dmis-lab/bern2 issues and pull requests

#72 - There is a problem with batch requests

Issue - State: open - Opened by togettoyou1 about 1 month ago

#71 - Bern2 is failing in API instance

Issue - State: closed - Opened by bikashpanda11 3 months ago - 10 comments

#70 - local instance of BERN2 fails to run

Issue - State: open - Opened by rafsanahmed 4 months ago

#69 - RESTful API method not working with Python

Issue - State: open - Opened by mtranchero 4 months ago - 1 comment

#68 - Plain text request is not working anymore with RESTful API nor website

Issue - State: open - Opened by bcourbon 4 months ago

#67 - Local service not starting correctly

Issue - State: open - Opened by markediger 5 months ago

#66 - Getting Timeout Errors while using Restful API method

Issue - State: closed - Opened by bikashpanda11 7 months ago - 2 comments

#65 - Max retries exceeded with url: /plain

Issue - State: open - Opened by luisenriqueramos1977 7 months ago

#64 - Restful API method throwing 500 INTERNAL SERVER ERROR

Issue - State: closed - Opened by bikashpanda11 7 months ago - 5 comments

#63 - fix no_cuda for BENR2 app file

Pull Request - State: closed - Opened by minstar 8 months ago

#62 - fix no_cuda for NER model

Pull Request - State: closed - Opened by minstar 8 months ago

#61 - Found no NVIDIA driver for CPU (run_bern2_cpu.sh)

Issue - State: closed - Opened by anopperl 8 months ago - 3 comments

#60 - localhost error

Issue - State: open - Opened by Morph0124 8 months ago - 2 comments

#59 - Connection refused error

Issue - State: closed - Opened by anopperl 8 months ago - 4 comments

#58 - NVIDIA Incompatibility

Issue - State: open - Opened by jessicapatricoski 10 months ago - 1 comment

#57 - Normalization giving the wrong species

Issue - State: open - Opened by duncster94 10 months ago

#56 - Train the model

Issue - State: open - Opened by Kik099 10 months ago - 5 comments

#55 - service down

Issue - State: open - Opened by qiuhaolu 12 months ago - 2 comments

#54 - nohup_multi_ner.out: list index out of range

Issue - State: closed - Opened by mjeensung about 1 year ago - 2 comments

#53 - bug in PMID REST-API: long publication titles get truncated after line break

Issue - State: closed - Opened by koernel2 about 1 year ago - 1 comment

#52 - I don't get "mutation" type on the local version

Issue - State: open - Opened by majdabd over 1 year ago - 15 comments

#51 - Got error when running run_eval.py

Issue - State: closed - Opened by shorlong over 1 year ago - 1 comment

#50 - 500 Error when calling API

Issue - State: closed - Opened by elorenzen-rancho over 1 year ago

#49 - You SSL certificate for http://bern2.korea.ac.kr has expired

Issue - State: closed - Opened by rlaurie over 1 year ago - 1 comment

#48 - Longer than 512 tokens

Issue - State: closed - Opened by jinniulema over 1 year ago - 2 comments

#47 - Annotation of pubmed23 baseline

Issue - State: closed - Opened by PubMedKG over 1 year ago - 1 comment

#46 - Use only NER

Issue - State: closed - Opened by Crispae almost 2 years ago - 1 comment

#45 - Use remote proxy

Pull Request - State: closed - Opened by zach-navina almost 2 years ago

#44 - Google Drive Link Not Found

Issue - State: closed - Opened by marjoleinpnnl almost 2 years ago - 3 comments

#43 - BERN2 RestfulAPI can't query plain text

Issue - State: closed - Opened by khoakoxoan almost 2 years ago - 2 comments

#42 - Unable to get response

Issue - State: open - Opened by Wickkey almost 2 years ago - 9 comments

#41 - Support batch

Pull Request - State: closed - Opened by zach-navina almost 2 years ago

#40 - Errors while extracting resource-file

Issue - State: closed - Opened by Bancherd-DeLong about 2 years ago - 5 comments

#39 - Unable to run it on Ubuntu 22. Anaconda already runs on port 8888. Response 403.

