Cookbook

Retrieve and annotate Entrez Gene IDS with the Entrez module.

Problem

If you deal with a large quantity of gene IDs (such as the ones produced by microarray analysis), annotating them is important if you want to determine their potential biological meaning. However, a lot of annotation systems are only web-based, or do not work with Python.

Solution

Thanks to the Entrez module it is possible to annotate batches of Entrez Gene IDs without trouble, using the “retrieve_ids” function provided below.

This example assumes you have a list of Entrez Gene IDs. Note: they should be stored as strings, rather than integers, even if they are numbers.


import sys

from Bio import Entrez

# *Always* tell NCBI who you are
Entrez.email = "your email here"

def retrieve_annotation(id_list):

    """Annotates Entrez Gene IDs using Bio.Entrez, in particular epost (to
    submit the data to NCBI) and esummary to retrieve the information.
    Returns a list of dictionaries with the annotations."""

    request = Entrez.epost("gene",id=",".join(id_list))
    try:
        result = Entrez.read(request)
    except RuntimeError as e:
        #FIXME: How generate NAs instead of causing an error with invalid IDs?
        print "An error occurred while retrieving the annotations."
        print "The error returned was %s" % e
        sys.exit(-1)

    webEnv = result["WebEnv"]
    queryKey = result["QueryKey"]
    data = Entrez.esummary(db="gene", webenv=webEnv, query_key =
            queryKey)
    annotations = Entrez.read(data)

    print "Retrieved %d annotations for %d genes" % (len(annotations),
            len(id_list))

    return annotations

As the function’s docstring says, the function returns a list of dictionaries, one for each gene, that you can use in any way you want. The following example prints out ID, Gene Symbol and Gene Name for a retrieved annotation:


def print_data(annotation):
    for gene_data in annotation:
        gene_id = gene_data["Id"]
        gene_symbol = gene_data["NomenclatureSymbol"]
        gene_name = gene_data["Description"]
        print "ID: %s - Gene Symbol: %s - Gene Name: %s" % (gene_id, gene_symbol, gene_name)

Tao Liu expanded on this code with a full example of converting between Entrez IDs and RefSeq IDs.

Retrieve and annotate Entrez Gene IDS with the Entrez module.

Problem

Solution

More