Hello. I installed BERN2 in my VM (Ubuntu 18.04 x64, 1 GPU). It succesfully installed, however, if I run example post script on READAME.md, then the below error occured. (Server console log)

[23/Mar/2022 06:02:40.831728] [550f7242b14dc039a8a5ee6aa9233f3472dd7b4a33484f5955175a4d] GNormPlus 0.0001380443572998047 sec
Traceback (most recent call last):
  File "/home/vessl/BERN2/bern2/bern2.py", line 106, in annotate_text
    output = self.tag_entities(text, base_name)
  File "/home/vessl/BERN2/bern2/bern2.py", line 358, in tag_entities
    async_result = loop.run_until_complete(self.async_ner(arguments_for_coroutines))
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/asyncio/base_events.py", line 587, in run_until_complete
    return future.result()
  File "/home/vessl/BERN2/bern2/bern2.py", line 491, in async_ner
    result = await asyncio.gather(*coroutines)
  File "/home/vessl/BERN2/bern2/bern2.py", line 533, in _ner_wrap
    with open(output_mtner, 'r', encoding='utf-8') as f:
FileNotFoundError: [Errno 2] No such file or directory: './multi_ner/output/550f7242b14dc039a8a5ee6aa9233f3472dd7b4a33484f5955175a4d.PubTator.json'

[2022-03-23 06:02:41,425] ERROR in app: Exception on /plain [POST]
Traceback (most recent call last):
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 2073, in wsgi_app
    response = self.full_dispatch_request()
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 1518, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 1516, in full_dispatch_request
    rv = self.dispatch_request()
  File "/home/vessl/miniconda3/envs/bern2/lib/python3.7/site-packages/flask/app.py", line 1502, in dispatch_request
    return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
  File "/home/vessl/BERN2/app/__init__.py", line 85, in plain_api
    return Response(json.dumps({"error_message": result_dict["error_message"]}), status=404, content_type='application/json')
NameError: name 'Response' is not defined
127.0.0.1 - - [23/Mar/2022 06:02:41] "POST /plain HTTP/1.1" 500 -

nohup_multi_ner.out log

MTNER init_t 28.547 sec.
1it [00:00, 185.89it/s]
Prediction: 100%|██████████| 1/1 [00:00<00:00,  2.28it/s]
Traceback (most recent call last):
  File "multi_ner/ner_server.py", line 91, in <module>
    run_server(mt_ner, args)
  File "multi_ner/ner_server.py", line 63, in run_server
    mtner_recognize(model, dict_path, base_name, args)
  File "multi_ner/ner_server.py", line 47, in mtner_recognize
    with open(output_mt_ner, 'w', encoding='utf-8') as f:
PermissionError: [Errno 13] Permission denied: 'multi_ner/output/550f7242b14dc039a8a5ee6aa9233f3472dd7b4a33484f5955175a4d.PubTator.json'

Thank you.

There are major issues in the data. Many files were just duplicates of one PMID's labelling. Is this intentional? I list the files of problem, and the pmid that it is filled up with in a table, following up with an example image of the issue. Look forward to your feedback.

| file # of problem 21n0XXX | file is filled up with only |
|---|---| | 713, 714, 715, 716, 717, 718, 719 | pmid: 22137675 | | 740, 741, 742 | pmid: 23065850 | | 748, 749 | pmid: 23334882 | | 758, 759 | pmid: 23630654 | | 766, 767 | pmid: 23886943 | | 779, 780, 781, 782 | pmid: 24335088 | | 788, 789, 790, 791 | pmid: 24595986 | | 813, 812, 811, 810 | pmid: 25329600 |

example image (21n0713.json)

Hello! I was testing the local deployment of Bern2 and it seems to work fine when submitting plain text. With PMID I get the following error:

Traceback (most recent call last): File "", line 1, in File "", line 2, in query_pmid File "/Users/franciscos/opt/anaconda3/lib/python3.8/site-packages/requests/models.py", line 910, in json return complexjson.loads(self.text, **kwargs) File "/Users/franciscos/opt/anaconda3/lib/python3.8/json/init.py", line 357, in loads return _default_decoder.decode(s) File "/Users/franciscos/opt/anaconda3/lib/python3.8/json/decoder.py", line 337, in decode obj, end = self.raw_decode(s, idx=_w(s, 0).end()) File "/Users/franciscos/opt/anaconda3/lib/python3.8/json/decoder.py", line 355, in raw_decode raise JSONDecodeError("Expecting value", s, err.value) from None json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

Any idea how I can fix this? Thanks in advance and thanks for building such a nice tool

Hi,

First of all, thanks for the great work!

