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io.github.msdk:msdk-db-mona

MassBank of America (MoNA), is an auto curating repository for storing, comparing and querying mass spectra of chemical compounds. It is metadata centric and it was designed to allow easy integration into other tools by utilize its REST based application programming interface. At the current time it contains over 200k predicted and 40k unique experimental mass spectra and their associated metadata. The predicted spectra were obtained by utilizing the lipid blast library and the experimental spectra were acquired from 30 different facilities all over the world, including several major research facilities in the United States and Japan. MoNA is utilizing the InChI Key as unique identifier for chemicals and is designed for easy scalability and expendability. This is realized by utilizing common applications like nginx, grails, AngularJS, postgresSQL and tomcat. MoNA is currently integrated in applications like MSDial, BinBase, MZMine and the statistics package R. This was accomplished by utilizing its REST based API, which is also utilized by its main AngularJS based web interface. We consider MoNA to be highly useful for crosslinking mass spectra in publications, identification of unknowns and integration in data acquisition software. This package provides you with access to the REST api of the main MoNA installation.

License

License
GroupId

GroupId

io.github.msdk
ArtifactId

ArtifactId

msdk-db-mona
Last Version

Last Version

0.0.27
Release Date

Release Date
Type

Type

jar
Description

Description

MassBank of America (MoNA), is an auto curating repository for storing, comparing and querying mass spectra of chemical compounds. It is metadata centric and it was designed to allow easy integration into other tools by utilize its REST based application programming interface. At the current time it contains over 200k predicted and 40k unique experimental mass spectra and their associated metadata. The predicted spectra were obtained by utilizing the lipid blast library and the experimental spectra were acquired from 30 different facilities all over the world, including several major research facilities in the United States and Japan. MoNA is utilizing the InChI Key as unique identifier for chemicals and is designed for easy scalability and expendability. This is realized by utilizing common applications like nginx, grails, AngularJS, postgresSQL and tomcat. MoNA is currently integrated in applications like MSDial, BinBase, MZMine and the statistics package R. This was accomplished by utilizing its REST based API, which is also utilized by its main AngularJS based web interface. We consider MoNA to be highly useful for crosslinking mass spectra in publications, identification of unknowns and integration in data acquisition software. This package provides you with access to the REST api of the main MoNA installation.

Download msdk-db-mona

Filename Size
msdk-db-mona-0.0.27.pom
msdk-db-mona-0.0.27.jar 35 KB
msdk-db-mona-0.0.27-sources.jar 22 KB
msdk-db-mona-0.0.27-javadoc.jar 123 KB
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How to add to project

<!-- https://jarcasting.com/artifacts/io.github.msdk/msdk-db-mona/ -->
<dependency>
    <groupId>io.github.msdk</groupId>
    <artifactId>msdk-db-mona</artifactId>
    <version>0.0.27</version>
</dependency>
// https://jarcasting.com/artifacts/io.github.msdk/msdk-db-mona/
implementation 'io.github.msdk:msdk-db-mona:0.0.27'
// https://jarcasting.com/artifacts/io.github.msdk/msdk-db-mona/
implementation ("io.github.msdk:msdk-db-mona:0.0.27")
'io.github.msdk:msdk-db-mona:jar:0.0.27'
<dependency org="io.github.msdk" name="msdk-db-mona" rev="0.0.27">
  <artifact name="msdk-db-mona" type="jar" />
</dependency>
@Grapes(
@Grab(group='io.github.msdk', module='msdk-db-mona', version='0.0.27')
)
libraryDependencies += "io.github.msdk" % "msdk-db-mona" % "0.0.27"
[io.github.msdk/msdk-db-mona "0.0.27"]

Dependencies

compile (8)

Group / Artifact Type Version
io.github.msdk : msdk-datamodel jar 0.0.27
com.eclipsesource.minimal-json : minimal-json jar 0.9.2
commons-lang : commons-lang jar 2.4
org.glassfish.jersey.media : jersey-media-json-jackson jar 2.17
org.glassfish.jersey.core : jersey-client jar 2.17
org.slf4j : slf4j-api jar 1.7.26
com.google.code.findbugs : jsr305 jar 3.0.2
com.google.guava : guava jar 27.1-jre

test (5)

Group / Artifact Type Version
junit : junit jar 4.12
org.mockito : mockito-core jar 2.27.0
org.hamcrest : hamcrest-library jar 1.3
com.github.stefanbirkner : system-rules jar 1.16.1
org.slf4j : slf4j-simple jar 1.7.26

Project Modules

There are no modules declared in this project.

About MSDK

Build Status Maven Central

Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing mass spectrometry data. The goals of the library are to provide a flexible data model with Java interfaces for mass-spectrometry related objects (including raw spectra, processed data sets, identification results etc.) and to integrate the existing algorithms that are currently scattered around various Java-based graphical tools.

Java version

MSDK requires Java runtime (JRE) version 8 or newer.

Usage

API

Please see the complete MSDK API.

Maven artifacts

MSDK jars are automatically deployed to Maven Central. In order to use MSDK, simply add the following dependency to your pom.xml:

 <dependency>
    <groupId>io.github.msdk</groupId>
    <artifactId>msdk-all</artifactId>
    <version>0.0.27</version>
 </dependency>

Development

Tutorial

Please read our brief tutorial on how to contribute new code to MSDK.

Code style

  • We use the Google Java Style Guide (https://github.com/google/styleguide)
  • You can use the eclipse-java-google-style.xml file to automatically format your code in the Eclipse IDE
  • Please write JavaDoc comments as full sentences, starting with a capital letter and ending with a period. Brevity is preferred (e.g., "Calculates standard deviation" instead of "This method calculates and returns a standard deviation of given set of numbers").

Logging

MSDK uses the SLF4J library for logging. This library can forward all logging calls to your favorite logging framework (java.util.logging, Apache log4j, or others). Please see SLF4J documentation for details.

Building

See the BUILD.md file

io.github.msdk

Mass Spectrometry Development Kit (MSDK)

MSDK is a collaborative project developing a Java library of algorithms for mass spectrometry data processing.

Versions

Version
0.0.27
0.0.26
0.0.25
0.0.24
0.0.23
0.0.22
0.0.21
0.0.20
0.0.19
0.0.18
0.0.17
0.0.16
0.0.15
0.0.14
0.0.13
0.0.12
0.0.11
0.0.10
0.0.9
0.0.8
0.0.7
0.0.6
0.0.5
0.0.4
0.0.3
0.0.2