Identifying Scientific Project-generated Data Citation from Full-text Articles: An Investigation of TCGA Data Citation
Article Category: Research Paper
Published Online: Sep 01, 2017
Page range: 32 - 44
Received: Jan 20, 2016
Accepted: May 15, 2016
DOI: https://doi.org/10.20309/jdis.201612
Keywords
© 2016 Jiao Li, Si Zheng, Hongyu Kang, Zhen Hou, Qing Qian
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.
Purpose
In the open science era, it is typical to share project-generated scientific data by depositing it in an open and accessible database. Moreover, scientific publications are preserved in a digital library archive. It is challenging to identify the data usage that is mentioned in literature and associate it with its source. Here, we investigated the data usage of a government-funded cancer genomics project, The Cancer Genome Atlas (TCGA), via a full-text literature analysis.
Design/methodology/approach
We focused on identifying articles using the TCGA dataset and constructing linkages between the articles and the specific TCGA dataset. First, we collected 5,372 TCGA-related articles from PubMed Central (PMC). Second, we constructed a benchmark set with 25 full-text articles that truly used the TCGA data in their studies, and we summarized the key features of the benchmark set. Third, the key features were applied to the remaining PMC full-text articles that were collected from PMC.
Findings
The amount of publications that use TCGA data has increased significantly since 2011, although the TCGA project was launched in 2005. Additionally, we found that the critical areas of focus in the studies that use the TCGA data were glioblastoma multiforme, lung cancer, and breast cancer; meanwhile, data from the RNA-sequencing (RNA-seq) platform is the most preferable for use.
Research limitations
The current workflow to identify articles that truly used TCGA data is labor-intensive. An automatic method is expected to improve the performance.
Practical implications
This study will help cancer genomics researchers determine the latest advancements in cancer molecular therapy, and it will promote data sharing and data-intensive scientific discovery.
Originality/value
Few studies have been conducted to investigate data usage by government-funded projects/programs since their launch. In this preliminary study, we extracted articles that use TCGA data from PMC, and we created a link between the full-text articles and the source data.