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Package Bio :: Package WWW :: Module NCBI |
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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. _openFunction Summary | |
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efetch(db[, cgi][...]) -> handle | |
elink([, cgi][...]) -> handle | |
epost(db, id[, cgi]) -> handle | |
esearch(db, term[, cgi][...]) -> handle | |
pmfetch(db, id, report=None, mode=None, cgi="http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi") | |
pmneighbor(pmid, display, cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi') -> handle | |
pmqty(db, term, dopt=None, cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi') -> handle | |
query(cmd, db, cgi='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi', **keywds) -> handle | |
_open(cgi, params={}, get=1) -> UndoHandle |
Function Details |
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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. |
_open(cgi, params={}, get=1)_open(cgi, params={}, get=1) -> UndoHandle 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. |
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