How To Get Pubmed Id Given A NLM Catalog Id?
Hi,
I am trying to get pubmed id with bio for all papers that an article was cited by.
For example this nlmcatalog (ID: 0407712) http://www.ncbi.nlm.nih.gov/pubmed?LinkName=nlmcatalog_pubmed&from_uid=407712
Python 2.7.11+ (default, Apr 17 2016, 14:00:29) [GCC 5.3.1 20160413] on linux2 Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio import Entrez
>>>Entrez.email = "A.N.Other@example.com"
>>> results = Entrez.read(Entrez.elink(dbfrom="nlmcatalog", db="pubmed",LinkName="nlmcatalog_pubmed", from_uid="407712"))
>>>results
[{u'LinkSetDb': [], u'DbFrom': 'nlmcatalog', u'IdList': ['407712'], u'LinkSetDbHistory': [], u'ERROR': []}]
do not have any result,Where did it go wrong?
Thanks.
1 answer
bash version of the eutils produces following results.
esearch -db nlmcatalog -query 407712|elink -target pubmed
Retrying elink, step 2: Query failed on MegaLink server
Retrying elink, step 2: Query failed on MegaLink server
Retrying elink, step 2: Query failed on MegaLink server
Query failed on MegaLink server
Replicate for debugging with:
edirutil -db nlmcatalog -web NCID_1_74199717_130.14.18.34_9001_1465910322_504824782_0MetA0_S_MegaStore_F_1 -key 1 -count 1 -step 1 -seconds 12.671 | elink -target pubmed
Automatically switching to -batch mode
LinkSetDb missing in batch elink result
<ENTREZ_DIRECT>
<Db>pubmed</Db>
<WebEnv>NCID_1_74199717_130.14.18.34_9001_1465910322_504824782_0MetA0_S_MegaStore_F_1</WebEnv>
<QueryKey>1</QueryKey>
<Count>0</Count>
<Step>2</Step>
</ENTREZ_DIRECT>
Elink acheck test indicates non-zero count expected
<WebEnv>NCID_1_36836734_130.14.22.215_9001_1465910252_1701363647_0MetA0_S_MegaStore_F_1</WebEnv>
<QueryKey>1</QueryKey>
<Count>0</Count>
<Step>2</Step>
</ENTREZ_DIRECT>
Elink acheck confirmation test failed
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