Translating existing strings into HPO terms about pyhpo HOT 2 CLOSED

Hi,
If Ontology.search performs a substring match on all term names and synonyms. This will only work if your term is a substring. It does not work for strings with character mismatches.
The order it returns results is random and not sorted. This was done for performance reasons, i.e. you will get your first result even though it did not yet finish checking all HPO terms in the Ontology.

For your use case you'd have to implement a matching/search function yourself. You would have to do something like

1. Get all names and synonyms for every HPO term
2. Search this list of strings, allowing for mismatches

For (1), you could do something like

strings: Dict[str, List[HPOTerm]] = {}

def name_to_term(name: str, term: HPOTerm):
    if name not in strings:
        strings[name] = [term]


for term in Ontology:
    name_to_term(term.name, term)
    for syn in term.synonym:
        name_to_term(syn, term)

Then compare your search query with the keys of strings and return the associated HPOTerms.

from pyhpo.

Thank you very much for your pointers!
I will reopen this issue if I run into any troubles.

from pyhpo.