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

Merpy ignoring strings from lexicon #4

Open
SIRConceicao opened this issue Nov 12, 2020 · 0 comments
Open

Merpy ignoring strings from lexicon #4

SIRConceicao opened this issue Nov 12, 2020 · 0 comments

Comments

@SIRConceicao
Copy link
Member

Hello,

I have found a bug that ignores specific strings from the input lexicon.

In this case the strings that I detected are "A2M" and "A1BG".

The code that I used to test this lexicon is the following:

import merpy 

merpy.download_mer()

geneSyn=merpy.create_lexicon_from_file("gene_synonyms_lexicon.txt", "geneSyn")
merpy.process_lexicon("geneSyn")

#Examples
print(merpy.get_entities("The genes encoding myeloperoxidase (MPO) and alpha(2)-macroglobulin (A2M)", "geneSyn"))

print(merpy.get_entities("The association between polymorphisms in the alpha-2-macroglobulin (a2m) gene", "geneSyn"))

print(merpy.get_entities("The gene A2M with A1BG and NAT1 are", "geneSyn"))

print(merpy.get_entities("fragment of A1BG in urine in SRNS", "geneSyn"))

The file in use:
gene_synonyms_lexicon.txt

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