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A full SpaCy pipeline and models for scientific/biomedical documents.

Project description

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.

Installation

Installing scispacy requires two steps: installing the library and intalling the models. To install the library, run:

pip install scispacy

to install a model (see our full selection of available models below), run a command like the following:

pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.2.0/en_core_sci_sm-0.2.0.tar.gz

Note: We strongly recommend that you use an isolated Python environment (such as virtualenv or conda) to install scispacy. Take a look below in the "Setting up a virtual environment" section if you need some help with this. Additionally, scispacy uses modern features of Python and as such is only available for Python 3.6 or greater.

Setting up a virtual environment

Conda can be used set up a virtual environment with the version of Python required for scispaCy. If you already have a Python 3.6 or 3.7 environment you want to use, you can skip to the 'installing via pip' section.

  1. Follow the installation instructions for Conda.

  2. Create a Conda environment called "scispacy" with Python 3.6:

    conda create -n scispacy python=3.6
    
  3. 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
    

Now you can install scispacy and one of the models using the steps above.

Once you have completed the above steps and downloaded one of the models below, you can load a scispaCy model as you would any other spaCy model. For example:

import spacy
nlp = spacy.load("en_core_sci_sm")
doc = nlp("Alterations in the hypocretin receptor 2 and preprohypocretin genes produce narcolepsy in some animals.")

Note on upgrading

If you are upgrading scispacy, you will need to download the models again, to get the model versions compatible with the version of scispacy that you have. The link to the model that you download should contain the version number of scispacy that you have.

Available Models

To install a model, click on the link below to download the model, and then run

pip install </path/to/download>

Alternatively, you can install directly from the URL by right-clicking on the link, selecting "Copy Link Address" and running

pip install CMD-V(to paste the copied URL)
Model Description Install URL
en_core_sci_sm A full spaCy pipeline for biomedical data with a ~100k vocabulary. Download
en_core_sci_md A full spaCy pipeline for biomedical data with a ~360k vocabulary and 50k word vectors. Download
en_core_sci_lg A full spaCy pipeline for biomedical data with a ~785k vocabulary and 600k word vectors. Download
en_ner_craft_md A spaCy NER model trained on the CRAFT corpus. Download
en_ner_jnlpba_md A spaCy NER model trained on the JNLPBA corpus. Download
en_ner_bc5cdr_md A spaCy NER model trained on the BC5CDR corpus. Download
en_ner_bionlp13cg_md A spaCy NER model trained on the BIONLP13CG corpus. Download

Additional Pipeline Components

AbbreviationDetector

The AbbreviationDetector is a Spacy component which implements the abbreviation detection algorithm in "A simple algorithm for identifying abbreviation definitions in biomedical text.", (Schwartz & Hearst, 2003).

You can access the list of abbreviations via the doc._.abbreviations attribute and for a given abbreviation, you can access it's long form (which is a spacy.tokens.Span) using span._.long_form, which will point to another span in the document.

Example Usage

import spacy

from scispacy.abbreviation import AbbreviationDetector

nlp = spacy.load("en_core_sci_sm")

# Add the abbreviation pipe to the spacy pipeline.
abbreviation_pipe = AbbreviationDetector(nlp)
nlp.add_pipe(abbreviation_pipe)

doc = nlp("Spinal and bulbar muscular atrophy (SBMA) is an \
           inherited motor neuron disease caused by the expansion \
           of a polyglutamine tract within the androgen receptor (AR). \
           SBMA can be caused by this easily.")

print("Abbreviation", "\t", "Definition")
for abrv in doc._.abbreviations:
	print(f"{abrv} \t ({abrv.start}, {abrv.end}) {abrv._.long_form}")

>>> Abbreviation	 Span	    Definition
>>> SBMA 		 (33, 34)   Spinal and bulbar muscular atrophy
>>> SBMA 	   	 (6, 7)     Spinal and bulbar muscular atrophy
>>> AR   		 (29, 30)   androgen receptor

UmlsEntityLinker (Alpha feature)

The UmlsEntityLinker is a SpaCy component which performs linking to the Unified Medical Language System. Note that this is currently an alpha feature. The linker simply performs a string overlap search on named entities, comparing them with a knowledge base of 2.7 million concepts using an approximate nearest neighbours search.

Because this component is a little rough around the edges, you may want to play around with some of the parameters below to adapt to your use case (higher precision, higher recall etc).

