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A smorgasbord architecture for coreference resolution in biomedical text
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README_factuality.md Minor updates Jan 10, 2019
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README.md

Bio-SCoRes

A smorgasbord architecture for coreference resolution in biomedical text

Bio-SCoRes is a general, modular framework for coreference resolution in biomedical text. It is underpinned by a smorgasbord architecture, and incorporates a variety of coreference types (anaphora, appositive, etc.), their textual expressions (definite noun phrases, possessive pronouns, etc.) and allows fine-grained specification of coreference resolution strategies.

This Bio-SCoRes distribution includes the coreference resolution framework components and the linguistic components they rely on, as well as the coreference resolution pipelines that were used to evaluate the tool. These components are implemented in Java and are available from the URL: https://github.com/kilicogluh/Bio-SCoRes.

Prerequisites

  • Java (jar files have been generated with 1.8, though it is possible to recompile with 1.7)
  • Ant (needed for recompilation, version 1.8 was used for compilation)

Directory Structure

bin directory contains scripts to run sample coreference resolution pipelines and evaluate them.

dist directory contains libraries distributed with Bio-SCoRes. These are the following:

  • ling.jar: Contains the core linguistic components used by Bio-SCoRes.
  • bioscores.jar: Contains the coreference resolution components.
  • coreftasks.jar: Contains the coreference resolution pipelines.

To use Bio-SCoRes from your application, ensure that the first two jar files are included in your classpath. The third jar file (coreftasks.jar) is required if you plan to use/adapt the example coreference resolution pipelines described in the PLOS ONE article.

DATA directory contains the SPL drug coreference corpus and various input and output files derived from it, as well input and output files for the BioNLP protein coreference dataset experiments.

lib directory contains third-party libraries required by the system (see Note regarding Stanford Core NLP below.)

resources directory contains WordNet dictionary files that are required by the system.

The top level directory contains ant build file as well as properties files used by the pipelines.

  • coref_spl.properties: Properties for the SPL pipelines.
  • coref_bionlp.properties: Properties for the BioNLP pipeline.
  • coref.properties: Properties for the generic pipeline.
  • build.xml: Ant build file for all components.

Usage

If you're only interested in seeing the capabilities of Bio-SCoRes, a good starting point is to run the scripts provided in the bin directory, which correspond to the pipelines described in the PLOS ONE article and use the data provided. These scripts do not require any arguments and point to existing input and output directories under DATA. They can be modified to fit individual needs (see the Note below regarding i2b2/VA corpus).

  • splGoldMentions: The script for running coreference resolution on structured drug label (SPL) dataset with gold coreferential mentions. In other words, only mention-referent linking is performed.

  • splGoldEntities: The script for running coreference resolution on structured drug label (SPL) dataset with gold named entities. This pipeline consists of coreferential mention detection and mention-referent linking.

  • bionlp: The script for running anaphora/appositive resolution on BioNLP'11 Shared Task coreference dataset. This pipeline consists of mention detection and mention-referent linking.

  • genericPipeline: The script for running a generic pipeline. Input to this script is an input directory with text files and corresponding term annotations in brat standoff format and an output directory, where the results are written in the same standoff format. Note that to be effective, the term-related domain knowledge should have been introduced to the system as properties (See the Note below).

The evaluation scripts in the same directory (*Evaluate) can be used to evaluate the output generated by the system using one of the aforementioned scripts. For example, splGoldMentionsEvaluate script evaluates the results generated using splGoldMentions. The evaluation script will calculate precision, recall, and F1. In addition, true positives, false positives and negatives can be printed out. To ensure the integrity of the distribution, you can compare the the evaluation results generated with those in Evaluation directory to ensure that they match.

If you're interested in incorporating Bio-SCoRes into your NLP pipeline, a good starting point is the source code for the pipelines (each in its respective subpackage in tasks.coref.* package).

  • SPLCoreferencePipeline: The entry point for splGoldMentions and splGoldEntities scripts. It makes the most extensive use of the framework (all mention and coreference types).

  • BioNLPCoreferencePipeline: The entry point for bionlp script. This is the simplest pipeline and only performs anaphora and appositive resolution.

The generic pipeline mentioned above uses the corresponding class gov.nih.nlm.bioscores.core.GenericCoreferencePipeline.

To adapt a pipeline to your needs, it makes most sense to start with adapting loadStrategies() method where the coreference resolution strategies are defined. Components of each strategy are implemented in various gov.nih.nlm.bioscores.* subpackages. New components can also be defined by implementing interfaces such as Agreement, CandidateFilter, PostScoringCandidateFilter. Modifying the post-processing steps to tailor the coreference links generated by the system is the logical next step; postProcessing() method of the pipeline class deals with this task.

Note on Named Entity Recognition

Bio-SCoRes does not provide a named entity recognition module. However, for it to have some degree of success, it requires that terms (drugs, disorders, etc.) in the text have already been labeled and semantic types/groups that are relevant to the task have been introduced to the framework via java properties. You can examine coref*.properties files at the top level directory to get a feel for how semantic information can be defined within the framework. For example, coref_spl.properties contains mostly drug-related settings used by the SPL pipelines, while coref_bionlp.properties includes gene/protein related settings. Note that, in addition to semantic types/groups, these configuration files may define word lists for hypernyms (i.e., high level terms) and event triggers (for example, 'phosphorylation' for gene/proteins) of relevant semantic groups, which can be exploited by the Agreement methods of the framework. In their absence, the system can still generate results, but the performance is likely to suffer. See the PLOS ONE article for more details.

Note on the i2b2/VA corpus

Due to usage restrictions, we do not include data derived from the i2b2/VA corpus and experiment results based on this corpus. The corpus can be obtained from http://www.i2b2.org/NLP/Coreference and the XML input expected by the i2b2 pipeline can be generated using the tasks.coref.i2b2.I2B2ToXMLWriter class included. I2B2CoreferencePipeline in the same package can be used to perform coreference resolution on this input. The i2b2 pipeline reported in the paper was evaluated using the i2b2 coreference scorer, which can be obtained from the same URL.

Note on Stanford CoreNLP package

Stanford CoreNLP model jar file that is needed for processing raw text for lexical and syntactic information (stanford-corenlp-3.3.1-models.jar) is not included with the distribution due to its size. It can be downloaded from http://stanfordnlp.github.io/CoreNLP/ and copied to lib directory.

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