Module org.monarchinitiative.hpotextmining.core

Package org.monarchinitiative.hpotextmining.core.miners

Interface TermMiner

All Known Implementing Classes:

BiolarkTermMiner, SciGraphTermMiner

public interface TermMiner

Classes implementing this interface are able to mine a set of MinedTerms from given query.

The query is a free text, usually containing a description of a clinical situation of the patient/proband. The aim of the text-mining is to identify a set of HPO terms that represent patient's phenotype. Terms may be either present or absent (see MinedTerm for more info). Set of identified terms is presented to the user/curator for further approval/rejection.

Since:

0.2

Version:

0.2.1

Author:

Daniel Danis

Method Summary

Modifier and Type	Method	Description
Collection<MinedTerm>	doMining(String query)	Parse given query String and return set of SimpleMinedTerms representing HPO terms identified in the query.

Method Details

doMining

Collection<MinedTerm> doMining(String query)
                        throws TermMinerException

Parse given query String and return set of SimpleMinedTerms representing HPO terms identified in the query.

The mining process might be blocking so it would be nice to perform the mining on another thread than the event loop thread of a Gui.

Parameters:

query - String containing text about to be searched for HPO terms

Returns:

Set of SimpleMinedTerms representing HPO terms and their positions in the query text

Throws:

TermMinerException - if there is any problem with HPO mining