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I'm trying to reproduce a complex manual search on NCBI using BioPython, but obviously something is not right. My command line is not working, but I'd especially like a way to have an accurate search where I can select only the genomes related to a published paper. Is there an easy way to do that?

I want to limit my results to only those genomes that i) have an NCBI BioProject entry and ii) that BioProject entry contains a Publications field.

For example, let's say I want all the genomes of Microbacterium, the latest version, from RefSeq and not partial (this is what I tried to write but something is not working) and I would like to add one more filter. Take, among the remaining/selected genomes, only the ones related to published papers.

For this strain, we have a related paper: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA669461/

For this one, we do not: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA608230/

and I really would like to not have to check 100 genomes manually, but I don't know how to manage it.

I tried:

query = "Microbacterium[Organism] AND latest refseq[filter] AND (all[filter] NOT
partial[filter])"
handle = Entrez.esearch(term=query, db="Assembly", retmax=600)
ids = Entrez.read(handle)["IdList"]

And after this, I'm just using a for loop to get genomes, but my query is not good and it is not handling the problem of the publication.

Thanks for any help!

Edit : as I need to search in the db Assembly unfortunately the answer with the flag author or date is not working

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Entrez has the tags [journal], [volume], [page number], [title], [year] and [author] to identify all sequences from a given publication. You will find a full list of tags here from the drop down menu.

Thus,

query = "Microbacterium[Organism] AND Nature[Journal] AND 528[volume] AND Bai[author] AND 364[page number]"

This will identify all Microbacterium genome sequences associated with Bai et al (2015) Nature 528:364- and is here.

For practical purposes I routinely search using the organism and author tags for their sequence output.

The example given (post-edit) was

Kim KK et al., "Microbacterium aquimaris sp. nov., isolated from seawater.", Int J Syst Evol Microbiol, 2008 Jul;58(Pt 7):1616-20

query = "Microbacterium[Organism] AND 58[volume] AND Kim[author] AND 1616[page number] AND 2008[year]"

I removed the [journal] tag because the abbreviation it uses is a bit unusual and replaced it with [year]. Still works here.

From the comments ... if only published sequences were required then using the range function and [publication date] is one way in ...

query = "Microbacterium[Organism] AND 2000/1/1:2020/1/1[publication date]"

The best strategy is to use the [author] because data production tends to be dominated by a small number of groups.

Comments of Comments

Why isn't searching working. The following search works

query = "Microbacterium[Organism] AND (all[filter] NOT partial[filter])"

The term it doesn't like is latest refseq[filter] if that is removed it will work. refseq works, but it doesn't like latest.

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  • $\begingroup$ I think the OP wants to limit the results to only those genomes whose NCBI BioProject entry includes a Publications field. $\endgroup$
    – terdon ♦
    Commented Feb 8, 2023 at 19:03
  • $\begingroup$ @terdon I don't believe there is a tag [publication], there is [publication date], which is better than [year]. However, it's the same answer, the sequence output of most fields are represented only by a small number of authors and only those authors are searched. $\endgroup$
    – M__ ♦
    Commented Feb 8, 2023 at 19:08
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    $\begingroup$ @M__ thanks a lot for your help ! your range idea it's pretty clever, it will already be much better than checking by hand! $\endgroup$
    – Marine Bergot
    Commented Feb 8, 2023 at 20:28
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    $\begingroup$ @M__ by the way, do you have any idea why my current research is not returning anything? $\endgroup$
    – Marine Bergot
    Commented Feb 8, 2023 at 20:35
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    $\begingroup$ @M__ thanks for your answer. I arrived in the same point but i need both, latest and refseq. For me latest is working with organism and no partial but refseq is not working even alone. do you have results with Microbacterium[Organism] AND refseq[Filter]? could it be related to version ? $\endgroup$
    – Marine Bergot
    Commented Feb 8, 2023 at 21:35

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