miRAFinder and GeneAFinder scripts: large-scale searching for miRNA and related information in indexed literature abstracts

Olga Berillo, Mireille Régnier, INRIA/LIX team AMIB, École Polytechnique, Palaiseau, France, Anatoly Ivashchenko

2014

Full text Open access: Hybrid Metadata (CSL-JSON)

DOI 10.6026/97320630010539

Data confidence 70 medium

How this score is calculated

It is built from checkable properties of the record itself: whether the article has a DOI, how many independent sources confirmed its data, whether the required fields are filled in, and how recent the latest confirmation is. Disagreement between sources and a missing identifier lower it. A value of 80 or above means the record was published without further checking; 60 to 79 means it is published at reduced confidence, with a manual check advisable. A record verified by an editor by hand is never pushed below 90 by a recalculation. This scores our data about the article, not the article itself.

Abstract

UNLABELLED: In recent times, information on miRNAs and their binding sites is gaining momentum. Therefore, there is interest in the development of tools extracting miRNA related information from known literature. Hence, we describe GeneAFinder and miRAFinder scripts (open source) developed using python programming for the semi-automatic extraction and arrangement of updated information on miRNAs, genes and additional data from published article abstracts in PubMed. The scripts are suitable for custom modification as per requirement. AVAILABILITY: miRAFinder and GeneAFinder scripts are free and available for download at http://sites.google.com /site/malaheenee/software.