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

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 (will go away Dec 2002) 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. 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
Function Summary
  efetch(db, cgi, **keywds)
efetch(db[, cgi][...]) -> handle
  elink(cgi, **keywds)
elink([, cgi][...]) -> handle
  epost(db, id, cgi, **keywds)
epost(db, id[, cgi]) -> handle
  esearch(db, term, cgi, **keywds)
esearch(db, term[, cgi][...]) -> handle
  pmfetch(db, id, report, mode, cgi)
pmfetch(db, id, report=None, mode=None, cgi="http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi")
  pmneighbor(pmid, display, cgi)
pmneighbor(pmid, display, cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi') -> handle
  pmqty(db, term, dopt, cgi, **keywds)
pmqty(db, term, dopt=None, cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi') -> handle
  query(cmd, db, cgi, **keywds)
query(cmd, db, cgi='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi', **keywds) -> handle

Function Details

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

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.

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

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.

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

epost(db, id[, 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/epost_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)

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.

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

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. 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.

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

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

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.

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

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

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.

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

query(cmd, db, cgi='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi', **keywds) -> 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/linking.html

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

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