Linking Genes/Diseases To Pubmed Ids

Hello everyone,

reading this post

How Do People Go About Pubmed Text Mining

I am asking myself if there are lists, which link gene IDs to pubmed IDs. I found some papers addressing this problem. But since text mining is just a small piece of my current project, I don't want to invest that much time only for the linking. Or are there maybe cross references in other databases? I know that the ENSEMBL DB stores links for gene/OMIM. I also found some references for pubmed in ENSEMBL, but the amount of links seems to be really rare.

With best,

Mario

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written 13.6 years ago by Mdeng

4 answers

It's not clear from your question whether you want to use only Ensembl gene IDs or if you're interested in linking any gene ID to a PubMed ID.

If the latter: you can cross-reference any two Entrez databases (e.g. gene and pubmed) using ELink. For example, to link Entrez Gene IDs 110011,110012 to PubMed:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=pubmed&id=110011,110012

The XML output:


http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_101123.dtd">
<eLinkResult>

    <LinkSet>
        <DbFrom>gene</DbFrom>
        <IdList>
            <Id>110011</Id>
            <Id>110012</Id>
        </IdList>
        <LinkSetDb>
            <DbTo>pubmed</DbTo>
            <LinkName>gene_pubmed</LinkName>
            <Link>
                <Id>21677750</Id>
            </Link>
            <Link>
                <Id>21267068</Id>
            </Link>
            <Link>
                <Id>18799693</Id>
            </Link>
            <Link>
                <Id>17967808</Id>
            </Link>
            <Link>
                <Id>17360631</Id>
            </Link>
            <Link>
                <Id>16141073</Id>
            </Link>
            <Link>
                <Id>16141072</Id>
            </Link>
            <Link>
                <Id>15890843</Id>
            </Link>
            <Link>
                <Id>14610273</Id>
            </Link>
            <Link>
                <Id>12972506</Id>
            </Link>
            <Link>
                <Id>12904583</Id>
            </Link>
            <Link>
                <Id>12477932</Id>
            </Link>
            <Link>
                <Id>12466851</Id>
            </Link>
            <Link>
                <Id>12242242</Id>
            </Link>
            <Link>
                <Id>11256068</Id>
            </Link>
            <Link>
                <Id>11217851</Id>
            </Link>
            <Link>
                <Id>11076861</Id>
            </Link>
            <Link>
                <Id>11042159</Id>
            </Link>
            <Link>
                <Id>10349636</Id>
            </Link>
                <Link>
                <Id>8889548</Id>
            </Link>
            <Link>
                <Id>8589719</Id>
            </Link>
        </LinkSetDb>
        <LinkSetDb>
            <DbTo>pubmed</DbTo>
            <LinkName>gene_pubmed_rif</LinkName>
            <Link>
                <Id>17360631</Id>
            </Link>
            <Link>
                <Id>15890843</Id>
            </Link>
            <Link>
                <Id>12242242</Id>
            </Link>
        </LinkSetDb>
    </LinkSet>
</eLinkResult>

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written 13.6 years ago by Neilfws

Although a bit out of date, you should be able to find this data at http://www.pubmed2ensembl.org/. However, as Ensembl gene ids are stable it is easy to map them across releases.

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written 13.6 years ago by Casey Bergman

You should also have a look at the following: http://meshop.oicr.on.ca/meshop/index.html

Corresponding litterature: http://www.ncbi.nlm.nih.gov/pubmed?term=meshop

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written 13.6 years ago by Anthony Mathelier

Hello everyone,

these things are exactly what I am looking for. I already knew pubmed2ensembl, but I can revert the (maybe) outdated ENSEMBL IDs. Also ELink looks nice.

Thanks!

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written 13.6 years ago by Mdeng