eutils -- a simplified interface to NCBI E-Utilities

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eutils is a Python package to simplify searching, fetching, and parsing records from NCBI using their E-utilities_ interface.

News

• 0.6.0 was released on 2019-12-17. Support for Python 2.7 has been dropped. See the 0.6 ChangeLog <https://eutils.readthedocs.io/en/stable/changelog/0.6.html>_.

Documentation

See https://eutils.readthedocs.io/en/stable/

Features

• simple Pythonic interface for searching and fetching
• automatic query rate throttling per NCBI guidelines
• optional sqlite-based caching of compressed replies
• "façades" that facilitate access to essential attributes in replies

A Quick Example

As of May 1, 2018, NCBI throttles requests based on whether a client is registered. Unregistered clients are limited to 3 requests/second; registered clients are granted 10 requests/second, and may request more. See the NCBI Announcement <https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/>_ for more information.

The eutils package will automatically throttle requests according to NCBI guidelines (3 or 10 requests/second without or with an API key, respectively).

::

$ pip install biocommons.eutils $ ipython

import os from biocommons.eutils import Client

Initialize a client. This client handles all caching and query

throttling. For example:

ec = Client(api_key=os.environ.get("NCBI_API_KEY", None))

search for tumor necrosis factor genes

any valid NCBI query may be used

esr = ec.esearch(db='gene',term='tumor necrosis factor')

esearch returns a list of entity IDs associated with your search. preview some of them:

esr.ids[:5] [136114222, 136113226, 136112112, 136111930, 136111620]

fetch data for an ID (gene id 7157 is human TNF)

egs = ec.efetch(db='gene', id=7157)

One may fetch multiple genes at a time. These are returned as an

EntrezgeneSet. We'll grab the first (and only) child, which returns

an instance of the Entrezgene class.

eg = egs.entrezgenes[0]

Easily access some basic information about the gene

eg.hgnc, eg.maploc, eg.description, eg.type, eg.genus_species ('TP53', '17p13.1', 'tumor protein p53', 'protein-coding', 'Homo sapiens')

get a list of genomic references

sorted([(r.acv, r.label) for r in eg.references]) [('NC_000017.11', 'Chromosome 17 Reference GRCh38...'), ('NC_018928.2', 'Chromosome 17 Alternate ...'), ('NG_017013.2', 'RefSeqGene')]

Get the first three products defined on GRCh38

[p.acv for p in eg.references[0].products][:3] ['NM_001126112.2', 'NM_001276761.1', 'NM_000546.5']

As a sample, grab the first product defined on this reference (order is arbitrary)

mrna = [i for i in eg.references[0].products if i.type == "mRNA"][0] str(mrna) 'GeneCommentary(acv=NM_001126112.2,type=mRNA,heading=Reference,label=transcript variant 2)'

mrna.genomic_coords provides access to the exon definitions on this reference

mrna.genomic_coords.gi, mrna.genomic_coords.strand ('568815581', -1)

mrna.genomic_coords.intervals [(7687376, 7687549), (7676520, 7676618), (7676381, 7676402), (7675993, 7676271), (7675052, 7675235), (7674858, 7674970), (7674180, 7674289), (7673700, 7673836), (7673534, 7673607), (7670608, 7670714), (7668401, 7669689)]

and if the mrna has a product, the resulting protein:

str(mrna.products[0]) 'GeneCommentary(acv=NP_001119584.1,type=peptide,heading=Reference,label=isoform a)'

Important Notes

• You are encouraged to browse issues <https://github.com/biocommons/eutils/issues>_. Please report any issues you find.
• Use a pip package specification to ensure stay within minor releases for API stability. For example, eutils >=0.6,<0.7.

Developing and Contributing

Contributions of bug reports, code patches, and documentation are welcome!

Development occurs in the default branch. Please work in feature branches or bookmarks from the default branch. Feature branches should be named for the eutils issue they fix, as in 121-update-xml-facades. When merging, use a commit message like "closes #121: update xml facades to new-style interface". ("closes #n" is recognized automatically and closes the ticket upon pushing.)

The included Makefile automates many tasks. In particular, make develop prepares a development environment and make test runs unittests. (Please run tests before committing!)

Again, thanks for your contributions.

.. _E-utilities: http://www.ncbi.nlm.nih.gov/books/NBK25499/

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