Module org.monarchinitiative.hpotextmining.core

Package org.monarchinitiative.hpotextmining.core.miners.biolark

Class BiolarkTermMiner

java.lang.Object

org.monarchinitiative.hpotextmining.core.miners.biolark.BiolarkTermMiner

All Implemented Interfaces:

TermMiner

public class BiolarkTermMiner
extends Object
implements TermMiner

This TermMiner uses Biolark web API to discover positions of HPO terms within provided query.

WarningThis Miner might not be working properly at the moment since the Biolark API is not running. Use SciGraphTermMiner instead

Since:

0.2

Version:

0.2.1

Author:

Daniel Danis

Constructor Summary

Constructors

Constructor	Description
BiolarkTermMiner(URL server)
BiolarkTermMiner(URLConnection connection)

Method Summary

Modifier and Type	Method	Description
Set<MinedTerm>	doMining(String query)	Performs mining of the provided text using Biolark service; query String is sent to the Biolark 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

BiolarkTermMiner

public BiolarkTermMiner(URLConnection connection)

BiolarkTermMiner

public BiolarkTermMiner(URL server)
                 throws IOException

Throws:

IOException

Method Details

doMining

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

Performs mining of the provided text using Biolark service; query String is sent to the Biolark 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