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Using Entrez Utilities to query the Nucleotide database by collection_date

Greetings,

I was wondering if there was a way to query the NCBI nucleotide database using E-utilities by collection_date. In the image below I retrieved GenBank file data. Column E is the collection date.

Is the only way to query by collection_date is to download all of the genbank files, save their collection date, and then sort them?

Thank you for the help!

enter image description here

ncbi entrez
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updated by spence.lank • spence.lank • written by anomalous.lexeme • anomalous.lexeme

1 answer

Using Entrezdirect. Date in last column is collection date. No way to query using it though. Could be wrong.

$ esearch -db nuccore -query "coronavirus" | esummary | xtract -pattern DocumentSummary -element Caption,SubName 

OQ355523    SARS-CoV-2/human/USA/NY_MEDDAC_FD_643/2023|Homo sapiens|SARS-CoV-2|USA|2023-01-09
OQ355522    SARS-CoV-2/human/USA/NY_MEDDAC_FD_642/2023|Homo sapiens|SARS-CoV-2|USA|2023-01-11
OQ355521    SARS-CoV-2/human/USA/NY_MEDDAC_FD_641/2023|Homo sapiens|SARS-CoV-2|USA|2023-01-11
OQ355520    SARS-CoV-2/human/USA/NY_MEDDAC_FD_640/2023|Homo sapiens|SARS-CoV-2|USA|2023-01-09
OQ355519    SARS-CoV-2/human/USA/NY_MEDDAC_FD_639/2023|Homo sapiens|SARS-CoV-2|USA|2023-01-05

Perhaps something like this to look for a specific date

$ esearch -db nuccore -query "coronavirus" | esummary | xtract -pattern DocumentSummary -element Caption,SubName | grep 2023-01-11 
OQ355522    SARS-CoV-2/human/USA/NY_MEDDAC_FD_642/2023|Homo sapiens|SARS-CoV-2|USA|2023-01-11
OQ355521    SARS-CoV-2/human/USA/NY_MEDDAC_FD_641/2023|Homo sapiens|SARS-CoV-2|USA|2023-01-11
OQ353253    SARS-CoV-2/human/USA/NV-CDC-LC0994357/2023|Homo sapiens|SARS-CoV-2|USA: Nevada|Nasal Swabs|2023-01-11
OQ353252    SARS-CoV-2/human/USA/WA-CDC-LC0994972/2023|Homo sapiens|SARS-CoV-2|USA: Washington|Nasal Swabs|2023-01-11
OQ353251    SARS-CoV-2/human/USA/KY-CDC-LC0994843/2023|Homo sapiens|SARS-CoV-2|USA: Kentucky|Nasal Swabs|2023-01-11
OQ353250    SARS-CoV-2/human/USA/WV-CDC-LC0994837/2023|Homo sapiens|SARS-CoV-2|USA: West Virginia|Nasal Swabs|2023-01-11
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written by GenoMax GenoMax

That looks pretty useful. I'll give that a try as well. Thank you very kindly for the help.

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written by anomalous.lexeme • anomalous.lexeme

The number of columns returned by the query in the "|" delimited portion of the data is inconsistent. Is it possible to normalize the number of columns so it's easier to query the results?

enter image description here

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written by spence.lank • spence.lank

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