Package Bio :: Package WWW :: Module NCBI
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Module NCBI

source code

Provides code to access NCBI over the WWW.

The main Entrez web page is available at: http://www.ncbi.nlm.nih.gov/Entrez/

A list of the Entrez utilities is available at: http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html

Documentation for the e-utilies are available at: http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

The main Blast web page is available at: http://www.ncbi.nlm.nih.gov/BLAST/

Functions: query Query Entrez; retrieve results in HTML format. pmfetch Retrieve results using a unique identifier. pmqty Search PubMed. pmneighbor Return a list of related articles for a PubMed entry.

efetch Access the efetch script. _open

Functions [hide private]
handle
query(cmd, db, cgi='http://www.ncbi.nlm.nih.gov/sites/entrez', **keywds)
Query Entrez and return a handle to the results, consisting of a web page in HTML format.
source code
 
pmfetch(db, id, report=None, mode=None, cgi="http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi")
Query PmFetch and return a handle to the results.
source code
handle
pmqty(db, term, dopt=None, cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi')
Query PmQty and return a handle to the results.
source code
handle
pmneighbor(pmid, display, cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi')
Query PMNeighbor and return a handle to the results.
source code
handle
epost(db, id, cgi=...)
Query Entrez and return a handle to the results.
source code
 
efetch(db, cgi='http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi', **keywds)
efetch(db[, cgi][...]) -> handle
source code
 
esearch(db, term, cgi='http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi', **keywds)
esearch(db, term[, cgi][...]) -> handle
source code
 
elink(cgi='http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi', **keywds)
elink([, cgi][...]) -> handle
source code
UndoHandle
_open(cgi, params={}, get=1)
Open a handle to Entrez.
source code
Variables [hide private]
  __warningregistry__ = {('Bio.WWW.NCBI is deprecated. The funct...
Function Details [hide private]

query(cmd, db, cgi='http://www.ncbi.nlm.nih.gov/sites/entrez', **keywds)

source code 

Query Entrez and return a handle to the results, consisting of a web page in HTML format. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helplinks.chapter.linkshelp

Raises an IOError exception if there's a network error.

Returns: handle

pmfetch(db, id, report=None, mode=None, cgi="http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi")

source code 

Query PmFetch and return a handle to the results. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch_help.html

Raises an IOError exception if there's a network error.

pmqty(db, term, dopt=None, cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi')

source code 

Query PmQty and return a handle to the results. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty_help.html

Raises an IOError exception if there's a network error.

Returns: handle

pmneighbor(pmid, display, cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi')

source code 

Query PMNeighbor and return a handle to the results. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor_help.html

Raises an IOError exception if there's a network error.

Returns: handle

epost(db, id, cgi=...)

source code 

Query Entrez and return a handle to the results. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/epost_help.html

Raises an IOError exception if there's a network error.

Returns: handle

efetch(db, cgi='http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi', **keywds)

source code 

efetch(db[, cgi][...]) -> handle

Query Entrez and return a handle to the results. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html

Raises an IOError exception if there's a network error.

esearch(db, term, cgi='http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi', **keywds)

source code 

esearch(db, term[, cgi][...]) -> handle

Query Entrez and return a handle to the results. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html

Raises an IOError exception if there's a network error.

elink(cgi='http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi', **keywds)

source code 

elink([, cgi][...]) -> handle

Query Entrez and return a handle to the results. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/entrez/query/static/elink_help.html

Raises an IOError exception if there's a network error.

_open(cgi, params={}, get=1)

source code 

Open a handle to Entrez. cgi is the URL for the cgi script to access. params is a dictionary with the options to pass to it. get is a boolean that describes whether a GET should be used. Does some simple error checking, and will raise an IOError if it encounters one.

Returns: UndoHandle

Variables Details [hide private]

__warningregistry__

Value:
{('Bio.WWW.NCBI is deprecated. The functions in Bio.WWW.NCBI are now a\
vailable from Bio.Entrez; except for the pm* functions which the NCBI \
have retired.',
  <type 'exceptions.DeprecationWarning'>,
  33): 1}