Finding papers, importing, and exporting data


Overview

iCite is currently built on top of data from PubMed. Users can find papers in iCite in three ways: entering a query into the PubMed Search Bar, uploading a file with the PubMed IDs of a portfolio of articles, or pasting a list of PubMed IDs into the text box.


PubMed Search Bar

Enter keywords, author names, year ranges, Medical Subject Heading terms, etc. into the PubMed Search Bar and click "Process" to search.

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Searches are routed through the National Library of Medicine's Entrez sevice and should closely, but not exactly, match the same query results in PubMed (exceptions include very new articles that haven't been processed in iCite yet). Examples:

  • neuronal migration calcium
  • hutchins bi[author]
  • axon guidance 2011:2012[Date - Publication]
  • crispr[MeSH Terms] drosophila[MeSH Terms]
  • covid-19 review[Publication Type]

Loading PubMed IDs into iCite

Go to iCite's New Analysis page. Then, either:

  1. upload your spreadsheet or text file with the list of PMIDs to be analyzed, or

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  1. paste a list of PMIDs into the text box

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Finally, click "Process" to proceed to the next page.


Gathering data from PubMed

Use this method to search for papers in a topic area or for individual authors. The following method is for identifying articles about "neuronal migration" published between 2010 and 2013. Be thoughtful! Newly published articles will not have any citation statistics associated with them, but the default sorting option in PubMed is newest to oldest. Use date filters to help select articles that have been around long enough for meaningful citation counts to accrue.

  1. Go to PubMed.
  2. Search for the topic of interest ("neuronal migration" for example)
  3. On the left sidebar, find "Publication dates" and choose "Custom range"

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  1. Type in a year range (2010 to 2013) and click "Apply"

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  1. There are two options for retrieving the PubMed IDs (PMIDs).
    • If you just want the top 20, you can click on "Summary" and change the view format to "PMID List":

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  • This displays a list of PubMed IDs that can be copied and pasted into iCite.
  • If you want the full list, choose "Send to", "Choose Destination: File", and then change "Format: Summary" to "Format: PMID List" and click "Create File"

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  • This will download a file called "pubmed_result.txt" containing up to 5000 PubMed IDs to whichever folder is the default save location for this browser. Generally, this is in the user's "Download" folder.

Downloading article-level data from iCite

iCite users can download the article-level data underlying the summary statistics. Use the "Export" button to download the selected results as a spreadsheet.

Clicking this button will download the selected (but not the deselected) articles as a spreadsheet with additional bibliometric information. This will appear in your web browser's default download folder.


Coverage information

Note that in some cases, PMIDs cannot be matched to citation records. In this case, a warning appears:

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Clicking "View details" displays the list of missing articles and common reasons why the PMIDs were not matched:

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Most often, this occurs because articles are outside the year range for available citation data. iCite currently has citation data for papers from 1995-present, but note that papers published in the most recent year (some of which are only a few months old) have not had enough time to accrue a meaningful citation count. For this reason, only articles that are at least a year old are available for calculating RCR. Recent papers may also show stronger seasonality patterns and discrepancies because of online publication preceding print publication. Papers that are published early in the calendar year or with long online-only publication periods will have a longer period in which to accrue citations.