May 14, 2021

New Journal Article: “Wide-Open: Accelerating Public Data Release by Automating Detection of Overdue Datasets”

The following article was published today by PLOS Biology.

Title

Wide-Open: Accelerating Public Data Release By Automating Detection Of Overdue Datasets

Authors

 Source

PLOS Biology
PLoS Biol 15(6): e2002477
https://doi.org/10.1371/journal.pbio.2002477

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.

Direct to Full Text Article

Coverage

Text-Mining Tool Seeks Out ‘hidden Data (via Nature)

Two popular repositories that offer researchers the option to keep genetics data hidden, for example, are the Gene Expression Omnibus (GEO) and the Sequence Read Archive (SRA), both run by the US National Center for Biotechnology Information. Both sites require data sets to be made open when papers are published. But in practice, scientists often forget to do this, says Maxim Grechkin, a computer scientist at the University of Washington in Seattle.

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About Gary Price

Gary Price (gprice@mediasourceinc.com) is a librarian, writer, consultant, and frequent conference speaker based in the Washington D.C. metro area. Before launching INFOdocket, Price and Shirl Kennedy were the founders and senior editors at ResourceShelf and DocuTicker for 10 years. From 2006-2009 he was Director of Online Information Services at Ask.com, and is currently a contributing editor at Search Engine Land.

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