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Published 20 hours ago • verified publisher icon bio-ontology-research-group

Strings for SemanticSimilarity.groovy

Open nklsbckmnn opened this issue 1 year ago • 4 comments

Thanks for sharing this. What are the strings that SemanticSimilarity.groovy requires as arguments? semantic-similarity.ipynb only provides integers.

nklsbckmnn avatar May 16 '23 16:05 nklsbckmnn

Hi, It needs a PPI file from STRING Database which is available in the data folder downloaded from here https://doi.org/10.5281/zenodo.3779900

coolmaksat avatar May 17 '23 05:05 coolmaksat

Thanks. Just to make sure... so it's

!groovy el-embeddings/SemanticSimilarity -ia data/train/{org_id}.annotation.txt -is data/train/{org_id}.protein.links.v11.0.txt -o data/train/{org_id}.sim_resnik.txt instead of

!groovy SemanticSimilarity -i data/train/{org_id}.annotation.txt -s 0 -o data/train/{org_id}.sim_resnik.txt

?

nklsbckmnn avatar May 17 '23 07:05 nklsbckmnn

Yes, that's right

coolmaksat avatar May 17 '23 07:05 coolmaksat

Thanks 🙏

nklsbckmnn avatar May 17 '23 08:05 nklsbckmnn