Esummary

entrezpy.esummary.esummarizer.Esummarizer implements the E-Utility ESummary [0]. Esummarizer fetches document summaries for UIDs in the requested database. Summaries can contain abstracts, experimental details, etc

Usage

import entrezpy.esummary.esummarizer

e = entrezpy.esummary.esummarizer.Esummarizer(tool,
                                              email,
                                              apikey=None,
                                              apikey_var=None,
                                              threads=None,
                                              qid=None)

analyzer = e.inquire('db' : 'pubmed', 'id' : [11850928, 11482001])
print(analyzer.get_result().summaries)

Esummarizer

entrezpy.esummary.esummarizer.Esummarizer

param str tool:string with no internal spaces uniquely identifying the software producing the request, i.e. your tool/pipeline.
param str email:
 a complete and valid e-mail address of the software developer and not that of a third-party end user. entrezpy is a library, not a tool.
param str apikey:
 NCBI API key
param str apikey_var:
 NCBI API key
param int threads:
 number of threads
param str qid:Unique Esummary query id. Will be generated if not given.

Supported E-Utility parameter

Parameters are passed as dictionary to entrezpy.esummary.esummarizer.Esummarizer.inquire() and are expected to be the same as those for the E-Utility [0]. For example:

{{'db' : 'pubmed','id' : [11237011,12466850]}

Parameter   Type
E-Utility    
db str
id list
WebEnv string
retstart int
retmax int
retmode JSON, enforced by entrezpy

Not supported E-Utility parameter

Parameter   Type
E-Utility    
retmode JSON, enforced by entrezpy
version XML specific parameter

Result

Instance of entrezpy.esummary.esummary_result.EsummaryResult.

If retmax = 0 or retmode = count no UIDs are returned. If usehistory is True (default), WebEnv and query_key for the request is returned.

  • count : number of found UIDs for request
  • retmax : number of UIDs to retrieve
  • retstart : number of first UID to retrieve
  • uids : list of fetched UIDs

Approach

  1. Parameters are checked and the request size is configured
  2. UIDs are posted to NCBI
  3. If no errors were encountered, returns the analyzer with the result storing the WebEnv and query_key for the UIDs.