dmis-lab / BioSyn

ACL'2020: Biomedical Entity Representations with Synonym Marginalization
https://arxiv.org/abs/2005.00239
MIT License
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What's the role of "class" field in query files? #7

Closed amirj closed 3 years ago

amirj commented 3 years ago

In the following example, "SpecificDisease", "Modifier" and "CompositeMention" are playing any role in the algorithm?

10441573||444|459||SpecificDisease||ovarian cancers||D010051
10441573||492|498||Modifier||cancer||D009369
10441573||655|683||CompositeMention||breast cancer|ovarian cancer||D001943|D010051
mjeensung commented 3 years ago

Hi amirj

In BioSyn, only mentions and CUIs are used. (Please see https://github.com/dmis-lab/BioSyn/blob/ed9dc962e806e4f6c453652f111eb7c01ffaabec/src/biosyn/data_loader.py#L62)

When you construct new query files, you should just fill the class field with any characters like '-'.

amirj commented 3 years ago

Thanks :-)