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Scrape biological data from websites

Project description

#Bioscraping

Web scrapers to interact with remote databases programatically in Python that makes a local cache of web data with sqlite3 to prevent excessive web traffic.

So far, implemented:

  • [Uniprot](http://uniprot.org) by uniprot protein ID. (e.g. ‘Q8BP71’)
  • [PubMed](www.ncbi.nlm.nih.gov/pubmed/) by PMID (e.g. ‘24213538’)

#Install

##Python 2.7.x and 3.x pip install bioscraping

#Test

Real unit tests are absent, but you can test basic functionality with python test/not_a_real_test.py.

#Usage

##PubMed

from bioscraping import PubMedClient

pubmed = PubMedClient()

defaults to writing a file called .bioscraping.pubmed.sqlite.db. Use PubMedClient(“:memory:”) for in-memory data storage.

pubmed.fetch(<PMID>)

Returns text with author and abstract for PMID.

##Uniprot

from bioscraping import UniprotClient

uniprot = UniprotClient()

defaults to writing a file called .bioscraping.uniprot.sqlite.db. Use UniprotClient(“:memory:”) for in-memory data storage.

uniprot.fetch(<Uniprot ID>)

Returns a dictionary of data parsed from xml.

#Buyer beware

UniprotClient has a potential race condition and tempfile needs to be implemented before it is safe for concurrent processes. (see TODO)

Project details


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