scispacy | full spaCy pipeline and models | Natural Language Processing library
kandi X-RAY | scispacy Summary
kandi X-RAY | scispacy Summary
This repository contains custom pipes and models related to using spaCy for scientific documents. In particular, there is a custom tokenizer that adds tokenization rules on top of spaCy's rule-based tokenizer, a POS tagger and syntactic parser trained on biomedical data and an entity span detection model. Separately, there are also NER models for more specific tasks.
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Top functions reviewed by kandi - BETA
- Create a TensorFlow annotation file
- Read full PubMed mentions from a directory
- Remove overlapping entities
- Returns the path to a file or URL
- Return a MedMentionExample from a string
- An iterator that yields examples from a file
- Evaluate the sentence splitting
- Creates a combined rule tokenizer
- Return the combined rule prefixes
- Removes newlines from text
- Read the concept details from the MRCONSO
- Read the header of the ULS file
- Read data from a tsv file
- Parse sentence
- Loads the parser data for a given path
- Load nearest neighbors index
- Read word frequencies
- Return a local path or a local path
- Evaluate a nlp model
- Read UUMLS types
- Return a generator that yields spacy examples from a directory
- Read all PubMed mentions from a directory
- Count the words in a text file
- Merge counts
- Creates a new corpus from a tsv file
- Replaces the tokenizer with the combined tokenizer
- Create a combined rule model
- R Parallelize a function on an iterator
scispacy Key Features
scispacy Examples and Code Snippets
Lines of Code : 195License : Non-SPDX (NOASSERTION)
Copyclinspacy_output_file %>%
bind_clinspacy_embeddings(mtsamples[1:5, 1:2])
#> clinspacy_id note_id description emb_001 emb_002 emb_003
#> 1 1 1 A 23-year-old clinspacy_output_file %>%
bind_clinspacy_embeddings(mtsamples[1:5, 1:2],
type = 'cui2vec')
#> clinspacy_id note_id description emb_001 emb_002 em clinspacy_output_file =
mtsamples[1:5, 1:2] %>%
clinspacy(df_col = 'description',
return_scispacy_embeddings = TRUE,
verbose = FALSE,
output_file = file.path(rappdirs::user_data_dir('clinspacy'),
Community Discussions
Trending Discussions on scispacy
QUESTION
I am working on extracting entities from scientific text (I am using scispacy) and later I will want to extract relations using hand-written rules. I have extracted entities and their character span successfully, and I can also get the pos and dependency tags for tokens and noun chunks. So I am comfortable with the two tasks separately, but I want to bring the two together and I have been stuck for a while.
The idea is that I want to be able to write rules such as: (just an example) if in a sentence/clause there are two entities where the first one is a 'DRUG/CHEMICAL' + is the subject, and the second one is a 'DISEASE' + is an object --> (then) infer 'treatment' relation between the two.
If anyone has any hints on how to approach this task, I would really appreciate it. Thank you!
S.
What I am doing to extract entities:
doc = nlp(text-with-more-than-one-sent)
for ent in doc.ents:
ANSWER
Answered 2022-Apr-04 at 05:21You can use the merge_entities mini-component to convert entities to single tokens, which would simplify what you're trying to do. There's also a component to merge noun chunks similarly.
QUESTION
import spacy
import scispacy
nlp = spacy.load('en_core_sci_lg')
for text1 in df1['priceDescription']:
doc1 = nlp(text1)
for text2 in df2['Description']:
doc2 = nlp(text2)
similarity = doc1.similarity(doc2)
#print(doc1.text, doc2.text, similarity)
output = (f'{doc1.text:26} | {doc2.text:26} | {similarity:.2}')
print(output)
ANSWER
Answered 2021-Dec-13 at 04:04This takes the strings you were previously printing to stdout, and instead gathers them into a list and returns the list. For future reference, you should note how little I had to change to make this work.
QUESTION
I found this below code from kaggel, every time I run the code gets ValueError. This is because of new version of SpaCy.Please Help Thanks in advance
...ANSWER
Answered 2021-Mar-02 at 05:15The way add_pipe works changed in v3; components have to be registered, and can then be added to a pipeline just using their name. In this case you have to wrap the LanguageDetector like so:
QUESTION
This code works as expected when using Spacy 2.3.1, but throws an exception on the third line when using Spacy 3.0.1 (we also updated scispacy from .0.2.5 to 0.4.0:
...ANSWER
Answered 2021-Mar-08 at 10:36UmlsEntityLinker is indeed a custom component from scispacy.
It looks like the v3 equivalent is:
QUESTION
What this message is about? How to remove this warning message.Thank You.
...ANSWER
Answered 2021-Mar-03 at 09:16The lemmatizer is a separate component from the tagger in spacy v3. Disable the lemmatizer along with the tagger to avoid these warnings:
QUESTION
With Gensim, there are three functions I use regularly, for example this one:
...ANSWER
Answered 2020-Dec-08 at 19:42A possible way to achieve your goal would be to:
- parse you documents via
nlp.pipe- collect all the words and pairwise similarities
- process similarities to get the desired results
Let's prepare some data:
QUESTION
I am trying to build NER model of clinical data using ScispaCy in colab. I have installed packages like this.
...ANSWER
Answered 2020-Dec-05 at 14:10I hope I am not too late... I believe you are very close to the correct approach.
I will write my answer in steps and you can choose where to stop.
Step 1)
QUESTION
I have installed all the packages. while importing them am getting an error like "cannot import name 'combined_rule_sentence_segmenter'". How to import packages properly.
...ANSWER
Answered 2020-Sep-15 at 13:25use en_core_sci_sm-0.2.5 instead of en_core_sci_sm-0.2.0
!pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.2.5/en_core_sci_sm-0.2.5.tar.gz
QUESTION
I want to build a model similar to sciSpacy, but for another domain. How should I go about this?
...ANSWER
Answered 2020-Apr-22 at 08:20You'll have to first make sure you have enough training data about your new domain. If you want to have a Named Entity Recognizer, you need texts annotated with named entities. If you want to have a parser, you need texts with dependency annotations. If you want a POS tagger, you need texts annotated with POS tags, etc.
Then you can create a new blank model, add the component(s) to them you need, and start training those:
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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Install scispacy
Follow the installation instructions for Conda.
Create a Conda environment called "scispacy" with Python 3.6: conda create -n scispacy python=3.6
Activate the Conda environment. You will need to activate the Conda environment in each terminal in which you want to use scispaCy. source activate scispacy
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