Summer 2019 data resources & skills

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Finding data in PubMed

Data filters in PubMed and PubMed Central (PMC) allow you to locate journal articles with associated data sets.

For PubMed, conduct a search using your keywords. Then add in data[filter].
Example of a search string: (diabetes AND data[filter])

The results will be citations with related data links in either the Secondary Source ID field or the LinkOut – Other Literature Resources field. Both fields are located below the abstract. These data links may be to records in other National Library of Medicine (NLM) databases or external data repositories.

For PubMed Central, you have three different methods for finding specific types of associated data: 

• Use has suppdata[filter] to find articles with associated supplementary material.
• Use has data avail[filter] to find articles that include a data availability or data accessibility statement.
• Use has data citations[filter] to find articles that include data citation(s).

Alternatively, use has associated data[filter] to find all articles with any type of data section described above.

Sharing Data in PubMed Central

NLM is encouraging all researchers to share their data. They provide three methods of data sharing within PubMed Central:

• Datasets up to 2 GB can be uploaded to PubMed Central and are associated directly with the publication.
• Datasets up to 20 GB are encouraged to be uploaded to repositories like Dryad or Figshare. A link in the article to the Data’s DOI can be added.
• Datasets in the terabyte range can use National Institutes of Health-managed repositories to upload data and share via a link.

If you need assistance getting started or following best practices, contact the library or visit our new data services guide. The data services guide provides resources and helpful information on all aspects of the data life cycle.

by Adrienne Brodie, MLS, liaison librarian for ATSU-ASHS & ATSU-SOMA