bern | neural named entity recognition and multi-type | Natural Language Processing library
kandi X-RAY | bern Summary
kandi X-RAY | bern Summary
BERN is a BioBERT-based multi-type NER tool that also supports normalization of extracted entities. This repository contains the official implementation of BERN. You can use BERN at or host your own server by following the description below. Please refer to our paper (Kim et al., IEEE Access 2019) for more details. This project is done by DMIS Laboratory at Korea University. The description below gives instructions on hosting your own BERN. Please refer to for the RESTful Web service of BERN.
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Top functions reviewed by kandi - BETA
- Handle GET request
- Convert a list of bern dictionaries into a string
- Converts a Pubtator XML document to a dictionary
- Recognize the input
- Convert entity to Publish annotation
- Return a Pubmed annotation
- Transformer transformer model
- Attention layer
- Apply dropout to input tensor
- Convert PMC ID to Pubtator
- Replace spaces
- Build model_fn
- Convert examples to features
- Perform normalization
- Download a PMC XML file
- Checks for Bernstein errors
- Creates attention mask from input tensors
- Test for stress test
- Embed word embedding
- Convert PubMed XML to Pubmed
- Recognize the input dataset
- Benchmark a test
- Convert a pubtator string to a dict
- Embedding postprocessor
- Convert Pubtator XML to a list of dicts
- Get MPC archive
- Handle POST request
- Recognize a given etype
bern Key Features
bern Examples and Code Snippets
Community Discussions
Trending Discussions on bern
QUESTION
In powershell I'm using
...ANSWER
Answered 2022-Mar-28 at 14:22Yes, you can use the static method IsDaylightSavingTime on the TimeZoneInfo class to get this information from a desired DateTime:
QUESTION
I built upon this thread to plot a spatial heatmap. The difference is that I do not want to compute the density of points because I already have the value for the level of "heat". In detail I want to plot the population density of the canton of Berne (Switzerland) with colour gradients.
The population data is from the Swiss statistical office and counts the inhabitants per hectare (100m x 100m squares), downloadable here (the "STATPOP2020.csv" file). Building on jlhoward answer in thread my code so far is:
...ANSWER
Answered 2022-Mar-20 at 14:15The problem, as you have already established, is that you want a contour map that represents population density, not the density of measurements, which is what stat_density_2d does. It is possible to create such an object in R, but it is difficult when the measurements are not spaced regularly on a grid (as is the case with this data). It may be best to use geom_point here for that reason:
QUESTION
I recently had an issue with a simple JS game, which I asked about here: Issue with negative scores in a simple JS game
It was fixed after I was advised to fix the else if statement. After that it worked fine.
I copied this game and swapped out the maths guessing part for a capital city guessing part, leaving everything else the same. The structure of the if/else if statements remains the same. However I am having the same issue again with the score not calculating correct, it starts increasing by more than 1x each time a question is answered.
The JS is:
...ANSWER
Answered 2022-Mar-20 at 04:21The problem is you keeping assigning the eventListener to the document.querySelector(".buttons") which cause problems.
Every time you trigger the game function, you will assign a new eventListener to .buttons which makes your every time you click the .button, you will trigger the game function for not only one time which makes the score doesn't work as you expected.
You could use Chrome developer tool to check that (if you are using chrome)
QUESTION
I'm a Scrapy enthusiast into scraping for 3 months. Because I really enjoy scraping, I ended up being frustrated and excitedly purchased a proxy package from Leafpad.
Unfortunetaly, when I uploaded them to my Scrapy spider, I recevied ValueError:
I used scrapy-rotating-proxies to integrate the proxies. I added the proxies which are not numbers but string urls like below:
...ANSWER
Answered 2022-Feb-21 at 02:25The way you have defined your proxies list is not correct. You need to use the format username:password@server:port and not server:port:username:password. Try using the below definition:
QUESTION
please I need help with my Java program. I am a beginner so it's really confusing for me. I am trying to build a multiple Question Trivia program. Whereby a user is prompted with a question and they have to choose from the given answers. If they get it right or wrong they are told, and also shown the time they took to answer the question. Now the problem is after they submit their answer to a question, they would be prompted if they want to play again and another question would come up. I have 2 lists 1 for questions ad 1 for answers I am iterating through the two lists with 2 for loops simultaneously so I am able to check if their input is the same as the answer for that question. I am stuck on getting out of the second loop so I can proceed with other questions, I have tried breaking the loop but it breaks and doesn't prompt the user for their answer. How can I solve this please. Here is my code Below, the main program starts at the for-loop
...ANSWER
Answered 2022-Mar-09 at 02:35Consider the following code. I have removed the timers for simplicity, and have converted it into a simple loop without any repeat code. Try running this yourself and note the changes from your code:
QUESTION
I am trying to download the HTML code of a website with requests and parse it with beautiful soup to get the source code of some images I want to download.