I tried to download the pre-processed PubMed annotations, but got a server error: ERR_EMPTY_RESPONSE. Is there any other way to download the data?

    I am running into same issue as @yuetieqi-meow 

No issue encountered in installation, and when I ran the test, in the nohup_bern2.out: `[01/Oct/2022 17:54:12.841469] id: 9f85ebe7f122e750ca113ce20ef88f448960721e701cd1cc3e1650e2 [Errno 111] Connection refused [01/Oct/2022 17:54:12.899379] [9f85ebe7f122e750ca113ce20ef88f448960721e701cd1cc3e1650e2] GNormPlus 0.0003619194030761719 sec [01/Oct/2022 17:54:13.614587] [9f85ebe7f122e750ca113ce20ef88f448960721e701cd1cc3e1650e2] tmVar 2.0 0.7597899436950684 sec [01/Oct/2022 17:54:13.801885] [9f85ebe7f122e750ca113ce20ef88f448960721e701cd1cc3e1650e2] Multi-task NER 0.9021279811859131 sec, #entities: 2 Traceback (most recent call last): File "/home/kun/anaconda3/envs/bern2/lib/python3.7/shutil.py", line 566, in move os.rename(src, real_dst) FileNotFoundError: [Errno 2] No such file or directory: './resources/GNormPlusJava/output/9f85ebe7f122e750ca113ce20ef88f448960721e701cd1cc3e1650e2.PubTator' -> './resources/tmVarJava/input/9f85ebe7f122e750ca113ce20ef88f448960721e701cd1cc3e1650e2.PubTator.PubTator.Gene'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/media/kun/Storage/BERN2/bern2/bern2.py", line 107, in annotate_text output = self.tag_entities(text, base_name) File "/media/kun/Storage/BERN2/bern2/bern2.py", line 376, in tag_entities shutil.move(output_gnormplus, input_tmvar_gene) File "/home/kun/anaconda3/envs/bern2/lib/python3.7/shutil.py", line 580, in move copy_function(src, real_dst) File "/home/kun/anaconda3/envs/bern2/lib/python3.7/shutil.py", line 266, in copy2 copyfile(src, dst, follow_symlinks=follow_symlinks) File "/home/kun/anaconda3/envs/bern2/lib/python3.7/shutil.py", line 120, in copyfile with open(src, 'rb') as fsrc: FileNotFoundError: [Errno 2] No such file or directory: './resources/GNormPlusJava/output/9f85ebe7f122e750ca113ce20ef88f448960721e701cd1cc3e1650e2.PubTator'`

No other issues found on other log files: nohup_disease_normalize.out: Sieve loading .. 2628 ms, Ready nohup_gene_normalize.out: Ready (port 18888) nohup_gnormplus.out: Starting GNormPlus Service at 127.0.1.1:18895 Loading Gene Dictionary : Processing ... Loading Gene Dictionary : Processing Time:9.951sec Ready nohup_multi_ner.out: `MTNER init_t 13.013 sec.

0it [00:00, ?it/s] 1it [00:00, 34.71it/s]

Prediction: 0%| | 0/1 [00:00<?, ?it/s] Prediction: 100%|██████████| 1/1 [00:00<00:00, 1.37it/s] Prediction: 100%|██████████| 1/1 [00:00<00:00, 1.37it/s]nohup_tmvar.out:Starting tmVar 2.0 Service at 127.0.1.1:18896 Reading POS tagger model from lib/taggers/english-left3words-distsim.tagger ... done [1.5 sec]. Loading tmVar : Processing Time:1.739sec Ready input/9f85ebe7f122e750ca113ce20ef88f448960721e701cd1cc3e1650e2.PubTator - (PubTator format) : Processing Time:0.521sec ner success = 9f85ebe7f122e750ca113ce20ef88f448960721e701cd1cc3e1650e2.PubTator`

I noticed when I ran the test case, the nohup_bern2.out nohup_multi_ner.out and nohup_tmvar.out logs are updated, but nohup_gnormplus.out is not (the other two normalize.out log files are not, and I assume because they are not executed because NER encounters error). This sounds like GNormPlus not executed at all? Any ideas on this?

