Task-Oriented Recipes

Validate and Update Seeds

1. Construct the term list:

   from pandasaurus.curie_validator import CurieValidator
   
   terms = CurieValidator.construct_term_list(seeds)
   

2. Catch validation errors:

   from pandasaurus.utils.pandasaurus_exceptions import InvalidTerm, ObsoletedTerm
   
   try:
       CurieValidator.get_validation_report(terms)
   except InvalidTerm as err:
       print(err)
   except ObsoletedTerm as err:
       print(err)
   

3. Replace obsoleted terms programmatically:

   query = Query(seeds)
   query.update_obsoleted_terms()
   

Contextual Enrichment

Gather all terms that are part_of a context and enrich them:

q = Query(kidney_terms, force_fail=True)
enriched = q.contextual_slim_enrichment(["UBERON:0000362"])  # renal medulla

Parent-only Enrichment

Use pandasaurus.query.Query.parent_enrichment() for a one-hop graph:

q = Query(seeds)
parent_df = q.parent_enrichment()

Export to Graph

After any enrichment call:

graph_df = q.graph_df  # pandas DataFrame
rdflib_graph = q.graph

Use pandasaurus.graph.graph_generator to further manipulate the graph or export as needed.