help pmidfetch                                                   (version 1.0) 
Daniel Elwood Cook {}         

pmidfetch-- Retreive publication information from Pubmed for a set of PMIDs (Pubmed Identifier). The following information is retrieved:

Title Volume Issue Page Date Affiliation Abstract (upto 244 characters) Authors (upto 244 characters) Mesh Terms (upto 244 characters)


pmidfetch pmid_list , bundle(integer)


pmidfetch uses the efetch utilities provided by the NCBI (National Center for Biotechnology Information) to retrieve information for a given list of PMIDs (Pubmed Identifiers).

You should use pmidfetch for data management/retrieval purposes primarily. It creates several variables with set names and fills them with data. It will overwrite pre-existing data in these variables (example: Gene_ID, Chr_ID, Alleles).

Ideally, you'll use this plugin to annotate a dataset you have by running it on only the set of snps from the set and merging or by taking care with the names of the variables in your set.

One thing you might try: pmidfetch downloads the MeSH terms (MeSH = Medical Subject Headings) and authors for a given publication.

You can use the strmatch function to identify authors or to classify publications by subject.

pmidfetch can handle duplicates.


Follow the command with the name of a variable specifying a list of SNPs. Your list can be numeric, ignoring the rs prefix, or a string with or without the rs prefix. pmidfetch will work with both and download a large amount of data for each set.

The option bundle can be used to adjust how many records Stata will attempt to download at once. pmidfetch works by downloading a set of records for your list of snps, parsing each set out, add the data to your dataset, and move onto the next set. This was necessary due to string length limitations within Stata.