Originally posted by @kunlu-ou in https://github.com/dmis-lab/BERN2/issues/24#issuecomment-1264506002

I'm trying to run locally and following the steps described in README, I get this

[21/Jan/2022 11:56:35.780036] id: 7bb79cf620bd0ba345504784f5aaa6ad48394bcd1cf10b7e29964e05
[21/Jan/2022 11:56:36.632464] [7bb79cf620bd0ba345504784f5aaa6ad48394bcd1cf10b7e29964e05] tmVar 2.0 0.8203573226928711 sec
[21/Jan/2022 11:56:38.605409] [7bb79cf620bd0ba345504784f5aaa6ad48394bcd1cf10b7e29964e05] GNormPlus 2.742703914642334 sec
Traceback (most recent call last):
  File "/Users/dima/code/BERN2/bern2/bern2.py", line 105, in annotate_text
    output = self.tag_entities(text, base_name)
  File "/Users/dima/code/BERN2/bern2/bern2.py", line 290, in tag_entities
    async_result = loop.run_until_complete(self.async_ner(arguments_for_coroutines))
  File "/Users/dima/opt/anaconda3/envs/bern2/lib/python3.7/asyncio/base_events.py", line 587, in run_until_complete
    return future.result()
  File "/Users/dima/code/BERN2/bern2/bern2.py", line 417, in async_ner
    result = await asyncio.gather(*coroutines)
  File "/Users/dima/code/BERN2/bern2/bern2.py", line 459, in _ner_wrap
    with open(output_mtner, 'r', encoding='utf-8') as f:
FileNotFoundError: [Errno 2] No such file or directory: './multi_ner/output/7bb79cf620bd0ba345504784f5aaa6ad48394bcd1cf10b7e29964e05.PubTator.json'

The only thing I've changed is removing transferring models to cuda, since I don't have GPU on my current machine.

Great to see that BERN2 normalizes entities to compact identifiers in resource:identifier format. I noticed that there is an opportunity to standardize the prefixes used with Bioregistry:

• NCBITaxon prefix as per http://bioregistry.io/registry/ncbitaxon
• NCBIGene prefix as per http://bioregistry.io/registry/ncbigene

FYI I didn't check all the entity types BERN2 is capable of tagging for whether they use the preferred prefix.

@cthoyt might also be helpful here.

Hello, I posted my error a few days ago in this and I retried a few times these days. I found it's really hard for me to fix it because all logs except nohup_bern2.out goes well. Here is my lastest nohup_bern2.out:

[08/May/2022 19:28:51.930673] id: 1c3d05e08ffc1ca51c537406a8e2342fd5c546912049d73bd31e0427
[Errno 111] Connection refused
[08/May/2022 19:28:52.126999] [1c3d05e08ffc1ca51c537406a8e2342fd5c546912049d73bd31e0427] GNormPlus 0.0005352497100830078 sec
[08/May/2022 19:29:07.017467] [1c3d05e08ffc1ca51c537406a8e2342fd5c546912049d73bd31e0427] Multi-task NER 14.890285730361938 sec, #entities: 2
[08/May/2022 19:29:26.444897] [1c3d05e08ffc1ca51c537406a8e2342fd5c546912049d73bd31e0427] tmVar 2.0 34.42515420913696 sec
Traceback (most recent call last):
  File "/home/scholar1/anaconda3/envs/bern2/lib/python3.7/shutil.py", line 566, in move
    os.rename(src, real_dst)
FileNotFoundError: [Errno 2] No such file or directory: './resources/GNormPlusJava/output/1c3d05e08ffc1ca51c537406a8e2342fd5c546912049d73bd31e0427.PubTator' -> './resources/tmVarJava/input/1c3d05e08ffc1ca51c537406a8e2342fd5c546912049d73bd31e0427.PubTator.PubTator.Gene'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/scholar1/bern2/BERN2/bern2/bern2.py", line 106, in annotate_text
    output = self.tag_entities(text, base_name)
  File "/home/scholar1/bern2/BERN2/bern2/bern2.py", line 371, in tag_entities
    shutil.move(output_gnormplus, input_tmvar_gene)
  File "/home/scholar1/anaconda3/envs/bern2/lib/python3.7/shutil.py", line 580, in move
    copy_function(src, real_dst)
  File "/home/scholar1/anaconda3/envs/bern2/lib/python3.7/shutil.py", line 266, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/home/scholar1/anaconda3/envs/bern2/lib/python3.7/shutil.py", line 120, in copyfile
    with open(src, 'rb') as fsrc:
FileNotFoundError: [Errno 2] No such file or directory: './resources/GNormPlusJava/output/1c3d05e08ffc1ca51c537406a8e2342fd5c546912049d73bd31e0427.PubTator'

127.0.0.1 - - [08/May/2022 19:29:27] "POST /plain HTTP/1.1" 404 -

and all other 5 logs just similar as I posted here

Thank you!

