DataONE:GEO reuse study/Phase 1

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==Research Plan==
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==Aim==
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* Query PubMed Central for GEO accession number patterns
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* Only look at one year of PMC because deposit rate (and possibly spectrum) not constant over time
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==Open Questions==
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==Background==
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* Also look at Highwire Press, Google Scholar, other full text sources?
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** More difficult because can't process queries automatically
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* Look for accession number patterns for datasets and data series?
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==Limitations==
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==Methods==
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===Important for argument===
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===Overview===
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This is a conservative estimate because:
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* Using the method outlined at [[DataONE:Protocols/Find_GEO_reuses]]:
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* Many papers not in PMC  (source for percentages?)
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** Query GEO for all GDS and GDS accession numbers for datasets submitted in 2007
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* Many data citations not attributed using accession numbers (source for percentages?)
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** Query PubMed Central for these accession numbers in the full text of PMC papers published between 1900 and 2009
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===Less important for argument===
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** Enumerate the PMC papers that reused GEO data
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* Doesn't capture reuse outside the peer-reviewed literature (for example, reuse during training)
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** Estimate what percent of these papers depended on the GEO data for their scientific contribution
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* Deposits into PMC not stable over time, distribution may change over time
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===Details===
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* see [[DataONE:Protocols/Find_GEO_reuses]]
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==Results==
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==Discussion==

Current revision

Contents

Aim

Background

Methods

Overview

  • Using the method outlined at DataONE:Protocols/Find_GEO_reuses:
    • Query GEO for all GDS and GDS accession numbers for datasets submitted in 2007
    • Query PubMed Central for these accession numbers in the full text of PMC papers published between 1900 and 2009
    • Enumerate the PMC papers that reused GEO data
    • Estimate what percent of these papers depended on the GEO data for their scientific contribution

Details

Results

Discussion

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