DataONE:GEO reuse study/Phase 1

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==Research Plan==
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==Aim==
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===Overview===
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* Query GEO for all GDS and GDS accession numbers for datasets submitted in 2007
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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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* Enumerate the PMC papers that reused GEO data
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* Estimate what percent of these papers depended on the GEO data for their scientific contribution
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===Query details===
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==Background==
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* accession number formats:
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** look at both GSE and GDS accession numbers
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** use both the raw ID number like 200007572 and the stripped version without the 200... prefix.  For example, search for both 200007572 and 7572
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** search for both accession number right beside the prefix, and with one space in between, so "GSE 7572" and "GSE7572"
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===Exclude data creation studies===
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* spot-check to make sure accession number is in the context of reuse... looks like there may be a few mentions in the context of depost in which the article is not tagged with pmc_gds[filter] (example: PMCID 2396644)
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** do this for all the PMC article hits?  looks like there are a few missing the filter, and it matters because it would erroneously inflate our reuse estimate
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** could use query from my BioLink paper: 
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  (geo OR omnibus)
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  AND microarray
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  AND "gene expression"     
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  AND accession
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  NOT (databases
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        OR user OR users
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        OR (public AND accessed)
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        OR (downloaded AND published))
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** or the more simple: 
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  "gene expression omnibus” AND (submitted OR deposited)
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** to do this transparently, query PMC results for each of these words:
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*** submitted
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*** deposited
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*** user*
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*** public
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*** accessed
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*** downloaded
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*** published
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===Estimate time lag for reuse===
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To estimate time lag:
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* extract year
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===Estimate what percentage of reusers weren't the original authors===
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* see if AND pubmed_gds and NOT pmc_gds have any author overlaps?  (note AND should be pubmed!)
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* other idea:  institution comparison using medline info
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* better than submitter, because submitter not the whole story
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* better than institution, because institution not precise in submission
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===Estimate what percent of reuse created "new science"===
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* classify if methods or informatics:
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** journal name has informatics
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** mesh term for methods?
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* look at mesh overlap?
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* look for metaanalysis mesh term?
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===Estimate what percent of these papers depended on the GEO data for their scientific contribution===
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** Any good ideas on how to do this efficiently?
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*** find those which are/are not in informatics journals
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*** that use "methods" MeSH terms
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*** ??
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===Estimate the fraction of all papers that are in PMC===
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* use "gene expression profiling"[mesh] query in PMC vs PubMed over time period in question to get relevant estimate
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** restrict from 2007 to 2009
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** result: 
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  number of articles in PMC:  6311,
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  number of articles in PubMed:  21569,
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  so PMC contains 29.26% of related papers
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* so we should multiply our number of scientific papers by about 3 to get estimate for all of scientific publishing
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==Additional uses of this data collection==
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* could use this data to see how many publications use any one dataset
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* could use this data to look at average elapsed time between data submission and reuse, but only have short time period to consider... better off with data deposited longer ago
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* can't use this particular data to see how many datasets each publication uses, because only looking at datasets from a given year
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==Notes==
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* this query PMC full-text approach is similar (as per correspondence with GEO team) to that used by the GEO team to compile the 3rd party reuse page:  http://www.ncbi.nlm.nih.gov/projects/geo/info/ucitations.html
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* would be nice to figure out how to write all of these columns to google docs directly from code
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==Methods==
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===Overview===
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* Using the method outlined at [[DataONE:Protocols/Find_GEO_reuses]]:
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** Query GEO for all GDS and GDS accession numbers for datasets submitted in 2007
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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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** Enumerate the PMC papers that reused GEO data
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** Estimate what percent of these papers depended on the GEO data for their scientific contribution
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==Open Questions==
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===Details===
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* see [[DataONE:Protocols/Find_GEO_reuses]]
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==Limitations==
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==Results==
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===Important for argument===
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This is a conservative estimate because:
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*  our estimates do not consider reuses after our study timeframe
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** many datasets we are considering will continue to be used in the future... these reuses are obviously not continued in our estimate
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** could estimate this impact if we examine data deposited 7 years ago?
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* Many papers not in PubMed Central
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** using "gene expression profiling"[mesh] query in PMC vs PubMed over 2007-2009 suggests PMC contains 30% of all related papers in PubMed
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* our methods do not find studies that both create and reuse data
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** to narrow down our query results, we automatedly eliminate studies that create data... even though these same studies may also reuse data
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** we don't have an estimate of how many this is, would require manual inventory
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* Many data citations not attributed using accession numbers
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** don't have a good way to estimate this yet
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** would require a manual inventory, similar to Sarah's data citation inventory in DataONE summer 2010 project
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** maybe out-of-scope to get this estimate for this project, just admit it is an underestimate
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===Less important for argument===
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==Discussion==
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* Doesn't capture reuse outside the peer-reviewed literature (for example, reuse during training)
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* Deposits into PMC not stable over time, distribution may change over time
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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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