MiringValidator

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:
http://localhost:8080/MiringValidator

MIRING:

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

RULES

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

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