DataONE:GEO reuse study/Phase 1: Difference between revisions

Latest revision as of 13:58, 14 July 2010

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

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