dmis-lab bern issues - Githubissues

dmis-lab / bern

A neural named entity recognition and multi-type normalization tool for biomedical text mining

https://bern.korea.ac.kr

BSD 2-Clause "Simplified" License

173 stars 44 forks source link

issues

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Site is down

#52 gdilieto-unimib opened 1 year ago
0
can bern recognize cellLine entity?

#51 wenyuhaokikika opened 1 year ago
0
FILE DOWNLOAD ISSUE

#50 combax opened 2 years ago
0
tensorflow-gpu version

#49 wenyuhaokikika opened 2 years ago
0
Website seems to be down

#48 JaskaranKaurGill closed 2 years ago
2
The Certificate of BERN website expired

#47 ghostintheshellarise opened 2 years ago
8
How to run and use from google colab ?

#46 AmeerAlkhier opened 3 years ago
0
tmVar2sever running error

#45 xuehaoliu92 opened 3 years ago
0
Server offline

#44 shoaibb closed 3 years ago
2
[{'error': 'NER crash'}]

#43 NarenInD opened 3 years ago
0
HTTPConnectionPool(host='164.52.196.65', port=8888): Max retries exceeded with url: / (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fc1089f04a8>: Failed to establish a new connection: [Errno 111] Connection refused',))

#42 NarenInD opened 3 years ago
0
Disease normalizer isn't being given entire input text, only the keyword

#41 mukund109 opened 3 years ago
0
Don't have permission to push a new branch to make Pull Request

#40 avacaondata opened 3 years ago
0
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

#39 NarenInD opened 3 years ago
1
Containerization

#38 leonardomra opened 3 years ago
0
('Connection aborted.', RemoteDisconnected('Remote end closed connection without response',))

#37 NarenInD opened 3 years ago
0
/bern/logs/nohup_gnormplus.out: No such file or directory

#36 NarenInD closed 3 years ago
0
{'status': 'fail', 'message': 'JSON PARSE ERROR'}

#35 NarenBabuR opened 4 years ago
0
https://bern.korea.ac.kr/ not working

#34 NarenBabuR closed 4 years ago
2
Not working with tensorflow 2.0

#33 avacaondata opened 4 years ago
2
JSONDecodeError for input of big size

#32 NarenInD opened 4 years ago
1
vibrio cholerae getting classified with all possibilties

#31 NarenInD opened 4 years ago
0
Ending index is not correct in JSON for species category

#30 NarenInD closed 4 years ago
1
Not getting classified

#29 NarenInD opened 4 years ago
1
Is database of BERN IDs to other ontologies mappings available?

#28 saksham219 closed 4 years ago
1
Batch Processing for BERN server

#27 geekyogurt opened 4 years ago
1
How can I perform relation extraction?

#26 BharathRajaGajula opened 4 years ago
0
lib/PAM140-6.txt (No such file or directory)

#25 wanguan2000 closed 4 years ago
1
Need clarification on GNormPlus_180921.jar , tmVar2Server.jar and other normalizer jars

#24 rajeshkumargp opened 4 years ago
0
Usage of crfpp-0.58.tar.gz is in GNormplus and Tmvar

#23 rajeshkumargp opened 4 years ago
0
Could I use other port of Disease_normalizer_19.jar?

#22 shipse92 opened 4 years ago
0
Incomplete abstracts + duplicated entries in 18.4 mil Pubmed dump

#21 mukund109 opened 4 years ago
0
"setup.txt" file missing

#20 Sudeep09 opened 4 years ago
2
KeyError: 'disease'

#19 jamshaidsohail5 closed 4 years ago
4
PubTator FileNotFound Error

#18 jamshaidsohail5 closed 4 years ago
1
NER extraction of text seems not to be working

#17 amalic opened 4 years ago
9
Problems running bern in Docker

#16 amalic closed 4 years ago
2
Running BERN on Windows: requests.exceptions.ConnectionError

#15 ianovski closed 4 years ago
2
There is a bug when bern recognize the 'Excerpt' section in some papers, shown below.

#14 SongbiaoZhu opened 4 years ago
3
ModuleNotFoundError: No module named 'xmltodict' when running `tail -F logs/nohup_BERN.out`

#13 enzoampil closed 4 years ago
2
FileNotFoundError: [Errno 2] No such file or directory: 'biobert_ner/tmp/token_test_Thread-47.txt'

#12 clouwer closed 4 years ago
1
Switching off GNormPlus and tmVar; customizing BERN

#11 dimitrijenyc opened 4 years ago
1
Using pre-trained models directly to predict on example text

#10 Lahssiniabdel closed 4 years ago
1
Only Abstracts are getting tagged

#9 nakumgaurav closed 4 years ago
1
BERN Server killed while predicting for an article

#8 nakumgaurav closed 4 years ago
2
elapsed_time for raw text

#7 mjeensung closed 4 years ago
0
Guide to fine-tune!

#6 AndreasSaka closed 4 years ago
1
What does the start and end tag in entities represent?

#5 shivanik96 closed 4 years ago
5
PubTator file not found error

#4 dimitrijenyc closed 4 years ago
7
Kubernetes / Docker setup

#3 vineethvijay-MyT closed 4 years ago
1