Question: Problem With Entrez For Retrieving Papers Citing A Snp Through Biopython
0
gravatar for igor.fobia
6.5 years ago by
igor.fobia10
Italy
igor.fobia10 wrote:

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:

  1. 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
  2. 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!

python biopython snp entrez • 2.2k views
ADD COMMENTlink modified 6.5 years ago by Pierre Lindenbaum129k • written 6.5 years ago by igor.fobia10
1
gravatar for Pierre Lindenbaum
6.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

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>
ADD COMMENTlink written 6.5 years ago by Pierre Lindenbaum129k

Thank you, I'll try to translate your query into biopython and see what happens.

ADD REPLYlink written 6.5 years ago by igor.fobia10
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