[Biopython] [PubMed] How to view PMID-list on the website?
MX
m464983 at gmail.com
Tue Dec 8 04:01:36 UTC 2015
I had the similar need a few years ago and here is what I did:
1. test query usign NCBI PubMED site and my query looks like
query = Entrez.esearch(db="pubmed", term='(publisher[sb] AND ("%s"[Date -
Publication]:"%s"[Date - Publication])' % (last_update, current),
usehistory="y")
2. Process query results to get following parameters for retrieving xml
records
records=Entrez.read(query)
query.close()
count = int(records["Count"])
webenv = records["WebEnv"]
querykey = records["QueryKey"]
3. Retrieve the abstracts in xml format
#To control the size of file using 10000 as limit
batch_size = 10000
if batch_size>=count:
ofp=gzip.open("aName.xml.gz" % , 'w')
fetch_handle = Entrez.efetch(db="pubmed", rettype="MEDLINE",
retmode="xml", retstart=0, retmax=batch_size, webenv=webenv,
query_key=querykey)
data = fetch_handle.read()
fetch_handle.close()
ofp.write(data)
ofp.close()
else:
num=count/batch_size+1
for i in range(num):
ofp=gzip.open("PubMed_%s.xml.gz" % i, 'w')
start = i*batch_size
end = min(count, start+batch_size)
print "Going to download record %i to %i" % (start+1, end)
fetch_handle = Entrez.efetch(db="pubmed", rettype="MEDLINE",
retmode="xml", retstart=start, retmax=batch_size, webenv=webenv,
query_key=querykey)
data = fetch_handle.read()
fetch_handle.close()
ofp.write(data)
ofp.close()
Hope it has some useful information.
Ming
On Thu, Dec 3, 2015 at 6:38 AM, <c.buhtz at posteo.jp> wrote:
> A little bit off-topic.
>
> I did some search/fetch/analyse with Entrez and and the end I have a
> list of PubMed-IDs (e.g. in a text-file, on id per line) - nearly 1000.
>
> How can I view/display that list on the Pubmed-Website? I mean I want
> to search for all PMIDs on the Website and show the result.
> --
> GnuPGP-Key ID 0751A8EC
> _______________________________________________
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