Bio_Eutils

Introduction

Bio_Eutils is the standalone version of the Entrez and Medline BioPython modules. It is used to access to the NCBI E-utilities - a set of (web)services to query Entrez databases.

Version

The latest version of the module follows the latest biopython release: 1.65 at this time.

Installation

The main purpose of this module is to keep the installation step as small and simple as possible. Hence the module comes with no other dependencies. You can either choose to clone the repository or install it from pip.

Clone the module from Github

git clone git://github.com/jmaupetit/Bio_Eutils.git
cd Bio_Eutils
python setup.py install

Install from PyPI with pip

pip install Bio_Eutils

Usage

A sample script to fetch references from J. Monod follows.

from Bio_Eutils import Entrez, Medline
Entrez.email = "me@myself.org"

# Search for PMIDs from author text based search
handle = Entrez.esearch(db="pubmed", retmax=100, term="monod j[author]")
pub_search = Entrez.read(handle)
handle.close()

# Fetch matching entries
handle = Entrez.efetch(db='pubmed', id=pub_search['IdList'], retmax=20, rettype="medline", retmode="text")
pub_items = Medline.parse(handle)

# Work with it
for pub_item in pub_items:
    print "*" * 10
    print "%s - %s." % (
        pub_item.get("TI","?"),
        ", ".join(pub_item.get("AU","?"))
        )

handle.close()

For more informations about the Entrez and Medline modules, refer to the Biopython documentation.

Running tests

If you want to contribute to this project, you may want to run tests. This could be achieve via:

$ cd Tests
$ python run_tests.py

Disclaimer

Please not that J. Maupetit is not the author of the Bio.Entrez and Bio.Medline packages. He only maintains this standalone version for his own usage. The Bio.* modules are distributed under the Biopython license agreement (see LICENSE).