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