Tanggal :September 27, 2020

bpy13. Using einfo EUtil in Biopython

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We can use Bio.Entrez.einfo to find information about databases. If we call einfo without any parameter, it will return the name of all the databases. However, if we put in a particular db, such as ‘pubmed’, it will return information about this database.

For Entrez.email, you should give your email. Biopython returns a dictionary of length 1, with the result in key ‘DbInfo”. Some information about the database is printed such as its name and count.

The dictionary within the result is iterated over (with i being the current subkey). We list all the field names and their description.


# bpy13.py
from __future__ import print_function, division
from Bio import Entrez

Entrez.email = "[email protected]"
handle = Entrez.einfo(db="pubmed")
record = Entrez.read(handle)
handle.close()
db = record['DbInfo']
name = db['MenuName']
dbName = db['DbName']
desc = db['Description']
count = db['Count']
print(" - ".join([name,dbName,desc,count]))
for i in db['FieldList']:
print(i['Name'],end='t')
print(i['Description'])

#PubMed - pubmed - PubMed bibliographic record - 24738242
#ALL All terms from all searchable fields
#UID Unique number assigned to publication
#FILT Limits the records
#TITL Words in title of publication
#WORD Free text associated with publication
#MESH Medical Subject Headings assigned to publication
#MAJR MeSH terms of major importance to publication
#AUTH Author(s) of publication
#JOUR Journal abbreviation of publication
#AFFL Author's institutional affiliation and address
#ECNO EC number for enzyme or CAS registry number
#SUBS CAS chemical name or MEDLINE Substance Name
#PDAT Date of publication
#EDAT Date publication first accessible through Entrez
#VOL Volume number of publication
#PAGE Page number(s) of publication
#PTYP Type of publication (e.g., review)
#LANG Language of publication
#ISS Issue number of publication
#SUBH Additional specificity for MeSH term
#SI Cross-reference from publication to other databases
#MHDA Date publication was indexed with MeSH terms
#TIAB Free text associated with Abstract/Title
#OTRM Other terms associated with publication
#INVR Investigator
#COLN Corporate Author of publication
#CNTY Country of publication
#PAPX MeSH pharmacological action pre-explosions
#GRNT NIH Grant Numbers
#MDAT Date of last modification
#CDAT Date of completion
#PID Publisher ID
#FAUT First Author of publication
#FULL Full Author Name(s) of publication
#FINV Full name of investigator
#TT Words in transliterated title of publication
#LAUT Last Author of publication
#PPDT Date of print publication
#EPDT Date of Electronic publication
#LID ELocation ID
#CRDT Date publication first accessible through Entrez
#BOOK ID of the book that contains the document
#ED Section's Editor
#ISBN ISBN
#PUBN Publisher's name
#AUCL Author Cluster ID
#EID Extended PMID
#DSO Additional text from the summary
#AUID Author Identifier
#PS Personal Name as Subject
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