ANSWER
Answered 2022-Feb-02 at 19:55You need change line 6 with this images = soup.find_all('img') and add all this to an array than remove data:image/gif...
QUESTION
I'm implementing a simple conversion string to integer convertor in F#; the logic is, e.g from string to uint32:
ANSWER
Answered 2022-Jan-21 at 18:52You can do something like this:
QUESTION
I am having trouble adding a comma after the city in a column with City State Zip.
Example:
New Bern NC 27856
Wilson NC 27866
Desired Result:
New Bern, NC 27856
Wilson, NC 27866
I am struggling because some cities are more than one word, so I cant use a substitute function. Also, text to columns is a mess when trying to manipulate city, state zip.
Any suggestions?
THANK YOU!
...ANSWER
Answered 2022-Jan-05 at 17:40I just tried this and it worked fine:
QUESTION
Currently, I'm building a dashboard for my home where I get temperature values from the Honeywell API. I'm trying to loop through a complex JSON that I got from the API to get all the device current temperatures.
Since I'm quite new to Python I have no clue how to get this sorted. Here is an example response:
...ANSWER
Answered 2022-Jan-03 at 20:35Looks like you've got a list containing one big dictionary. That dictionary has a devices key-value pair, where the value is a list of dictionaries, one for each device. If data is your JSON structure, you can iterate through the device-dictionaries in the following way:
QUESTION
I'm trying to call the REST API - such as https://randomuser.me/api/ and get the response logged and saved to a file in NestJS with Axios.
The rest call is in the Service class which is in turn is being accessed from the controller.
...ANSWER
Answered 2021-Nov-06 at 16:58Nest's HttpService returns an RxJS Observable which is kind of like a supercharged callback. By default await doesn't work on Observables, but Nest will handle the observable if you end up sending one back from your controller. To be able to await the observable, you need to wrap the observable in the lastValueFrom method from rxjs. If you want to just use Observables for the entire call, then you need to make use of .pipe and rxjs/operators, probably tap for logging. Something like this should do
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install bern
Install python packages
Install GNormPlus & run GNormPlusServer.jar FYI: Download Google Drive files with WGET: https://gist.github.com/iamtekeste/3cdfd0366ebfd2c0d805#gistcomment-2316906
Install tmVar2 & run tmVar2Server.jar
Download normalization resources and pre-trained BioBERT NER models
Run named entity normalizers
Run BERN server
Usage PMID(s) (HTTP GET) http://<YOUR_SERVER_ADDRESS>:8888/?pmid=<a PMID or comma seperate PMIDs>&format=<json or pubtator> Example: http://<YOUR_SERVER_ADDRESS>:8888/?pmid=30429607&format=json&indent=true Example: http://<YOUR_SERVER_ADDRESS>:8888/?pmid=30429607&format=pubtator Example: http://<YOUR_SERVER_ADDRESS>:8888/?pmid=30429607,29446767&format=json&indent=true Raw text (HTTP POST) POST Address: http://<YOUR_SERVER_ADDRESS>:8888 Set key, value of a body as follows: import requests import json body_data = {"param": json.dumps({"text": "CLAPO syndrome: identification of somatic activating PIK3CA mutations and delineation of the natural history and phenotype. PURPOSE: CLAPO syndrome is a rare vascular disorder characterized by capillary malformation of the lower lip, lymphatic malformation predominant on the face and neck, asymmetry, and partial/generalized overgrowth. Here we tested the hypothesis that, although the genetic cause is not known, the tissue distribution of the clinical manifestations in CLAPO seems to follow a pattern of somatic mosaicism. METHODS: We clinically evaluated a cohort of 13 patients with CLAPO and screened 20 DNA blood/tissue samples from 9 patients using high-throughput, deep sequencing. RESULTS: We identified five activating mutations in the PIK3CA gene in affected tissues from 6 of the 9 patients studied; one of the variants (NM_006218.2:c.248T>C; p.Phe83Ser) has not been previously described in developmental disorders. CONCLUSION: We describe for the first time the presence of somatic activating PIK3CA mutations in patients with CLAPO. We also report an update of the phenotype and natural history of the syndrome."})} response = requests.post('http://<YOUR_SERVER_ADDRESS>:8888', data=body_data) result_dict = response.json() print(result_dict)
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