Pubmed

Searching PubMed Programmatically

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Earlier this semester, we taught a workshop on how to use the NCBI Entrez Direct (EDirect) [1] tool to search and compile PubMed and related data from a Unix Shell. EDirect is a great tool and has an approachable learning curve. You may consider using EDirect if, for example, you would like to compile custom bibliographic datasets, perform many searches, or discover related linked data.

All of our workshop materials including code and slides are openly available on GitHub:

https://github.com/vfscalfani/EDirectChemInfo

Check it out and let us know if you have any questions. We would be happy to help you.

[1] https://www.ncbi.nlm.nih.gov/books/NBK179288/

MEDLINE Available for Finding Health Science Research

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Recently, UA Libraries subscribed to MEDLINE. The National Library of Medicine (NLM) produces MEDLINE, and NLM provides free access to MEDLINE through PubMed. MEDLINE is also accessed through an interface provided by Ovid, a commercial database vendor.

MEDLINE is an index that is used to find articles published in biomedical journals. MEDLINE covers the journal literature from 1948 to the present. It indexes article citations from over 4,000 medical journals and the entire database consists of over 11 million citations, many with abstracts.

Enhanced features make searching easier and more powerful. Each citation in Ovid indicates whether it can be found in a journal owned by the library. Alerting tools such as AutoAlerts and eTocs are available to keep up with new articles matching the search criteria and tables of contents for new journal issues.

To search Ovid MEDLINE, click on Databases/MEDLINE from the library’s home page. If you would like more information about this database, or if you would like a demonstration of it for a class, contact Mangala Krishnamurthy in Rodgers Library. Contact mkrishna@ua.edu.

Tags: database, Medicine, MeSH, NLM, Nursing

A Snapshot of PubMed Database

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This snapshot of PubMed database will give you basic information about this most relevant and beneficial online resource in the field of medicine and nursing.

A service of the National Library of Medicine, PubMed provides access to over 11 million MEDLINE citations back to the Mid-1960s.  It provides links to many sites providing full text articles and other related resources.

Coverage: full text articles (only up to the most recent six months). You can use the UA libraries collections and Interlibrary Service to get full text of articles that are not linked to in the PubMed database.

Link: http://www.lib.ua.edu/databases/ and use the alpha list on the right side to get to “P” to look for PubMed.

Direct Link: http://www.ncbi.nlm.nih.gov/pubmed?db=pubmed

Tips for searching:

Begin a basic search by entering a keyword (Medical Subject Heading – MeSH Term) into the search field. Then narrow the results with related keywords or by using filters (to limit) offered on the sides of the search results page. Manage Filters link is on the on the right side and more additional filters on the left side of the results page. You can select language, type of publication, years of publication and more to filter the search results

What is MeSH terms in PubMed?

Medical Subject Headings – MESH

MeSH is the National Library of Medicine’s controlled vocabulary thesaurus. It consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic.

If you would like more information about this database, or if you would like a demonstration of it for a class, contact Mangala Krishnamurthy in Rodgers Library. Contact mkrishna@ua.edu.