The splash, this is the reference documentation
C++ Java C# Python Scala HTML Other
Latest commit a17aa21 Dec 12, 2016 @ssmehta ssmehta committed on GitHub Merge pull request #32 from egonw/fix/citationR
Added a CITATION file for the R package (closes #30)

README.md

SPLASH

The Spectral Hash

The SPLASH (SPectraL hASH) is an unambiguous, database-independent spectral identifier, just as the InChIKey is designed to serve as a unique identifier for chemical structures. It contains separate blocks that define different layers of information, separated by dashes. For example, the full SPLASH of a caffeine mass spectrum above is splash10-0002-0900000000-b112e4e059e1ecf98c5f. The first block is the SPLASH identifier, the second and third are summary blocks, and the fourth is the unique hash block.

This repository contains:

  • The current reference implementations for the SPLASH written in Java
  • Additional implementations in C++, Python, C# and R
  • API wrappers in Scala and JavaScript
  • A Java validation tool
  • A web service with REST endpoints written in Java (accessible at http://splash.fiehnlab.ucdavis.edu) with Docker build files

SPLASH has been published in Nature Biotechnology. If using SPLASH, please cite:

Wohlgemuth, G, et al., SPLASH, a Hashed Identifier for Mass Spectra. Nature Biotechnology 34, 1099-101 (2016). doi:10.1038/nbt.3689

Contents

Java API

Building

To build the project, run all tests and install the SPLASH jar files in the local Maven repository, simply run:

mvn clean install

Maven Dependency

The reference implementation jar file is available from the Fiehn Lab Public Maven Repository:

<repository>
    <id>releases</id>
    <name>Fiehnlab Public Maven Repository</name>
    <url>http://gose.fiehnlab.ucdavis.edu:55000/content/groups/public</url>
</repository>

To use SPLASH in a Maven project, add the following section to the project's pom.xml file:

<dependency>
    <groupId>edu.ucdavis.fiehnlab.splash</groupId>
    <artifactId>core</artifactId>
    <version>1.8</version>
</dependency>

Usage

To generate a SPLASH for the following mass spectrum of caffeine with MassBank identifier PR100026,

m/z        intensity
138.0641   71.59
195.0815   261.7

build a Spectrum object from a list of ion-intnsity pairs and use the SplashFactory to utilize the default SPLASHer:

Splash splash = SplashFactory.create();
Spectrum spectrum = new SpectrumImpl(Arrays.asList(new Ion(138.0641, 71.59), new Ion(195.0815, 261.7)), SpectraType.MS);
String splash = splash.splashIt(spectrum);

Alternatively, you can also utilize the SplashUtil class to directly SPLASH a spectrum in a string representation:

String splash = SplashUtil.splash("138.0641:71.59 195.0815:261.7", SpectraType.MS);

We are also providing an easy way to connect a listener to the splashing algorithm, so that you can inspect the different blocks, before they are hashed. This can be done with directly adding a SplashListener to your Splash instance or alternativly using the util like this

String splash = SplashUtils.splash("138.0641:71.59 195.0815:261.7", SpectraType.MS, new SplashListener() {
    @Override
    public void eventReceived(SplashingEvent e) {}

    @Override
    public void complete(Spectrum spectrum, String splash) {}
});

Validation Tool

In addition to the reference implementations, we provide a simple validation tool that is used to ensure consistent and accurate SPLASH generation between tools and implementations. The latest jar file is available from the Fiehn Lab Public Maven Repository.

to run this tool (from the sources) please clone and build the project and afterwards run

java -jar validation-1.8.jar

For example, to validate a file against thr reference implementation, run the following from the project root:

java -jar validation/target/validation-1.8.jar -c -s 2 -t ms ./base-dataset/spectra/notsplashed/test-set-v1.csv base-dataset/spectra/test-set-with-splash-v1.csv

The specified flags indicate:

  • k = column number of the generated SPLASH
  • o = column number of the spectrum ID/origin
  • s = column number of the full mass spectrum in single-line string representation
  • t = type of spectrum to SPLASH (default: MS)
  • T = column delimiter
  • X = enable debug messages

The format for single-line string spectral representation follows:

ion:intensity ion:intensity ...

REST Service

The documentation for the REST service is available as a dedicated index page once you start the REST server using:

java -jar web/target/web-1.8.jar

If you like to use the official REST API, you can find it at: http://splash.fiehnlab.ucdavis.edu

Contributing

If you would like to contribute to this project, please feel submit issues or create a pull request.