How To Get Pubmed Id Given A NLM Catalog Id?

Question

[arching]

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 = "[e-mail]"
>>> 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.

Answer 1

[Sej Modha]

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