BIOBERT corpus

[naver]

BIOBERT corpus

[jhyuklee]

Please check here. Thanks.

[LivC193]

Hi,
This is the function I use to get Abstracts as well as other information:

try:
         handle = Entrez.efetch(db = 'pubmed',
                                retmode = 'text',
                                rettype = 'Abstract',
                                id = pubmed_id,
                                api_key = 'your api key')

         results = handle.read()
         rec_file = io.StringIO(results)
         medline_rec = Medline.read(rec_file)

         if 'AB' in medline_rec.keys():
             ab = medline_rec['AB']

AB is for abstract. You need your own api_key from pubmed and also read usage restrictions.

[jhyuklee]

Hi, did you check the README of our repository? There are links to the corpora. Regarding the original BERT corpus, please check from google's repository. Thanks.

[etetteh]

Thank you for your reply, but the only links I'm seeing those for the downstream tasks not the pubmed data itself.

…

On Fri, Feb 21, 2020, 00:52 Jinhyuk Lee ***@***.***> wrote: Hi, did you check the README of our repository? There are links to the corpora. Regarding the original BERT corpus, please check from google's repository. Thanks. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#17?email_source=notifications&email_token=AGZQ72H6RWHWK3NI3P7YZK3RD4QTRA5CNFSM4KYRKLRKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEMRDQ4I#issuecomment-589445233>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGZQ72EFWHYS5KVKEEICK5TRD4QTRANCNFSM4KYRKLRA> .

[etetteh]

Thanks so much for sharing. I download a file from pubmed that contains PMID(Pubmed ID), and found a way to download them in chunks using rentrez. I wish I could download the number of Abstracts at one time, but it's all well. I really appreciate the response from you

…

On Wed, Feb 26, 2020, 00:10 LivC182 ***@***.***> wrote: Hi, This is the function I use to get Abstracts as well as other information: try: handle = Entrez.efetch(db = 'pubmed', retmode = 'text', rettype = 'Abstract', id = pubmed_id, api_key = 'your api key') results = handle.read() rec_file = io.StringIO(results) medline_rec = Medline.read(rec_file) if 'AB' in medline_rec.keys(): ab = medline_rec['AB'] AB is for abstract. You need your own api_key from pubmed and also read usage restrictions. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#17?email_source=notifications&email_token=AGZQ72EAZFQATQ2X2FRIJTLREWXPXA5CNFSM4KYRKLRKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEM6E7HQ#issuecomment-591155102>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGZQ72EPAMP4V2YW2YO5MVLREWXPXANCNFSM4KYRKLRA> .