[BiO BB] Finding PMID related to MeSH terms

[Mike Marchywka]

> Could anyone give me some suggestions on how I can
> download all PMIDs at once? Or better, do anyone

I've never encountered a limitation with eutils:
( hit these links, I pulled them out of a script I use )

SNPHELPURL="http://www.ncbi.nlm.nih.gov/projects/SNP/SNPeutils.htm"
DBHELPURL="http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html"
#http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pccompound
#http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html
#http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?
#http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html#SequenceDatabases
SEARCHHELPURL="http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html"
#http://www.ncbi.nlm.nih.gov/entrez/query/static/help/helpdoc.html


I tried it myself, and it would have worked but I killed it:
$ eutilsnew -v -out junk "liver[mesh]"
Count is 327807
--21:46:17-- http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=biot
echmarchywka&email=marchywka at hotmail.com&rettype=abstract&retmode=text&retstart=
0&retmax=327807&db=Pubmed&query_key=1&WebEnv=0pNNCKO60mP4gg0SvlhFxs1uZ6fgH_IZxjO
ZEs3mmUL9qzejO1IO9A_Hsr at 1EDE7B35754BF7D0_0014SID
=> `junk'
Resolving eutils.ncbi.nlm.nih.gov... 130.14.29.110
Connecting to eutils.ncbi.nlm.nih.gov[130.14.29.110]:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [text/html]

[ <=> ] 230,932 42.60K/s



I could send you the script but it has a lot of idiosyncratic stuff for myself, there are good
examples on their site.



Mike Marchywka
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> Date: Mon, 3 Dec 2007 04:01:38 +0900
> From: s_uchida21 at yahoo.co.jp
> To: bio_bulletin_board at bioinformatics.org
> Subject: [BiO BB] Finding PMID related to MeSH terms
>
> Hello. I want to obtain all PMIDs related to a
> certain MeSH term. For example,
>
>>From MeSH homepage
> http://www.ncbi.nlm.nih.gov/sites/entrez?db=mesh,
>
> search "Liver"
>
> => click the "Links" for "1: Liver
> Year introduced: /cytology was LIVER CYTOLOGY
> 1964-1965"
>
> => jump to "PubMed" site
>
> Result display: "All: 327807 Review: 17161"
>
>
>>From the above result, I want to obatin all 327,807
> PMID. By using this PubMed website, I am only
> allowed to download 500 PMIDs each.
>
> Could anyone give me some suggestions on how I can
> download all PMIDs at once? Or better, do anyone
> know a FTP site where I can download all related
> PMIDs to MeSH terms?
>
> Thank you very much for your help in advance.
>
> Shizuka
>
>