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limit the number of efetch result

Dear all,

I am working around with recent EDirect (version 18.2). I had tried in order to limit the number of efetch result like following.

esearch -db pubmed -query "transcription regulation" | efetch -start 1 -stop 10 -format uid

I supposed this would have gave me 10 pmids but this code gave me millions of pmids.

Does someone know how to restrict the number of efetch results?

Thanks,

efetch edirect.
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written by tsutsui.data.analysis • tsutsui.data.analysis

2 answers

(I only know the web API) I usually use the parameter retmax for esearch . I think stop for efetch is for the start-end of the sequences.

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written by Pierre Lindenbaum Pierre Lindenbaum

As far as I understand, API works fine only if the number of result less than 10,000.
So following url give me error.

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=transcription[AND]regulation&retmax=10&retstart=10001

This is not very flexible. Do you know if there is any work around for API?
That's must be fine enough, using EDirtect is not mandatly.

Thanks.

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written by tsutsui.data.analysis • tsutsui.data.analysis

Start and Stop option works but you can use it only with one of the format options below for Pubmed records.

pubmed
                 abstract                    Abstract
                 bioc                        PubTator Central BioC XML
                 medline                     MEDLINE
                 native             asn.1    Pubmed-entry ASN.1
                 native             xml      PubmedArticleSet XML

You can get the UID first using

esearch -db pubmed -query "transcription" | efetch -format uid

and then fetch them in any batches that you want.

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written by GenoMax GenoMax

Thank you for your answer.
Since I was afraid that getting large number of IDs in one time affect server performance, I would like to get ids separately.

Taking advantage of your answer, I have tried following. This didn't restrict the number of result, neither.

esearch -db pubmed -query "transcription" | efetch -format medline -start 1 -stop 10 | grep "PMID- "

Do my understanding incorrect?

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written by tsutsui.data.analysis • tsutsui.data.analysis

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