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Search NCBI Databases with Bio.Entrez.esearch()
How to Search NCBI Databases with Bio.Entrez.esearch() function?
✍: FYIcenter.com
Bio.Entrez.esearch() function allows you to search NCBI Databases with a given criteria. It uses the Entrez Web services provided by www.ncbi.nlm.nih.gov.
1. Search in PubMed for publications that include Biopython in their title. It returns 3 matches.
fyicenter$ python >>> from Bio import Entrez >>> Entrez.email = "A.N.Other@example.com" >>> handle = Entrez.esearch(db="pubmed", term="biopython[title]", retmax="40") >>> record = Entrez.read(handle) >>> record {'Count': '3', 'RetMax': '3', 'RetStart': '0', 'IdList': ['34434786', '22909249', '19304878'], 'TranslationSet': [], 'QueryTranslation': '"biopython"[Title]' }
2. Search for the matK gene in Cypripedioideae orchids in GenBank.
>>> handle = Entrez.esearch( ... db="nucleotide", term="Cypripedioideae[Orgn] AND matK[Gene]", idtype="acc" ... ) >>> record = Entrez.read(handle) >>> record["Count"] >>> record["IdList"] ['NC_069974.1', 'NC_069973.1', 'NC_069972.1', 'NC_069971.1', 'NC_069970.1', ...]
⇒ Retrieve Record Summary with Bio.Entrez.esummary()
⇐ List NCBI Databases with Bio.Entrez.einfo()
2023-08-09, 302🔥, 0💬
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