Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

API: Resolving Former Taxon Names #20

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

API: Resolving Former Taxon Names #20

Angatar opened this issue Nov 25, 2024 · 0 comments

Comments

@Angatar
Copy link
Member

Angatar commented Nov 25, 2024

Description:
Currently, it is not possible to directly resolve a taxon's former names within the targeted ontology (e.g., ictv_latest). If the API well allows searching for exact matches on the label field in a specific ontology, to resolve a previous name of a taxon into its current name the user currently must:

  1. locate the former name in an earlier ICTV ontology version.
  2. Extract the corresponding ictv_id for that name.
  3. Query the release of interest (typically the latest) using this ictv_id.

This process is cumbersome and improvable, particularly for users who need to reconcile historical references with the latest taxonomy.

Current Problem:

  • Previous taxon names cannot be resolved directly in the latest ontology.

  • Cross-referencing historical data with the current taxonomy requires multiple queries an probably manual effort to only target ICTV ontologies.

Proposed Resolution:

  • Add to each taxon term in the ontology an obo_synonym and/or synonym metadata for each former names (labels) known from previous releases.
  • Ensure the obo_synonym/ synonym field is indexed for efficient querying... the help interface currently indicates it is possible to specify a list of fields to seek in,

This allows users to search for historical names and resolve them directly in the targeted ontology.

Example, for the species taxon Betacoronavirus pandemicum (ICTV ID 20040588), the term in the ontology should include its previous known names:

{
  "term_id": "20040588",
  "label": "Betacoronavirus pandemicum",
  "obo_synonym": "Severe acute respiratory syndrome-related coronavirus"
  "obo_synonym": "Severe acute respiratory syndrome coronavirus"
   "synonyms":["Severe acute respiratory syndrome-related coronavirus", "Severe acute respiratory syndrome coronavirus" ]
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant