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API: Resolve complex term situations (Abandoned, Split, Merged, Promoted) #19

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Angatar opened this issue Nov 25, 2024 · 0 comments
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Angatar commented Nov 25, 2024

Description:
The current API does not address complex term situations, such as abandoned, split, merged, or promoted terms from previous ICTV releases. These obsolete terms are not included in the ontology of the queried release, making it impossible to resolve references.

Current Problem:

  • Terms from earlier ICTV releases that are no longer valid in the current release are not included in the ontology.

  • Users cannot resolve these obsolete terms to their replacements or fallback terms (e.g., parent or merged taxa).

  • Example: The taxon Luteoviridae (ICTV Taxonomic ID 201903759) is absent in the ictv_2023 ontology. However, it should be included as an abandoned term metadata is_obsolete = true (maybe having an "Abandoned taxon" class as parent class ), with metadata pointing to its replacement, Tolivirales (ICTV ID 20190722). term_replaced_by: 20190722

Proposed Resolution:

Include all obsolete terms (i.e., ICTV IDs not present in the current release) as entries in the ontology, and tagging these terms as "obsoletes" having for parent class a synthetic "Abandoned taxon" class .
Add a term_replaced_by field in the metadata for these abandoned terms, indicating their replacement ICTV ID = fallback ID.

Therefore the "Luteoviridae" taxon that was abandoned should be represented in the ictv_2023 ontology and should basically allow to retrieve the following information

{
  "term_id": "201903759",
  "label": "Luteoviridae",
  "is_obsolete": true,
  "term_replaced_by": "20190722"
}
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