Module org.monarchinitiative.hpotextmining.core

Package org.monarchinitiative.hpotextmining.core.miners.scigraph

Class SciGraphTermMiner

java.lang.Object

org.monarchinitiative.hpotextmining.core.miners.scigraph.SciGraphTermMiner

All Implemented Interfaces:

TermMiner

public class SciGraphTermMiner
extends Object
implements TermMiner

This class allows using Monarch SciGraph Server for text mining. TODO: take out the server configuration parameters to generalize it (and merge it to AskTudorServer) if necessary

Since:

0.2.2

Version:

0.2.3

Author:

Aaron Zhang

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SciGraphTermMiner.ConnectionFactory	Each time the text mining is requested we send the query to the server using a new connection.

Constructor Summary

Constructors

Constructor	Description
SciGraphTermMiner(URL server)

Method Summary

Modifier and Type	Method	Description
Set<MinedTerm>	doMining(String query)	Performs mining of the provided text using SciGraph service; query String is sent to the SciGraph API and the Thread is blocked until a JSON response is received.

Methods inherited from class java.lang.Object

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

Constructor Details

SciGraphTermMiner

public SciGraphTermMiner(URL server)

Method Details

doMining

public Set<MinedTerm> doMining(String query)
                        throws TermMinerException

Performs mining of the provided text using SciGraph service; query String is sent to the SciGraph API and the Thread is blocked until a JSON response is received. The response is then decoded into MinedTerms.

Specified by:

doMining in interface TermMiner

Parameters:

query - String with text to be mined for HPO terms

Returns:

Set of MinedTerms representing identified HPO terms. The set is empty, if I/O error occurs or if URL/query are invalid

Throws:

TermMinerException - if there is any problem with HPO mining