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

[majdabd]

Hello! I installed the local version and ran a local server without any errors. However, my results do not include mutation entities (nor mutation type), even when my text is taken directly from the tmVar corpus. I downloaded the resources file that includes the tmVar2.0. The annotation I get for mutations is RNA and the ID is CUI-LESS. What might be the issue? Thanks

[mjeensung]

Hi @majdabd

Could you please provide any abstracts where you have encountered the issue? Also, does the BERN2 web demo annotate mutation entities when you input the abstract?

[majdabd]

Hello, yes the web demo works well in annotating mutation entities.

This is an example text where I don't get mutation annotations : "The chemokine receptor 1 CXCR-1 (or IL8R-alpha) is a specific receptor for the interleukin 8 (IL-8), which is chemoattractant for neutrophils and has an important role in the inflammatory response. The polymorphism rs2234671 at position Ex2+860G>C of the CXCR1 gene causes a conservative amino acid substitution (S276T). This single nucleotide polymorphism (SNP) seemed to be functional as it was associated with decreased lung cancer risk. Previous studies of our group found association of haplotypes in the IL8 and in the CXCR2 genes with the multifactorial disease chronic periodontitis. In this study we investigated the polymorphism rs2234671 in 395 Brazilian subjects with and without chronic periodontitis. FINDINGS: Similar distribution of the allelic and genotypic frequencies were observed between the groups (p>0.05). CONCLUSIONS: The polymorphism rs2234671 in the CXCR1 gene was not associated with the susceptibility to chronic periodontitis in the studied Brazilian population."

[mjeensung]

Thanks for sharing!

I'll try reproducing and figuring out the issue from my side and get back to you.

[majdabd]

Thank you for the help. To aid you in figuring out the issue, below is the log info from nohup_tmvar.out. I guess it is working well, but the annotation/normalization results do no appear in the final dictionary with the rest of the entities. I don't know why.

Starting tmVar 2.0 Service at 127.0.1.1:18896 Reading POS tagger model from lib/taggers/english-left3words-distsim.tagger ... done [0.9 sec]. Loading tmVar : Processing Time:0.943sec Ready input/b2752a1cbbb52dc62f2c250d8965d05c492c48c5fba7ba47cd0c4239.PubTator - (PubTator format) : Processing Time:0.313sec ner success = b2752a1cbbb52dc62f2c250d8965d05c492c48c5fba7ba47cd0c4239.PubTator output/b2752a1cbbb52dc62f2c250d8965d05c492c48c5fba7ba47cd0c4239.PubTator.PubTator.PubTator input/b2752a1cbbb52dc62f2c250d8965d05c492c48c5fba7ba47cd0c4239.PubTator.PubTator - (PubTator format) : Processing Time:0.067sec normalization success = b2752a1cbbb52dc62f2c250d8965d05c492c48c5fba7ba47cd0c4239.PubTator.PubTator|b2752a1cbbb52dc62f2c250d8965d05c492c48c5fba7ba47cd0c4239.PubTator.PubTator.Gene input/cf11c8c04d69ba408c1b70a52ec8455d6e92b9c63380bd2b6622c43f.PubTator - (PubTator format) : Processing Time:0.253sec ner success = cf11c8c04d69ba408c1b70a52ec8455d6e92b9c63380bd2b6622c43f.PubTator output/cf11c8c04d69ba408c1b70a52ec8455d6e92b9c63380bd2b6622c43f.PubTator.PubTator.PubTator input/cf11c8c04d69ba408c1b70a52ec8455d6e92b9c63380bd2b6622c43f.PubTator.PubTator - (PubTator format) : Processing Time:0.156sec normalization success = cf11c8c04d69ba408c1b70a52ec8455d6e92b9c63380bd2b6622c43f.PubTator.PubTator|cf11c8c04d69ba408c1b70a52ec8455d6e92b9c63380bd2b6622c43f.PubTator.PubTator.Gene input/000429bb9f1cf418a0781d70196549efc526804e4d5f0d6bf7b93f74.PubTator - (PubTator format) : Processing Time:0.213sec ner success = 000429bb9f1cf418a0781d70196549efc526804e4d5f0d6bf7b93f74.PubTator output/000429bb9f1cf418a0781d70196549efc526804e4d5f0d6bf7b93f74.PubTator.PubTator.PubTator input/000429bb9f1cf418a0781d70196549efc526804e4d5f0d6bf7b93f74.PubTator.PubTator - (PubTator format) : Processing Time:0.038sec normalization success = 000429bb9f1cf418a0781d70196549efc526804e4d5f0d6bf7b93f74.PubTator.PubTator|000429bb9f1cf418a0781d70196549efc526804e4d5f0d6bf7b93f74.PubTator.PubTator.Gene input/aa3e29d211ec15bde1fd17c39c2a870a19f8b7e5a5ab3970f8f13313.PubTator - (PubTator format) : Processing Time:0.156sec ner success = aa3e29d211ec15bde1fd17c39c2a870a19f8b7e5a5ab3970f8f13313.PubTator output/aa3e29d211ec15bde1fd17c39c2a870a19f8b7e5a5ab3970f8f13313.PubTator.PubTator.PubTator input/aa3e29d211ec15bde1fd17c39c2a870a19f8b7e5a5ab3970f8f13313.PubTator.PubTator - (PubTator format) : Processing Time:0.054sec normalization success = aa3e29d211ec15bde1fd17c39c2a870a19f8b7e5a5ab3970f8f13313.PubTator.PubTator|aa3e29d211ec15bde1fd17c39c2a870a19f8b7e5a5ab3970f8f13313.PubTator.PubTator.Gene

