Problem With Entrez For Retrieving Papers Citing A Snp Through Biopython
1
Give the rs number of a SNP (e.g. 1799853), I want to get the list of the paper citing this SNP, preferrably separating the ones with an 'Association Results' from the articles listed in 'Cited Variants', as shown in the GeneView box of the dbSNP page of the SNP (see link below):
http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1799853
Looking at the source of the previous page, I saw that the 'Cited Variants' are given by following link:
http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&DbFrom=snp&Cmd=Link&LinkName=snp_pubmed_cited&IdsFromResult=1799853
My problems are:
I cannot properly submit this query via Biopython Entrez, because no "id" is present; I can sumbit it with requests but then I have to parse the output. The Entrez query url, if pasted in a browser, leads to a Pubmed query url
Put apart the citation with Association Results. I haven't focused on this task yet, but again, looking at the source of the first link, it seems that these papers are extracted from the following link
http://www.genome.gov/gwastudies/index.cfm?snp=rs1799853
Thank you!
biopython
entrez
snp
python
• 3.0k views
using NCBI Utilities:
$ curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=snp&db=pubmed&retmode=xml&id=1799853 "
http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_101123.dtd ">
<eLinkResult>
<LinkSet>
<DbFrom>snp</DbFrom>
<IdList>
<Id>1799853</Id>
</IdList>
<LinkSetDb>
<DbTo>pubmed</DbTo>
<LinkName>snp_pubmed</LinkName>
<Link>
<Id>24368493</Id>
</Link>
<Link>
<Id>24019055</Id>
</Link>
<Link>
<Id>23691226</Id>
</Link>
<Link>
<Id>23587916</Id>
</Link>
<Link>
<Id>23473641</Id>
</Link>
<Link>
<Id>23133420</Id>
</Link>
<Link>
<Id>23130019</Id>
</Link>
<Link>
<Id>23081681</Id>
</Link>
<Link>
<Id>22676711</Id>
</Link>
<Link>
<Id>22569204</Id>
</Link>
<Link>
<Id>22486182</Id>
</Link>
<Link>
<Id>22118051</Id>
</Link>
<Link>
<Id>22010099</Id>
</Link>
<Link>
<Id>20808793</Id>
</Link>
<Link>
<Id>20733952</Id>
</Link>
<Link>
<Id>20585445</Id>
</Link>
<Link>
<Id>20555338</Id>
</Link>
<Link>
<Id>20459744</Id>
</Link>
<Link>
<Id>20214591</Id>
</Link>
<Link>
<Id>20149073</Id>
</Link>
<Link>
<Id>20082485</Id>
</Link>
<Link>
<Id>19955245</Id>
</Link>
<Link>
<Id>19761371</Id>
</Link>
<Link>
<Id>19538716</Id>
</Link>
<Link>
<Id>19422321</Id>
</Link>
<Link>
<Id>19300499</Id>
</Link>
<Link>
<Id>19228618</Id>
</Link>
<Link>
<Id>19223558</Id>
</Link>
<Link>
<Id>18992263</Id>
</Link>
<Link>
<Id>18992148</Id>
</Link>
<Link>
<Id>18990750</Id>
</Link>
<Link>
<Id>18752379</Id>
</Link>
<Link>
<Id>18680736</Id>
</Link>
<Link>
<Id>18662264</Id>
</Link>
<Link>
<Id>18596683</Id>
</Link>
<Link>
<Id>18574025</Id>
</Link>
<Link>
<Id>18547414</Id>
</Link>
<Link>
<Id>18466099</Id>
</Link>
<Link>
<Id>18305455</Id>
</Link>
<Link>
<Id>17387222</Id>
</Link>
<Link>
<Id>17048007</Id>
</Link>
</LinkSetDb>
<LinkSetDb>
<DbTo>pubmed</DbTo>
<LinkName>snp_pubmed_cited</LinkName>
<Link>
<Id>24368493</Id>
</Link>
<Link>
<Id>24019055</Id>
</Link>
<Link>
<Id>23691226</Id>
</Link>
<Link>
<Id>23587916</Id>
</Link>
<Link>
<Id>23473641</Id>
</Link>
<Link>
<Id>23133420</Id>
</Link>
<Link>
<Id>23130019</Id>
</Link>
<Link>
<Id>23081681</Id>
</Link>
<Link>
<Id>22676711</Id>
</Link>
<Link>
<Id>22569204</Id>
</Link>
<Link>
<Id>22486182</Id>
</Link>
<Link>
<Id>22118051</Id>
</Link>
<Link>
<Id>22010099</Id>
</Link>
<Link>
<Id>20808793</Id>
</Link>
<Link>
<Id>20733952</Id>
</Link>
<Link>
<Id>20585445</Id>
</Link>
<Link>
<Id>20555338</Id>
</Link>
<Link>
<Id>20459744</Id>
</Link>
<Link>
<Id>20214591</Id>
</Link>
<Link>
<Id>20149073</Id>
</Link>
<Link>
<Id>20082485</Id>
</Link>
<Link>
<Id>19955245</Id>
</Link>
<Link>
<Id>19761371</Id>
</Link>
<Link>
<Id>19538716</Id>
</Link>
<Link>
<Id>19422321</Id>
</Link>
<Link>
<Id>19300499</Id>
</Link>
<Link>
<Id>19228618</Id>
</Link>
<Link>
<Id>19223558</Id>
</Link>
<Link>
<Id>18992263</Id>
</Link>
<Link>
<Id>18992148</Id>
</Link>
<Link>
<Id>18990750</Id>
</Link>
<Link>
<Id>18752379</Id>
</Link>
<Link>
<Id>18680736</Id>
</Link>
<Link>
<Id>18662264</Id>
</Link>
<Link>
<Id>18596683</Id>
</Link>
<Link>
<Id>18574025</Id>
</Link>
<Link>
<Id>18547414</Id>
</Link>
<Link>
<Id>18466099</Id>
</Link>
<Link>
<Id>18305455</Id>
</Link>
<Link>
<Id>17387222</Id>
</Link>
<Link>
<Id>17048007</Id>
</Link>
</LinkSetDb>
</LinkSet>
</eLinkResult>
before adding your answer.
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Thank you, I'll try to translate your query into biopython and see what happens.