BIOLITMAP: a web-based geolocated and temporal visualization of the evolution of bioinformatics publications

Description

Code for the web-based geolocated and temporal visualization of bioinformatics research (BIOLITMAP): http://socialanalytics.bsc.es/biolitmap/.

Paper accepted to Oxford Bioinformatics.

Directory structure

• In /data the export of the BIOLITMAP SQL database is stored, as it was in December 2017.
• In /scripts the tools used for the NLP tasks are stored
• /scripts/src stores the codes related to the NLP, Clustering, Topic Modeling and Perplexity Analysis tasks.
• /scripts/vis stores the visualization created using the final Latent Dirichlet Allocation model, by employing the pyLDAvis package.
• /API stores the source codes of the REST API.

Getting the data from the REST API

We have deployed in our servers a REST API to gather the data from the map in JSON format, the following endpoints are available:

1. http://socialanalytics.bsc.es/biolitmap-api/biolitmap/list - To get the complete list of the data.
2. http://socialanalytics.bsc.es/biolitmap-api/biolitmap/filter/source/"journal" - To filter by source (e.g. Oxford Bioinformatics).
3. http://socialanalytics.bsc.es/biolitmap-api/biolitmap/filter/year/[+-]"year" - To filter by year (e.g. 2010), you can use the + and - symbols to query for greater-equal or less-equal, respectively (e.g. +2010 or -2010).
4. http://socialanalytics.bsc.es/biolitmap-api/biolitmap/filter/nameAffiliation/"institution" - To filter by research institution (e.g. University of Cambridge).

Example output from the /list endpoint

Getting the raw source data from Scopus

In order to obtain the raw source data with which this application has been built on, the following steps need to be followed:

1. Access to the Scopus (www.scopus.com) document search tool
2. Search the documents by using the following query:

ISSN ( 'JOURNAL_ISSN' ) AND ( LIMIT-TO ( PUBYEAR , 2017 ) OR LIMIT-TO ( PUBYEAR , 2016 ) OR LIMIT-TO ( PUBYEAR , 2015 ) OR LIMIT-TO ( PUBYEAR , 2014 ) OR LIMIT-TO ( PUBYEAR , 2013 ) OR LIMIT-TO ( PUBYEAR , 2012 ) OR LIMIT-TO ( PUBYEAR , 2011 ) OR LIMIT-TO ( PUBYEAR , 2010 ) OR LIMIT-TO ( PUBYEAR , 2009 ) OR LIMIT-TO ( PUBYEAR , 2008 ) OR LIMIT-TO ( PUBYEAR , 2007 ) OR LIMIT-TO ( PUBYEAR , 2006 ) OR LIMIT-TO ( PUBYEAR , 2005 ) ) AND ( LIMIT-TO ( EXACTKEYWORD , "Article" ) )

3. Export the documents in CSV format with the 'Export' option.

Journals

In this first version of the application, the articles from the following journals are extracted:

1. Oxford Bioinformatics (ISSN 1460-2059)
2. Nucleic Acids Research (ISSN 1362-4962)
3. BMC Bioinformatics (ISSN 1471-2105)
4. BMC Genomics (ISSN 1471-2164)
5. PLoS Computational Biology (ISSN 1553-734X)

Contact

You can contact the developers by sending an email to [email protected] or [email protected]

Preview