help genefetch                                                   (version 1.2) 
Daniel Elwood Cook {Danielecook@gmail.com}                   www.Elwoodcook.com
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    genefetch -- Retreive information from Pub Med for a set of Entrez Gene
    id's or Gene Names. The following information is retrieved:

         Gene Name
         Gene ID
         Full Name
         Species
         Location
         From (start bp)
         To (end bp)
         Chromosome

Syntax

    genefetch Gene_Names_OR_IDs , bundle(integer) organism(string)

Description

    genefetch uses the efetch utilities provided by the NCBI (National Center
    for Biotechnology Information) to retrieve information for a given list
    of Gene ID's or Gene Names (Single Nucleotide Polymorphims).

    You should use genefetch 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).

    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.

    genefetch can handle duplicates.

Usage

 Method 1: Providing Gene Names

    There are two ways to use genefetch. One is to provide a list of gene
    names. If you do this, genefetch will retrieve gene id's by performing
    searches on Pubmed's gene database and retrieving the top result.

    (!Important!) This method has the potential to retrieve incorrect
    information. However, as long as you use the HGNC approved symbol for
    your gene, genefetch should always retrieve the correct record.

    (!Important!) If you do provide a list of Gene Names and are working with
    a species other than homo sapiens, you must use the organism option,
    specifying the taxonomic name (e.g. Mus musculus, Rattus norvegicus,
    Nomascus leucogenys). If you do not specify an organism, it is set to
    homo sapien.

    I would recommend using a variable named gene containing a list of Gene
    names when using this method. This variable will remain intact when Gene
    information is retrieved and you can compare the Gene and Gene_Name
    variables to ensure that the correct record has been retrieved.

 Method 2: Providing a list of Gene IDs

    The second way to use genefetch is to provide it with a list of Entrez
    Gene ID's. This method will always pull in the correct Gene information
    provided the id exists.

    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.  genefetch 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.  genefetch 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.