monarch-initiative/HpoTextMining

Name: HpoTextMining

Owner: Monarch Initiative

Description: Perform text mining for identification of HPO terms in free text from scientific publication.

Created: 2017-06-20 20:52:42.0

Updated: 2017-11-09 17:19:23.0

Pushed: 2017-12-13 19:26:02.0

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Size: 1171

Language: Java

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README

HpoTextMining

HpoTextMining allows convenient curation of phenotype information

Aim

The aim of HpoTextMining is to allow easy & convenient curation of phenotypic information using Human Phenotype Ontology (HPO). The software is designed to be a plugin in more complex curation software built using JavaFX framework.

How to use

The HpoTextMining presents a dialog window to the curator/user. The dialog window consists of following subparts:

• approved terms table - table (at the bottom) that contains the approved phenotype terms. The terms which are inside the table will be returned as results after closing or hitting OK button of the dialog
• ontology tree pane - tree hierarchy of the ontology is displayed on the left side of the dialog. User can expand individual levels and add selected terms into the approved terms table
• text-mining pane - place where user submits a query text that is mined for HPO terms. Then, results of the analysis are presented in the same pane

How to use in JavaFX app

In order to use HpoTextMining in your project, add the following dependency into your pom.xml file.

endency>
<groupId>com.github.monarch-initiative</groupId>
<artifactId>hpotextmining-core</artifactId>
<version>0.2.1</version>
pendency>

Example usage

See Main and ApplicationConfig classes of the hpotextmining-demo module to see an example usage.