Hi:

Thank you very much for sharing your excellent work. While trying to extract the resource file, I ran into this error. Any suggestions as to the cause(s)?

tar -zxvf resources_v1.1.b.tar.gz . .

resources/tmVarJava/Database/var2rs_Xm.db resources/tmVarJava/Database/gene2rs.db tar: Skipping to next header tar: A lone zero block at 22871798 tar: Exiting with failure status due to previous errors .

Regards,

Bancherd

Hi @minstar & @mjeensung , I have attempted to install BERN2 locally, but I get the following error when I launch it:

Traceback (most recent call last):
  File "server.py", line 1, in <module>
    from app import create_app
  File "/Users/[myuser]/BERN2/app/__init__.py", line 129
    return render_template('result_text.html', result_items=res_items, latency = f'{latency*1000:9.2f}', result_str=json.dumps(result_dict, sort_keys=True, indent=4))

I have also seen that this error appears to keep server.py from running as it is not running when I run bash stop_bern2.sh. I get the following output

No ner_server.py found to stop.
Stopped GNormPlusServer.main.jar
Stopped tmVar2Server.main.jar
Stopped disease_normalizer_21.jar
Stopped gnormplus-normalization_21.jar
No server.py found to stop.

Finally, I still tried to submit the plain text and PMID examples listed under the local instillation instructions and I simply get no output even after waiting for several minutes. My thought process leads me to believe that the error in server.py is causing BERN2 to simply terminate and hence no outputs from the tutorial text and PMIDS.

Thanks for your help! Let me know if I can help with any additional files or insight.

Andrew

Very excited to see BERN2! Really nice work so far.

I'm looking to map certain mentions of proteins to standard identifiers. Here's a list of these proteins, where each protein is also followed by a direction of activity:

3 beta hydroxysteroid dehydrogenase 5 stimulator; AF4/FMR2 protein 2 inhibitor; Adenylate cyclase 2 stimulator; Alpha gamma adaptin binding protein p34 stimulator; BR serine threonine protein kinase 1 stimulator; Complement Factor B stimulator; DNA gyrase B inhibitor; Ectonucleotide pyrophosphatase-PDE-3 stimulator; Falcipain 1 stimulator; Homeobox protein Nkx 2.4 stimulator; ISLR protein inhibitor; Integrin alpha-IIb/beta-4 antagonist; Inter alpha trypsin inhibitor H5 stimulator; Interleukin receptor 17B antagonist; Isopropylmalate dehydrogenase stimulator; Methylthioadenosine nucleosidase stimulator; Patched domain containing protein 2 inhibitor; Protein FAM161A stimulator; Protocadherin gamma A1 inhibitor; Ring finger protein 4 stimulator; SMAD-9 inhibitor; Small ubiquitin related modifier 1 inhibitor; Sodium-dicarboxylate cotransporter-1 inhibitor; Sorting nexin 9 inhibitor; Sugar phosphate exchanger 2 stimulator; Transcription factor p65 stimulator; Tumor necrosis factor 14 ligand inhibitor; Ubiquitin-conjugating enzyme E21 stimulator; Unspecified ion channel inhibitor; Zinc finger BED domain protein 6 inhibitor

Using the nice web interface, I get:

So overall BERN2 does a good job recognizing the protein mentions. However, we actually already know what the protein text is, and are more interested in normalization. Most of the gene/protein mentions receive "ID: CUI-less". Any advice on how to improve the performance of named entity normalization for human proteins?

I see that the website notes that normalization is done by https://github.com/dmis-lab/BioSyn, so feel free to migrate this issue to that repo if it's best there.

I get the following error:

[Errno 2] No such file or directory : './resources/GNormPlusJava/output/2ec5cc999ceefc8f5a83a423fe6db771ab7868adf7fb74598c36ccd.PubTator' -> ./resources/tmVarJava/input/2ec5cc999ceefc8f5a83a423fe6db771ab7868adf7fb74598c36ccd.PubTator.PubTator.Gene

does anyone can help me fix this?

I'm not able to get response when I call the rest api. Could someone please help?

Can you please publish a video for the local installation. Trying on Ubuntu with already exiting environment of Jupyter. Nothing is running on 8888. 403 error.

Hi,

I am trying to install bern2 dependencies on mac Os Montery. When I run the below commands , I am getting package not found error for cudatoolkit and faiss-gpu. And these version are not available for osx. I confirmed it through conda search and also by searching on anaconda.org search packages.

Let me know if I can run this on osx ?

Dependencies : conda install pytorch==1.9.0 cudatoolkit=10.2 -c pytorch conda install faiss-gpu libfaiss-avx2 -c conda-forge

Thanks