following uses:

Name matching and reconciliation

  1. Name matching against another OpenRefine project (which might be a CSV, text file, or any other format supported by OpenRefine)
  2. Name reconciliation against EOL (fuzzy matching) and GBIF Nub (non-fuzzy matching) via Rod Page's reconciliation services.
  3. Name reconciliation against GBIF Checklist Bank using its API.

Retrieve higher taxonomy

  1. Retrieve higher taxonomy from ITIS using the getFullHierarchyFromTSN API call.
  2. Retrieve higher taxonomy from GBIF.

Given a name, return a list of all known synonyms.

  1. EOL provides this information through its pages API call.

See something wrong? Please let us know!