Name: miring-validator

Owner: NMDP/Be The Match Bioinformatics Research

Description: Semantic Validator for MIRING-compliant HML

Created: 2015-05-26 21:55:02.0

Updated: 2017-03-23 20:18:59.0

Pushed: 2016-12-13 15:25:54.0

Homepage: null

Size: 3484

Language: Java

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Semantic Validator for MIRING-compliant HML National Marrow Donor Program (NMDP)

This is a REST service that validates an HML file according to a MIRING checklist, and returns a XML report specifying any encountered MIRING or HML infractions.

You can import this project into eclipse (Import as a Maven Project), or use the text editor of your choice. I recommend you use java 1.8 and MAVEN to build.

Build MiringValidator.war file using MAVEN:
$ mvn clean install

Deploy /target/MiringValidator.war to your Tomcat 8.0 server, or run within MAVEN:
$ mvn clean install tomcat7:run-war

Once your tomcat server is running, you should find the web interface at:


MIRING stands for Minimum Information for Reporting Next Generation Sequence Genotyping, and represents a minimum checklist of data to be included in a NGS report.

MIRING is independant of data platform, but this validator is based on HML 1.0.1.

See a MIRING Compliant HML sample at http://schemas.nmdp.org

MIRING: http://biorxiv.org/content/early/2015/02/16/015230
HML: http://biorxiv.org/content/early/2015/02/06/014951

MIRING rules are based on 8 general elements:

MIRING Element 1 - Message Annotation

Message Generator Contact Information & Document Identification

MIRING Element 2 - Reference Context MIRING Element 3 - Full Genotype MIRING Element 4 - Consensus Sequence MIRING Element 5 - Novel Polymorphisms MIRING Element 6 - Platform Documentation MIRING Element 7 - Read Processing Documentation MIRING Element 8 - Primary Data

The validator further divides these elements into rules. For more information on MIRING elements and a rule ID reference, see http://miring.b12x.org/MoreInfo.html or the local github wiki HERE.

This validator engine is powered by SAX Parser and Probatron4j, an excellent implementation of Schematron

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.