Imageomics / Imageomics/TaxonoPy
genus: Calephelis species: laverna
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- Python
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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
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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