Wide-Open: Accelerating public data release by automating detection of overdue datasets

infodocketGARY's bookmarks 2017-06-08

Summary:

Abstract

 

 

Open data is a vital pillar of open science and a key enabler for reproducibility, data reuse, and novel discoveries. Enforcement of open-data policies, however, largely relies on manual efforts, which invariably lag behind the increasingly automated generation of biological data. To address this problem, we developed a general approach to automatically identify datasets overdue for public release by applying text mining to identify dataset references in published articles and parse query results from repositories to determine if the datasets remain private. We demonstrate the effectiveness of this approach on 2 popular National Center for Biotechnology Information (NCBI) repositories: Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA). Our Wide-Open system identified a large number of overdue datasets, which spurred administrators to respond directly by releasing 400 datasets in one week.

Link:

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2002477

From feeds:

Open Access Tracking Project (OATP) » peter.suber's bookmarks
Open Access Tracking Project (OATP) » infodocketGARY's bookmarks

Tags:

oa.data oa.new oa.speed oa.tools oa.floss oa.compliance oa.policies oa.policies.journals oa.open_science

Date tagged:

06/08/2017, 14:32

Date published:

06/08/2017, 13:29