  • resolve_abbreviations : bool = True, optional (default = False) Whether to resolve abbreviations identified in the Doc before performing linking. This parameter has no effect if there is no AbbreviationDetector in the spacy pipeline.
  • k : int, optional, (default = 30) The number of nearest neighbours to look up from the candidate generator per mention.
  • threshold : float, optional, (default = 0.7) The threshold that a mention candidate must reach to be added to the mention in the Doc as a mention candidate.
  • no_definition_threshold : float, optional, (default = 0.95) The threshold that a entity candidate must reach to be added to the mention in the Doc as a mention candidate if the entity candidate does not have a definition.
  • filter_for_definitions: bool, default = True Whether to filter entities that can be returned to only include those with definitions in the knowledge base.
  • max_entities_per_mention : int, optional, default = 5 The maximum number of entities which will be returned for a given mention, regardless of how many are nearest neighbours are found.

This class sets the ._.umls_ents attribute on spacy Spans, which consists of a List[Tuple[str, float]] corresponding to the UMLS concept_id and the associated score for a list of max_entities_per_mention number of entities.

You can look up more information for a given id using the umls attribute of this class:

print(linker.umls.cui_to_entity[concept_id])

Example Usage

import spacy
import scispacy

from scispacy.umls_linking import UmlsEntityLinker

nlp = spacy.load("en_core_sci_sm")

# This line takes a while, because we have to download ~1GB of data
# and load a large JSON file (the knowledge base). Be patient!
# Thankfully it should be faster after the first time you use it, because
# the downloads are cached.
# NOTE: The resolve_abbreviations parameter is optional, and requires that
# the AbbreviationDetector pipe has already been added to the pipeline. Adding
# the AbbreviationDetector pipe and setting resolve_abbreviations to True means
# that linking will only be performed on the long form of abbreviations.
linker = UmlsEntityLinker(resolve_abbreviations=True)

nlp.add_pipe(linker)

doc = nlp("Spinal and bulbar muscular atrophy (SBMA) is an \
           inherited motor neuron disease caused by the expansion \
           of a polyglutamine tract within the androgen receptor (AR). \
           SBMA can be caused by this easily.")

# Let's look at a random entity!
entity = doc.ents[1]

print("Name: ", entity)
>>> Name: bulbar muscular atrophy

# Each entity is linked to UMLS with a score
# (currently just char-3gram matching).
for umls_ent in entity._.umls_ents:
	print(linker.umls.cui_to_entity[umls_ent[0]])
	

>>> CUI: C1839259, Name: Bulbo-Spinal Atrophy, X-Linked
>>> Definition: An X-linked recessive form of spinal muscular atrophy. It is due to a mutation of the 
  				gene encoding the ANDROGEN RECEPTOR.
>>> TUI(s): T047
>>> Aliases (abbreviated, total: 50):
         Bulbo-Spinal Atrophy, X-Linked, Bulbo-Spinal Atrophy, X-Linked, ....
    
>>> CUI: C0541794, Name: Skeletal muscle atrophy
>>> Definition: A process, occurring in skeletal muscle, that is characterized by a decrease in protein content,
                fiber diameter, force production and fatigue resistance in response to ...
>>> TUI(s): T046
>>> Aliases: (total: 9):
         Skeletal muscle atrophy, ATROPHY SKELETAL MUSCLE, skeletal muscle atrophy, ....

>>> CUI: C1447749, Name: AR protein, human
>>> Definition: Androgen receptor (919 aa, ~99 kDa) is encoded by the human AR gene.
                This protein plays a role in the modulation of steroid-dependent gene transcription.
>>> TUI(s): T116, T192
>>> Aliases (abbreviated, total: 16):
         AR protein, human, Androgen Receptor, Dihydrotestosterone Receptor, AR, DHTR, NR3C4, ...

Citing

If you use ScispaCy in your research, please cite ScispaCy: Fast and Robust Models for Biomedical Natural Language Processing. Additionally, please indicate which version and model of ScispaCy you used so that your research can be reproduced.

@inproceedings{Neumann2019ScispaCyFA,
  title={ScispaCy: Fast and Robust Models for Biomedical Natural Language Processing},
  author={Mark Neumann and Daniel King and Iz Beltagy and Waleed Ammar},
  year={2019},
  Eprint={arXiv:1902.07669}
}

ScispaCy is an open-source project developed by the Allen Institute for Artificial Intelligence (AI2). AI2 is a non-profit institute with the mission to contribute to humanity through high-impact AI research and engineering.

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