Answers.Body: <p>Conversion using <code>R</code>:</p>
  <pre><code>library(biomaRt)
  
  mart &lt;- useDataset(&quot;hsapiens_gene_ensembl&quot;, useMart(&quot;ensembl&quot;))
  
      genes &lt;- getBM(
        filters=&quot;ensembl_gene_id&quot;,
        attributes=c(&quot;ensembl_gene_id&quot;, &quot;entrezgene_id&quot;),
        values=ensembl.genes,
        mart=mart)
  </code></pre>
  <p>Where <code>ensembl.genes</code> is a vector of Ensembl gene IDs.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-08-05T22:23:06.367Z
Answers.Text: As of 2021-08-05, the attributes argument should be set to `attributes = c("ensembl_gene_id", "entrezgene_id")`. I believe that the `"_id"` appendage has been added to the attribute since this answer was first posted.
Answers.UserDisplayName: Gabriel J. Odom
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-01-18T16:01:17.680Z
Answers.LastActivityDate: 2023-09-07T16:15:48.133Z
Answers.LastEditDate: 2023-09-07T16:15:48.133Z
Answers.UserDisplayName: Peter
Answers.Body: <p>The ID you need is the NCBI gene ID, which is the same as the EntrezGene ID. </p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-06T11:29:32.903Z
Answers.Text: Thank you Ian, it seems working. Anyway, there is no a one-to-one matching (i.e., some Ensembl IDs do not have an NCBI counterpart). Is it normal?
Answers.UserDisplayName: floatingpurr
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-06T11:59:23.847Z
Answers.Text: Yes. See my answer to your other question. https://bioinformatics.stackexchange.com/a/2474/235
Answers.UserDisplayName: Ian Sudbery
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-09-06T11:22:30.280Z
Answers.LastActivityDate: 2017-09-06T11:22:30.280Z
Answers.UserDisplayName: Ian Sudbery
Body: <p>Well, I'm trying to convert a list of Human Gene referenced by Ensembl Gene IDs to Entrez Gene IDs. I <a href="https://bioinformatics.stackexchange.com/questions/2462/missing-data-mappings-in-mygene-info-while-trying-to-convert-genes-ensembl-ids-t">have been advised</a> to use <a href="http://www.ensembl.org/biomart/martview/" rel="noreferrer">biomart</a>.</p>
  
  <p>I tried to get a kind of conversion table for all human genes. I don't know if my settings are wrong, but I didn't find any checkbox for Entrez Gene Id in the section <code>Attributes</code> > <code>External References</code>. I've just found the Entrez transcript name ID (see below), but it's not what I need.</p>
  
  <p><a href="https://i.sstatic.net/VWtTT.png" rel="noreferrer"><img src="https://i.sstatic.net/VWtTT.png" alt="enter image description here"></a></p>
  
  <p>How can I use <em>biomart</em> for such a conversion?</p>
  
  <p><strong>Edit:</strong></p>
  
  <p><strike>According to <a href="https://youtu.be/DXPaBdPM2vs?t=1m50s" rel="noreferrer">this video tutorial</a> EntrezGene ID should be an option in biomart (see screenshot below).</strike></p>
  
  <p>That video tutorial is outdated.</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-06T11:50:38.200Z
Comments.Text: That tutorial is 8 years old.
Comments.UserDisplayName: Emily_Ensembl
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-09-06T11:55:22.653Z
Comments.Text: Yes, @Emily_Ensembl. I'm sorry, I had gotten it from an old documentation page : )
Comments.UserDisplayName: floatingpurr
Tags: <gene><public-databases><biomart><conversion>
Title: Converting Ensembl Gene IDs to Entrez Gene IDs through biomart
ThreadText: # Converting Ensembl Gene IDs to Entrez Gene IDs through biomart
  
  (Asked by: username_0 on 2017-09-06)
  
  Well, I'm trying to convert a list of Human Gene referenced by Ensembl Gene IDs to Entrez Gene IDs. I [have been advised](https://bioinformatics.stackexchange.com/questions/2462/missing-data-mappings-in-mygene-info-while-trying-to-convert-genes-ensembl-ids-t) to use [biomart](http://www.ensembl.org/biomart/martview/).
  
  I tried to get a kind of conversion table for all human genes. I don't know if my settings are wrong, but I didn't find any checkbox for Entrez Gene Id in the section `Attributes` > `External References`. I've just found the Entrez transcript name ID (see below), but it's not what I need.
  
  [![enter image description here](https://i.sstatic.net/VWtTT.png)](https://i.sstatic.net/VWtTT.png)
  
  How can I use *biomart* for such a conversion?
  
  **Edit:**
  
  According to [this video tutorial](https://youtu.be/DXPaBdPM2vs?t=1m50s) EntrezGene ID should be an option in biomart (see screenshot below).
  
  That video tutorial is outdated.
  
  **Tags:** gene, public-databases, biomart, conversion
  
  > **Comments:**
  > **username_1**: That tutorial is 8 years old.  
  > **username_0**: Yes, @username_1. I'm sorry, I had gotten it from an old documentation page : )  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_4 on 2017-09-06. Score: 8 | Accepted answer
  
  The ID you need is the NCBI gene ID, which is the same as the EntrezGene ID.
  
  > **Comments:**
  > **username_0**: Thank you Ian, it seems working. Anyway, there is no a one-to-one matching (i.e., some Ensembl IDs do not have an NCBI counterpart). Is it normal?  
  > **username_4**: Yes. See my answer to your other question. https://bioinformatics.stackexchange.com/a/2474/235  
  
  ---
  
  ### Answer by username_2 on 2018-01-18. Score: 8
  
  Conversion using `R`:
  
  ```
  library(biomaRt)
  
  mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
  
      genes <- getBM(
        filters="ensembl_gene_id",
        attributes=c("ensembl_gene_id", "entrezgene_id"),
        values=ensembl.genes,
        mart=mart)
  
  ```
  
  Where `ensembl.genes` is a vector of Ensembl gene IDs.
  
  > **Comments:**
  > **username_3**: As of 2021-08-05, the attributes argument should be set to `attributes = c("ensembl_gene_id", "entrezgene_id")`. I believe that the `"_id"` appendage has been added to the attribute since this answer was first posted.  
  
  ---
  
  