Imageomics / Imageomics/TaxonoPy

Add flag to toggle `"ForceAcceptedLastResort"` resolution

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Python
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Description

We may not always want to force unmatched taxonomic labels to be resolved to the source-provided labels. It could be helpful to push these into the "unresolved" bucket for potential review.

Example from TreeOfLife-10M re-resolution:

{"uuid": "1375e525-845c-492a-9a9c-5a4476750ec7", 
"source_id": "30030699", 
"scientific_name": "Giant stick insect", 
"phylum": null, 
"class": null, 
"order": null, 
"family": null, 
"genus": "Giant", 
"species": "Giant stick insect", 
"kingdom": null, 
"common_name": "Giant stick insect"}

This is an example of improperly labeled source data that was fed into the pipeline. Since there was no resolution profile to which it could match, this was forced through to resolve as provided by the source. In this case, we would not want such a resolution to be considered "resolved".

Alternatively (or additionally), we could consider a common-name match resolution option (all unresolved taxa from TreeOfLife-10M have common name labels, but no other taxa).

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by tracing the pipeline's ForceAcceptedLastResort resolution behavior and how unmatched taxa enter the "unresolved" bucket. Determine how a toggle should affect source-provided fallback labels, and whether common-name matching is in scope. Done means the chosen behavior is explicit and consistently distinguishes resolved from unresolved taxa.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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