| File | Date | Author | Commit |
|---|---|---|---|
| ABioNLP | 2018-02-28 |
Shyam Diwakar
|
[8e4420] Initial commit |
| DB_Sql | 2018-02-28 |
Shyam Diwakar
|
[8e4420] Initial commit |
| .gitattributes | 2018-02-28 |
Shyam Diwakar
|
[8e4420] Initial commit |
| README.md | 2018-02-28 |
Shyam Diwakar
|
[8dc3be] Updated README.md |
| Readme.txt | 2018-02-28 |
Shyam Diwakar
|
[8e4420] Initial commit |
This tool is part of the paper "Mining Scientific Articles for Inter-Relationships and Visualisation: Natural Language Processing for Systems Biology Modeling" by Nidheesh Melethadathil, Priya Chellaiah, Jaap Heringa, Bipin Nair and Shyam Diwakar. (manuscript submitted)
Code contributors: Nidheesh Melethdathil and Shyam Diwakar
Computational Neuroscience Lab, Amrita School of Biotechnology
Amrita Vishwa Vidyapeetham, Kollam, Kerala, India.
www.amrita.edu/compneuro
This framework uses different open source application and interfaces for article retrieval, document clustering and visualization. This is web based or runs on Tomcat with two other third party APIs for cluster label validation and visualization.
Installation requires following steps to be executed.
Download and install Java (https://java.com/en/download/) in the server.
Download and configure Tomcat (ideally through a IDE like NetBeans or Eclipse) webserver in the computer. Available at https://netbeans.org/downloads/.
a. In Netbeans 8 you may have to install the Tomcat plugin manually. After you download and extract Tomcat follow these steps:
b. Tools -> Plugins -> Available plugins, search for 'tomcat' and install the one named "Java EE Base plugin".
c. Restart Netbeans
d. On the project view (default left side of the screen), go to services, right click on Servers and then "Add Server"
e. Select Apache Tomcat, enter username and password and config the rest and finish.
Download and configure MySQL database. Preferably install WAMP server from following link. https://sourceforge.net/projects/wampserver/ in the server and import the tables from BioNLP.sql file available in the Db_Sql folder).
Download and configure Neo4j(https://neo4j.com/download/), the Graph database in the root folder.
Download and copy MetaMap, the UMLS Metathesaurus files available from https://metamap.nlm.nih.gov/JavaApi.shtml to root folder.
Server Side
1. Start three services of MetaMap (by executing the corresponding .bat files available in \public_mm_win32_main_2012\public_mm\bin folder)
a. Skrmedpostctl
b. Wsdserverctl
c. mmserver12
Start Neo4j database
Run the build for this NLP tool in NetBeans which will start Tomcat server and will make the NLP tool available at http://localhost:8080/project_new/.
Browser Side
1. Open the web application and provide authentication details like username and password.
Provide the search term, select the algorithm and specify the number of documents to be retrieved to submit the query.
Depends on selection of algorithm, user may provide different values for the parameters.
The results of retrieval after clustering is displayed as radial graphs like a star with nodes representing the cluster.
Click on the circle with cluster label to see the articles grouped in that cluster labels. These articles are listed in the right side section of the screen. Clicking on title of the articles will display the abstract for the paper.
