pt.ua.bioinformatics.coeus.api.plugins
Class OMIMPlugin

java.lang.Object
  pt.ua.bioinformatics.coeus.api.plugins.OMIMPlugin

public class OMIMPlugin
extends java.lang.Object

DiseaseCard plugin for OMIM data handling.

Generates initial gene and disease dataset based on OMIM's morbid map.

Constructor Summary

OMIMPlugin(Resource res)

Method Summary

java.util.HashMap<java.lang.String,Disease>	getDiseases()
java.util.HashMap<java.lang.String,Disease>	getGenotypes()
Resource	getRes()
void	itemize() OMIMPlugin controller.
void	setDiseases(java.util.HashMap<java.lang.String,Disease> diseases)
void	setGenotypes(java.util.HashMap<java.lang.String,Disease> genotypes)
void	setRes(Resource res)
void	triplify() Loads the in-memory data into COEUS SDB.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OMIMPlugin

public OMIMPlugin(Resource res)

Method Detail

getGenotypes

public java.util.HashMap<java.lang.String,Disease> getGenotypes()

setGenotypes

public void setGenotypes(java.util.HashMap<java.lang.String,Disease> genotypes)

getDiseases

public java.util.HashMap<java.lang.String,Disease> getDiseases()

setDiseases

public void setDiseases(java.util.HashMap<java.lang.String,Disease> diseases)

getRes

public Resource getRes()

setRes

public void setRes(Resource res)

itemize

public void itemize()

OMIMPlugin controller.

Workflow:

• Load genotype information from OMIM genemap
• Load phenotype information from OMIM morbidmap
• Import loaded dataset into COEUS SDB

triplify

public void triplify()

Loads the in-memory data into COEUS SDB.

Workflow

• Loads genotypes
• Loads genes for each genotype
• Loads genotypes for each genotype
• Loads genes for each phenotype