clulab / reach

Reach Biomedical Information Extraction

Version Matrix

Build Status Maven Central

Reach

What is it?

Reach stands for Reading and Assembling Contextual and Holistic Mechanisms from Text. In plain English, Reach is an information extraction system for the biomedical domain, which aims to read scientific literature and extract cancer signaling pathways. Reach implements a fairly complete extraction pipeline, including: recognition of biochemical entities (proteins, chemicals, etc.), grounding them to known knowledge bases such as Uniprot, extraction of BioPAX-like interactions, e.g., phosphorylation, complex assembly, positive/negative regulations, and coreference resolution, for both entities and interactions.

Reach is developed using Odin, our open-domain information extraction framework, which is released within our processors repository.

Please scroll down to the bottom of this page for additional resources, including a Reach output visualizer, REST API, and datasets created with Reach.

Licensing

This project is, and will always be, free for research purposes. However, starting with version 1.2, we are using a license that restricts its use for commercial purposes. Please contact us for details.

Changes

  • 1.4.0 - Require separate Processors Server (Reach is the client). Add CLUProcessor type.
  • 1.4.0 - Update to use Processors 6.1.5 (for refactored Client/Server). Update run scripts.
  • much more...

Authors

Reach was created by the following members of the CLU lab at the University of Arizona:

Citations

If you use Reach, please cite one of the following papers:

@Article{Escarcega:2018,
  author={Valenzuela-Esc{\'a}rcega, Marco A and Babur, {\"O}zg{\"u}n and Hahn-Powell, Gus and Bell, Dane and Hicks, Thomas and Noriega-Atala, Enrique and Wang, Xia and Surdeanu, Mihai and Demir, Emek and Morrison, Clayton T},
  title={Large-scale Automated Machine Reading Discovers New Cancer Driving Mechanisms},
  journal={Database: The Journal of Biological Databases and Curation},
  url={http://clulab.cs.arizona.edu/papers/escarcega2018.pdf},
  doi={10.1093/database/bay098},
  year={2018},
  publisher={Oxford University Press}
}
@inproceedings{Valenzuela+:2015aa,
  author    = {Valenzuela-Esc\'{a}rcega, Marco A. and Gustave Hahn-Powell and Thomas Hicks and Mihai Surdeanu},
  title     = {A Domain-independent Rule-based Framework for Event Extraction},
  organization = {ACL-IJCNLP 2015},
  booktitle = {Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics and the 7th International Joint Conference on Natural Language Processing of the Asian Federation of Natural Language Processing: Software Demonstrations (ACL-IJCNLP)},
  url = {http://www.aclweb.org/anthology/P/P15/P15-4022.pdf},
  year      = {2015},
  pages = {127--132},
  Note = {Paper available at \url{http://www.aclweb.org/anthology/P/P15/P15-4022.pdf}},
}

More publications from the Reach project are available here.

Installation

This software requires Java 1.8, Scala 2.11, and CoreNLP 3.x or higher.

The jar is available on Maven Central. To use, simply add the following dependency to your pom.xml:

<dependency>
   <groupId>org.clulab</groupId>
   <artifactId>reach_2.11</artifactId>
   <version>1.4.0</version>
</dependency>

The equivalent SBT dependencies are:

libraryDependencies ++= Seq(
    "org.clulab" %% "reach" % "1.4.0"
)

How to compile the source code

This is a standard sbt project, so use the usual commands (i.e. sbt compile, sbt assembly, etc.) to compile. Add the generated jar files under target/ to your $CLASSPATH, along with the other necessary dependency jars. Take a look at build.sbt to see which dependencies are necessary at runtime.

Running Reach

Processing a directory of .nxml papers

The most common use of Reach is to process a directory containing one or more papers in the proper formats. A Wiki page documents the supported input formats.

Some configuration is necessary before running Reach. Please refer to the Running Reach Wiki page for detailed information on configuring and running Reach.

The Interactive Shell

An interactive shell can be run from the command line to process small fragments of entered text. The shell is useful for reviewing and understanding the operation of Reach, including NER, entity, and event processing and rule debugging. To start a Reach shell, run the runReachShell.sh script:

runReachShell.sh

At the shell prompt enter :help to get a list of available commands.

Modifying the code

Reach builds upon our Odin event extraction framework. If you want to modify event and entity grammars, please refer to Odin's Wiki page for details. Please read the included Odin manual for details on the rule language and the Odin API.

Reach web services

We have developed a series of web services on top of the Reach library. All are freely available here.

Reach datasets

We have generated multiple datasets by reading publications from the open-access PubMed subset using Reach. All datasets are freely available here.

Funding

The development of Reach was funded by the DARPA Big Mechanism program under ARO contract W911NF-14-1-0395.