Klortho / python-eutils

Django project accessing PubMed backends

eutils

The eutils package contains wrapper functions for calling eutils. So far, it contains esearch and esummary. To use esearch:

import eutils
id = eutils.esearch("sra", term)

esummary takes a single id (multiple ids are not yet supported) and returns an object of class DocumentSummary, which has an attribute, xml, containing a parsed tree (an object of class XML from lxml).

import eutils
summary = eutils.esummary("sra", id)
parsed_tree = summary.xml

If no document is found, a NoSummaryFoundException is raised.

Additional modules exist that extend the esummary functionality to add data.

sra:

from eutils import sra
summary = sra.esummary(id)
title = summary.title

biosample:

from eutils import biosample
summary = biosample.esummary(id)
sra = summary.sra
sample_name = summary.sample_name

bioproject:

from eutils import bioproject
summary = bioproject.esummary(id)
organism = summary.organism
project_data_type = summary.project_data_type