Imageomics / Imageomics/TaxonoPy

genus: Calephelis species: laverna

Open
#16 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

edge case enhancement
Dominant language
Python
Stars
19
Forks
0
PR merge metrics
No merged PRs in 30d

Description

An entry "Calephelis laverna" whose resolution with GNVerifier using GBIF provides sparse yet confident rank hits at just the kingdom, genus, and species levels. The final resolution is, e.g.:

{
  "uuid": "109fff25-cccb-4c5f-823e-89da7d1c8d76",
  "scientific_name": "Calephelis laverna",
  "source_dataset": "unknown",
  "source_id": "20386037",
  "resolution_status": "EXACT_MATCH_PRIMARY_SOURCE_ACCEPTED_SIMPLE",
  "kingdom": "Animalia",
  "phylum": null,
  "class": null,
  "order": null,
  "family": null,
  "genus": "Calephelis",
  "species": "Calephelis laverna",
  "resolution_path": "RESOLVED",
  "resolution_strategy": "ExactMatchPrimarySourceAcceptedSimple",
  "final_query_term": "Calephelis laverna",
  "final_query_rank": "species",
  "final_data_source_id": 11,
  "common_name": "Animal"
}

This is a shortcoming of the GBIF Backbone Taxonomy.

It should be mitigated by detecting a sparse internal resolution (here, 4 missing values at internal ranks) by querying additional data providers (COL, OTOL) to either supplement or supplant this data.

For example, COL contains filled out hierarchy data:

Eukaryota (domain) >> Animalia (kingdom) >> Arthropoda (phylum) >> Insecta (class) >> Lepidoptera (order) >> Papilionoidea (superfamily) >> Riodinidae (family) >> Riodininae (subfamily) >> Riodinini (tribe) >> Calephelis (genus) >> Calephelis laverna (species)

The solution to this may also address #15.

Contributor guide

No contributing guide indexed for this repository

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 reviewing the existing GBIF resolution flow and issue #15, then identify where sparse internal ranks can trigger queries to COL and OTOL. Done means a sparse hierarchy can be supplemented or replaced with additional provider data while preserving the resolved taxon result.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data, databases
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.