text: user4413: I know that with GRCh38, it is possible to extract the matching RefSeq transcripts for Ensembl genes/transcripts/proteins using Biomart from Ensembl. 
  However, for GRCh37, this option does not exists. Using the following MySQL command returns Ensembl transcript IDs for matching RefSeq transcripts:
  mysql -u anonymous -h ensembldb.ensembl.org -A -P 3337 -D homo_sapiens_core_99_37 -e "SELECT transcript.stable_id, xref.display_label FROM transcript, object_xref, xref,external_db WHERE transcript.transcript_id = object_xref.ensembl_id AND object_xref.ensembl_object_type = 'Transcript' AND object_xref.xref_id = xref.xref_id AND xref.external_db_id = external_db.external_db_id AND external_db.db_name = 'RefSeq_mRNA';"
  
  Also, I was trying to play around with the databases schema but I am not able to find any solution to problem.
  Ultimately, I wish to obtain a table like the following:
  Gene stable ID      Transcript stable ID    Protein stable ID   RefSeq match transcript
  ENSG00000120329     ENST00000239451         ENSP00000239451     NM_031947.4
  ENSG00000164219     ENST00000419445         ENSP00000404676     NM_005023.4
  ENSG00000150594     ENST00000280155         ENSP00000280155     NM_000681.4
  ENSG00000113578     ENST00000337706         ENSP00000338548     NM_000800.5
  
  Thank you in advance.
  
  user73: Try the GRCh37 version of BioMart, and the External reference "RefSeq mRNA ID" / "RefSeq ncRNA ID":
  https://grch37.ensembl.org/biomart
  From the Perl code provided by BioMart, it looks like the field name should be "refseq_mrna" or "refseq_ncrna". I'm not sure how that translates to the SQL code.
  I feel compelled to add a caution to this, though. GRCh37 is a very old build, having been replaced by GRCh38 in December 2013. If possible, please find a way to use GRCh38 for your analysis instead, and don't create any new software that depends on GRCh37. For example, gnomAD v3 supports GRCh38 (see bioconductor, or here).
  
  user1332: The RefSeq match option in BioMart is from the Matched Annotation from NCBI and EBI (MANE) collaboration between RefSeq and Ensembl. It has only been calculated for the up-to-date gene annotation on GRCh38 so cannot be obtained on GRCh37. You can get mapping from Ensembl to RefSeq transcripts through BioMart as RefSeq mRNA ID (refseq_mrna in R) but this is not a perfect match like the MANE, it is a mapping based on sequence similarity and similar genomic location, and there can be mismatches between them.
  
original_text: 4413: <p>I know that with GRCh38, it is possible to extract the matching RefSeq transcripts for Ensembl genes/transcripts/proteins using Biomart from Ensembl. </p>
  
  <p>However, for GRCh37, this option does not exists. Using the following MySQL command returns Ensembl transcript IDs for matching RefSeq transcripts:</p>
  
  <pre><code>mysql -u anonymous -h ensembldb.ensembl.org -A -P 3337 -D homo_sapiens_core_99_37 -e "SELECT transcript.stable_id, xref.display_label FROM transcript, object_xref, xref,external_db WHERE transcript.transcript_id = object_xref.ensembl_id AND object_xref.ensembl_object_type = 'Transcript' AND object_xref.xref_id = xref.xref_id AND xref.external_db_id = external_db.external_db_id AND external_db.db_name = 'RefSeq_mRNA';"
  </code></pre>
  
  <p>Also, I was trying to play around with the <a href="https://www.ensembl.org/info/docs/api/core/diagrams/Core.svg" rel="nofollow noreferrer">databases schema</a> but I am not able to find any solution to problem.</p>
  
  <p>Ultimately, I wish to obtain a table like the following:</p>
  
  <pre><code>Gene stable ID      Transcript stable ID    Protein stable ID   RefSeq match transcript
  ENSG00000120329     ENST00000239451         ENSP00000239451     NM_031947.4
  ENSG00000164219     ENST00000419445         ENSP00000404676     NM_005023.4
  ENSG00000150594     ENST00000280155         ENSP00000280155     NM_000681.4
  ENSG00000113578     ENST00000337706         ENSP00000338548     NM_000800.5
  </code></pre>
  
  <p>Thank you in advance.</p>
   73: <p>Try the GRCh37 version of BioMart, and the External reference "RefSeq mRNA ID" / "RefSeq ncRNA ID":</p>
  
  <p><a href="https://grch37.ensembl.org/biomart" rel="nofollow noreferrer">https://grch37.ensembl.org/biomart</a></p>
  
  <p>From the Perl code provided by BioMart, it looks like the field name should be "refseq_mrna" or "refseq_ncrna". I'm not sure how that translates to the SQL code.</p>
  
  <p>I feel compelled to add a caution to this, though. GRCh37 is a very old build, having been <em>replaced</em> by GRCh38 in <a href="https://en.wikipedia.org/wiki/Reference_genome#Human_reference_genome" rel="nofollow noreferrer">December 2013</a>. If possible, please find a way to use GRCh38 for your analysis instead, and don't create any <em>new</em> software that depends on GRCh37. For example, gnomAD v3 supports GRCh38 (see <a href="https://bioconductor.org/packages/release/data/annotation/html/MafDb.gnomAD.r3.0.GRCh38.html" rel="nofollow noreferrer">bioconductor</a>, or <a href="https://macarthurlab.org/2019/10/16/gnomad-v3-0/" rel="nofollow noreferrer">here</a>).</p>
   1332: <p>The RefSeq match option in BioMart is from the <a href="http://www.ensembl.org/info/genome/genebuild/mane.html" rel="nofollow noreferrer">Matched Annotation from NCBI and EBI (MANE)</a> collaboration between RefSeq and Ensembl. It has only been calculated for the up-to-date gene annotation on GRCh38 so cannot be obtained on GRCh37. You can get mapping from Ensembl to RefSeq transcripts through BioMart as RefSeq mRNA ID (refseq_mrna in R) but this is not a perfect match like the MANE, it is a mapping based on sequence similarity and similar genomic location, and there can be mismatches between them.</p>
  