Biopython Entrez difference between nuccore and nucleotide databases
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7.0 years ago

Is there a difference between the nuccore and nucleotide entrez databases? In my simple tests they seem to return the same data. However the biopython tutorial makes use of both of them.

My testing from python:

Entrez.read(Entrez.einfo(db='nuccore'))["DbInfo"]["Description"]
'Core Nucleotide db'

Entrez.read(Entrez.einfo(db='nuccore'))["DbInfo"]["Count"]
'202831776'

Entrez.read(Entrez.einfo(db='nucleotide'))["DbInfo"]["Description"]
'Core Nucleotide db'

Entrez.read(Entrez.einfo(db='nucleotide'))["DbInfo"]["Count"]
'202831776'

I also tried using efetch and didn't see any differences in the returned data.

biopython entrez • 5.2k views
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I also looked for that and found: (Nucleic Acids Research, Volume 42, Issue D1, 1 January 2014, Pages D7–D17, Database resources of the National Center for Biotechnology Information) "GenBank is the primary nucleotide sequence archive at NCBI and is a member of the INSDC. Sequences from GenBank are available from three Entrez databases: Nucleotide, EST and GSS (specified as nuccore, nucest and nucgss within the E-utilities). The Nucleotide database contains all GenBank sequences except those within the EST or GSS GenBank divisions. The database also contains WGS sequences, Third Party Annotation (TPA) sequences and sequences imported from the Structure database." looks that it's the same.

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7.0 years ago
erictleung ▴ 100

When trying to figure out the difference between the two databases, I also ran the same commands on the database descriptions, which indicates to me that they are the same database.

In the Biopython tutorial under Chapter 9, it mentions "The Bio.Entrez module makes use of the Entrez Programming Utilities (also known as EUtils)." According to NCBI's book "Entrez Programming Utilities Help", the nuccore database is just E-utility database name corresponding to the Nucleotide Entrez database.

Additionally, going to the Nucleotide database on NCBI, I notice "nuccore" in the web address.

So I think they're the same database :)

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