How can one retrieve the list of PMIDs of abstracts associated with a MeSH term?

Question

[Arjun Krishnan]

I'm interested in retrieving the list of PubMed article identifiers (PMIDs) of all the articles in PubMed that is associated with a MeSH term like "Breast Neoplasms". I wish to repeat this for a number of MeSH terms, which therefore makes direct web-queries at http://www.ncbi.nlm.nih.gov/pubmed/ too painful.

Is there a way NCBI's E-utilities to do this efficiently from the linux command-line?

Answer 1

[Pierre Lindenbaum]

Used ncbi esearch with the MESH field modifier (as defined in http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed)

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=%22Breast+Neoplasms%22%5BMESH%5D

$ curl -s 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=%22Breast+Neoplasms%22%5BMESH%5D' | xmllint --format -
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD esearch 20060628//EN" "http://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060628/esearch.dtd">
<eSearchResult>
  <Count>221299</Count>
  <RetMax>20</RetMax>
  <RetStart>0</RetStart>
  <IdList>
    <Id>25668825</Id>
    <Id>25668824</Id>
    <Id>25668823</Id>
    <Id>25668822</Id>
    <Id>25647216</Id>
    <Id>25647215</Id>
    <Id>25647190</Id>
    <Id>25603628</Id>
    <Id>25597209</Id>
    <Id>25596051</Id>
    <Id>25596048</Id>
    <Id>25585789</Id>
    <Id>25585788</Id>
    <Id>25585780</Id>
    <Id>25585779</Id>
    <Id>25585778</Id>
    <Id>25585328</Id>
    <Id>25585323</Id>
    <Id>25577824</Id>
    <Id>25568923</Id>
  </IdList>
  <TranslationSet/>
  <TranslationStack>
    <TermSet>
      <Term>"Breast Neoplasms"[MESH]</Term>
      <Field>MESH</Field>
      <Count>221299</Count>
      <Explode>Y</Explode>
    </TermSet>
    <OP>GROUP</OP>
  </TranslationStack>
  <QueryTranslation>"Breast Neoplasms"[MESH]</QueryTranslation>
</eSearchResult>

Answer 2

[Chris S.]

Entrez Direct is another option

esearch -db pubmed -query "Burkholderia pseudomallei/metabolism[MESH]" | efetch -format uid
24866793
24626296
24595140
24502667
24462575
...

Answer 3

[Ram]

curl -vs 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=breast+neoplasms&retmode=text&retmax=1000' 2>&1 | grep "^<Id>"

should give you just the IDs with HTML tags. Use sed to remove the tags and transform in any way you'd like to see it.

Please note: I've set retmax to the 1000. You can change it to get IDs in batches of your preferred size. Update from Pierre is that this number cannot be >100,000.

Also, curl -vs writes to STDOUT without progress bar, 2>&1 combines STDERR and STDOUT so you can process the output directly through pipes.

[Pierre Lindenbaum]

FYI max(retmax)= 100,000

[Ram]

Ah, I see. Batches it is, then!