Issue - State: closed - Opened by zeusstuxnet about 2 years ago - 1 comment

#38 - BERN2 API endpoint not working

Issue - State: closed - Opened by Travis-Barton about 2 years ago - 2 comments

#37 - I'm running BERN2 but server can't be reached

Issue - State: closed - Opened by Ufifus about 2 years ago - 3 comments

#36 - I am running into same issue as @yuetieqi-meow

Issue - State: closed - Opened by kunlu-ou about 2 years ago - 7 comments

#35 - Resource file network error

Issue - State: closed - Opened by combax about 2 years ago - 2 comments

#34 - Syntax Error in server.py Causes BERN2 Local Installation to Not Work

Issue - State: closed - Opened by compbiolover over 2 years ago - 5 comments

#33 - Run BERN2 locally on Apple Silicon

Issue - State: closed - Opened by ghostintheshellarise over 2 years ago - 2 comments

#32 - linux cpu version upload

Pull Request - State: closed - Opened by minstar over 2 years ago

#31 - How disable some inner taggers

Issue - State: closed - Opened by mpperez3 over 2 years ago - 1 comment

#30 - Unable to install bern2 dependencies on Mac OS

Issue - State: closed - Opened by naveenjack over 2 years ago - 3 comments

#29 - Problems encountered trying to run BERN2 in windows

Issue - State: closed - Opened by SatanuG over 2 years ago - 4 comments

#28 - need gpu and FileNotFoundError

Issue - State: closed - Opened by zhangweizhenGitHub over 2 years ago - 2 comments

#27 - Support NRE of new category of terms?

Issue - State: closed - Opened by hh1985 over 2 years ago - 10 comments

#26 - Confusion about the differences between BERN & BERN2.

Issue - State: closed - Opened by sschet over 2 years ago - 1 comment

#25 - ERROR: 500 INTERNAL SERVER ERROR on web page when i try submit demo text

Issue - State: closed - Opened by Researcher-123 over 2 years ago - 3 comments

#24 - FileNotFoundError: [Errno 2]

Issue - State: closed - Opened by yuetieqi-meow over 2 years ago - 6 comments

#23 - Security Issue block abstract result

Issue - State: closed - Opened by JacopoBandoni over 2 years ago - 3 comments

#22 - bash run_bern2.sh

Issue - State: closed - Opened by venkateshkolli over 2 years ago - 1 comment

#21 - # install CRF

Issue - State: closed - Opened by venkateshkolli over 2 years ago - 1 comment

#20 - Entity normalization without NER

Issue - State: closed - Opened by pedroruas18 over 2 years ago - 1 comment

#19 - socket.gaierror: [Errno -2] Name or service not known

Issue - State: closed - Opened by shi4712shi over 2 years ago - 3 comments

#18 - fail to install BERN2 locally

Issue - State: closed - Opened by yuanhao96 over 2 years ago - 3 comments

#17 - FileNotFoundError: [Errno 2] for local server POST

Issue - State: closed - Opened by starmpcc over 2 years ago - 26 comments

#16 - update for cpu version

Pull Request - State: closed - Opened by minstar over 2 years ago

#15 - Bern2 local deployment can't query a PMID

Issue - State: closed - Opened by FCoroado over 2 years ago - 8 comments

#14 - bug fix of mutation end span in output format

Pull Request - State: closed - Opened by minstar over 2 years ago

#13 - fix overlap resolution

Pull Request - State: closed - Opened by minstar almost 3 years ago

#12 - Files are duplicated with same PMID

Issue - State: closed - Opened by ksj20 almost 3 years ago - 9 comments

#11 - Annotation download ERR_EMPTY_RESPONSE

Issue - State: closed - Opened by mbiemans almost 3 years ago - 8 comments

#10 - How can I make batch predictions?

Issue - State: closed - Opened by Tesla-jiang almost 3 years ago - 4 comments

#9 - Create LICENSE

Pull Request - State: closed - Opened by mjeensung almost 3 years ago

#8 - standardize prefixes using BioRegistry

Pull Request - State: closed - Opened by mjeensung almost 3 years ago - 4 comments

#7 - Where do raw data files for Cell Ontology and Cellosaurus come from

Issue - State: closed - Opened by cthoyt almost 3 years ago - 1 comment

#6 - Add missing requirement to requirements.txt

Pull Request - State: closed - Opened by cthoyt almost 3 years ago - 3 comments

#5 - Generate URLs using the Bioregistry

Pull Request - State: closed - Opened by cthoyt almost 3 years ago - 3 comments

#4 - Troubles running locally, FileNotFoundError

Issue - State: closed - Opened by dmytrobabych almost 3 years ago - 7 comments

GitHub / dmis-lab/bern2 issues and pull requests