Search genbank for records that have a specific field

HI!

Can I use andvanced search on NCBI (or some other method) to find Genbank records that have a specific field, independently of what that field contains?

Specifically I would like to filter records that have the "specimen_voucher" field under Features/Source. Or even more specifically I have a list of Genbank IDs and would like to filter out those that do not have this field.

genbank ncbi

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written 3.9 years ago by tbayer •

Can you provide example of GenBank ID. Without that information this is example query. Count field below shows how many entries.

Using Entrezdirect:

$ esearch -db biosample -query "specimen_voucher"
<ENTREZ_DIRECT>
  <Db>biosample</Db>
  <WebEnv>MCID_631896eb1fc13d1b281a6e9a</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>184220</Count>
  <Step>1</Step>

</ENTREZ_DIRECT>

For nucleotide database

$ esearch -db nuccore -query "specimen_voucher"
<ENTREZ_DIRECT>
  <Db>nuccore</Db>
  <WebEnv>MCID_6318970a4cbf63655f3cbfe7</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>65890</Count>
  <Step>1</Step>
</ENTREZ_DIRECT>

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written 3.9 years ago by GenoMax

Hi, thanks for the reply. An example record would be AF301461.1 with the specimen_voucher field.

Your example esearch -db nuccore -query "specimen_voucher would also find records that do not have the field, but where the text "specimen_voucher" appears anywhere in the title, no?

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written 3.9 years ago by tbayer •

While that field appears in GenBank format record it is not a directly queryable attribute AFAI see. You can find specific records that have a value in that field by

$ esearch -db nuccore -query "AF301461" | efetch -format gb | grep "/specimen_voucher"
                     /specimen_voucher="LSUMNS B-18658"

That field may also be empty

$ esearch -db nuccore -query "specimen_voucher" | efetch -format gb | grep -e "/specimen_voucher" -e ACCESSION
    ACCESSION   LC723704
                         /specimen_voucher="TNS:S. Chantanaorrapint & O. Suwanmala
    ACCESSION   LC723703
                         /specimen_voucher="TNS:S. Chantanaorrapint & O. Suwanmala
    ACCESSION   LC723702
                         /specimen_voucher="TNS:S. Chantanaorrapint & O. Suwanmala
    ACCESSION   LC723701
                         /specimen_voucher="TNS:S. Chantanaorrapint & O. Suwanmala
    ACCESSION   LC723700
                         /specimen_voucher="TNS:S. Chantanaorrapint & O. Suwanmala
    ACCESSION   LC723699
                         /specimen_voucher="TNS:S. Chantanaorrapint & O. Suwanmala
    ACCESSION   LC278102
                         /specimen_voucher="FRLM:34902"
    ACCESSION   LC036918
                         /specimen_voucher="HUMZ:198113"
    ACCESSION   LC021154
                         /specimen_voucher="FAKU:73708"
    ACCESSION   AB969934
                         /specimen_voucher="BSKU:62255"

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written 3.9 years ago by GenoMax

Thanks! As i wanted to retrieve all Genbank records that have this field downloading the full genbank format for grepping may take a while... I think I'll just search for that keyword via the online search for now and download all IDs in a file.

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written 3.9 years ago by tbayer •

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