[minstar]

@majdabd Thank you for your patience.

We reproduce the same issue in Java version 13. (especially openjdk 13.0.7 version)
We think that tmvar is normally operating on Java 8~11 version. (we use openjdk 1.8.0_352 in webserver)
Could you please check your Java version?

[majdabd]

Hello, this is the Java OpenJDK version on our cluster :
openjdk 11.0.20 2023-07-18
OpenJDK Runtime Environment (build 11.0.20+8-post-Ubuntu-1ubuntu122.04)
OpenJDK 64-Bit Server VM (build 11.0.20+8-post-Ubuntu-1ubuntu122.04, mixed mode, sharing)

Should I ask for a downgrade?

UPDATE : We did downgrade to Java 8 (openjdk 1.8.0_352) and it did not work.

Do you think if we use tmVar3.0 instead of tmVar2.0, we won't have this issue?

Thanks a lot for the help

[minstar]

Hi, does your output show the same result as before?

Could you please show the log info from nohup_tmvar.out?

We didn't try for the tmVar3.0 thus we don't really think that changing the version could resolve the issue.

[majdabd]

Hello. Yes, the same result as before, which is no tmVar results, no matter the Java version or text I use. Find below the log info from nohup_tmvar.out after I cleared everything and re-installed everything from the beginning:

Starting tmVar 2.0 Service at 127.0.1.1:18896
Reading POS tagger model from lib/taggers/english-left3words-distsim.tagger ... done [0.9 sec].
Loading tmVar : Processing Time:0.963sec
Ready
input/ac681be0f560890d622ea19f57f7e361f89d24214d3b63fd41545f7c.PubTator - (PubTator format) : Processing Time:0.227sec
ner success = ac681be0f560890d622ea19f57f7e361f89d24214d3b63fd41545f7c.PubTator
output/ac681be0f560890d622ea19f57f7e361f89d24214d3b63fd41545f7c.PubTator.PubTator.PubTator
input/ac681be0f560890d622ea19f57f7e361f89d24214d3b63fd41545f7c.PubTator.PubTator - (PubTator format) : Processing Time:0.123sec
normalization success = ac681be0f560890d622ea19f57f7e361f89d24214d3b63fd41545f7c.PubTator.PubTator|ac681be0f560890d622ea19f57f7e361f89d24214d3b63fd41545f7c.PubTator.PubTator.Gene

[minstar]

Sorry @majdabd

I've tried to simulate your situation several times in my environment, but I still can resolve the same issue by downgrading the JAVA version.
Also, I don't know why it keeps generating an error in your environment.

[majdabd]

Thanks, @minstar for the effort. I've been looking into the issue for a week now, and don't have the slightest clue why this is happening. I have installed and ran BERN2 on 4 different machines, using exactly the same steps as in the README and still, I never get "mutations" on any of them. Have you tried running it from scratch on a new machine? Thanks

[minstar]

I've tried to install BERN2 on 3 different machines same steps as suggested in README.
I'm sorry to say that I don't know why the mutation types aren't properly working.

[majdabd]

Hello @minstar . Is there a way to disable or ignore tmVar? If it is not working, I don't want the users of my app to needlessly download tmVar2.0 resources. Thanks

[minstar]

Hi @majdabd,
sorry for the late reply.

I think you could comment out the tmVar process in the bern2.py file.
If it is not working, please let me know.
I will help you in detail.

[DunCer]

I meet the same problem as you, but now I've solved it. I think you should check if the crf_test runs smoothly, Otherwise, you should re-check and install the CRF.

[mjeensung]

Thanks @DunCer for sharing your solution!