The datasets can be downloaded from zenodo.
The zip file contains two folders: RRID and antibody_specificity.
- RRID
- pair-file.xlsx - This file contains the pairs of snippet from antibody_specificity and snippet from rrid-snippet.xlsx file.
- rrid-snippet.xlsx - This file contains snippets of RRID (AB_xxxx).
- antibody_specificity
- dataset.xlsx - This file contains snippets which were labeled as positive, negative, or neutral.
- dataset_more_negative.xlsx - This file contains 65 more negative data which were also labeled as positive, negative, or neutral.
To use this dataset with this code.
- Extract zip file to this directory.
- For ABSA, convert dataset.xlsx and dataset_more_negative.xlsx into csv file with only SNIPPET and label as columns.
- For RRID Linking, convert pair-file.xlsx into csv file with id, PMID, RRID, Snippet_rdw, SNIPPET_3192antibody, and RRID GT as columns.
- Before training ABSA models, first cd into utils folder and run
python convert2seq.py