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Entrez esearch term format

I'm using biopython to perform an Entrez esearch of the NCBI taxonomy database. The term is the exact string as it appears in the database.

Entrez.read(Entrez.esearch(db='Taxonomy', term="Cupriavidus sp. HPC(L)"))

returns

{'QueryTranslation': 'Cupriavidus sp. HPC[All Names] AND (L[All Names])', 'IdList': [], 'Count': '0', 'RetStart': '0', 'ErrorList': {'FieldNotFound': [], 'PhraseNotFound': ['Cupriavidus', 'sp.', 'HPC', 'L']}, 'RetMax': '0', 'TranslationSet': [], 'WarningList': {'PhraseIgnored': [], 'QuotedPhraseNotFound': [], 'OutputMessage': ['No items found.']}}

This should return information on TaxID 1217418.

Thanks in advance.

entrez esearch ncbi biopython taxonomy
• 3,281 views • link
written by smiller smiller

I can replicate this empty results using NCBI commandline utils, it'd be interesting to find out how to tackle this.

esearch -db taxonomy -query "Cupriavidus sp HPC(L)"
• 0 views • link
written by Sej Modha Sej Modha

1 answer

SIMPLE AND OBVIOUS SOLUTION:

Enclose the search term in double quotes to make it literal.

Entrez.read(Entrez.esearch(db='Taxonomy', term="\"Cupriavidus sp. HPC(L)\""))

correctly returns

{'RetStart': '0', 'TranslationStack': [{'Count': '1', 'Field': 'All Names', 'Term': '"Cupriavidus sp. HPC(L)"[All Names]', 'Explode': 'N'}, 'GROUP'], 'IdList': ['1217418'], 'TranslationSet': [], 'Count': '1', 'RetMax': '1', 'QueryTranslation': '"Cupriavidus sp. HPC(L)"[All Names]'}

• 0 views • link
written by smiller smiller

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