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Corpus of Online Medical EnTities: the cometA corpus

Home Page: https://www.siphs.org

Jupyter Notebook 95.32% Python 4.68%
entity-linking bionlp nlp machine-learning deep-learning transformer

cometa's Issues

Download link not working

Hello,

Dropbox link is down. Can you provide an alternative download linke for COMETA corpus?

Thanks

Reproducing Stoilos Distance Based Result

Hi,

I am trying to reproduce your results on zero shot general dataset using Stoilos distance. I have used your pre-computed file term_onto_ed_dic_zeroshot_general.pkl. I took the first element with the smallest distance and counted as a hit if it was either match with the entity or its synonyms, but I am only getting accuracy of 0.3011.

Please let me know what you think. Thank you!

count = 0
corr = 0
for g in gold_entites_dict:
    if mid_to_idx[g] not in ONT_ED_DICT: continue
    count += 1
    label_id = label_ids[g]
    for term in dp.snomed.index_definition[str(dp.label_to_snomed_id[label_id])]:
        cur_result = int(term.lower() == ONT_ED_DICT[mid_to_idx[g]][0][0].lower())
        if cur_result == 1:
            corr += 1
            break

License information

Thank you so much for the great work. Can you specify the license for using the data, please?

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