text: user3119: I am playing with biomart in order to get the list of genes associated to a specific gene ontology (GO) term.
  So, if I use the webservice as in this query:
  I get at least 50 genes. If I download the file I can gen an exact count of them:
  $ cat mart_export.txt | wc -l
  347
  
  Now, I can do the same operation by using the R library biomaRt. Specifically:
  > ensembl <- useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset='hsapiens_gene_ensembl')
  > gene <- getBM(attributes = c('external_gene_name'), filters = 'go', values = 'GO:0030098', mart = ensembl)
  > unique(gene)
    external_gene_name
  1               SPI1
  2              PRKDC
  3                TOX
  4               LY6D
  5               CBFB
  6              IKZF1
  7               RELB
  8             FLT3LG
  
  By doing so, these are all the genes I retrieve. The two results are totally different and I don't know why it. All these eight genes are found in the biomart file (I grepped it, to be sure).
  I believe this is not an issue related to databases versions since I checked:
  >listMarts()
                 biomart               version
  1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 94
  2   ENSEMBL_MART_MOUSE      Mouse strains 94
  3     ENSEMBL_MART_SNP  Ensembl Variation 94
  4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 94
  
  and:
  >listDatasets(ensembl)
  ...
  38 Human genes (GRCh38.p12)
  ...
  
  Both are the same version used by biomart online.
  What is going on? Is it possible that biomart online is considering GO relations that are not specified in the R version?
  
  user1332: Sorry, this was my mistake in the last question. To search down the ontology, rather than just for the specific association with a term, biomaRt needs a different filter: 'go_parent_term'.
  Try:
  gene <- getBM(attributes = c('external_gene_name'), filters = 'go_parent_term', values = 'GO:0030098', mart = ensembl)
  
  
original_text: 3119: <p>I am playing with biomart in order to get the list of genes associated to a specific gene ontology (GO) term.</p>
  
  <p>So, if I use the webservice as in this <a href="http://www.ensembl.org/biomart/martview/b222cd479ae7a7ab534cc7d672a80df5" rel="nofollow noreferrer">query</a>:</p>
  
  <p>I get at least 50 genes. If I download the file I can gen an exact count of them:</p>
  
  <pre><code>$ cat mart_export.txt | wc -l
  347
  </code></pre>
  
  <p>Now, I can do the same operation by using the R library biomaRt. Specifically:</p>
  
  <pre><code>&gt; ensembl &lt;- useEnsembl(biomart="ENSEMBL_MART_ENSEMBL", dataset='hsapiens_gene_ensembl')
  &gt; gene &lt;- getBM(attributes = c('external_gene_name'), filters = 'go', values = 'GO:0030098', mart = ensembl)
  &gt; unique(gene)
    external_gene_name
  1               SPI1
  2              PRKDC
  3                TOX
  4               LY6D
  5               CBFB
  6              IKZF1
  7               RELB
  8             FLT3LG
  </code></pre>
  
  <p>By doing so, these are all the genes I retrieve. The two results are totally different and I don't know why it. All these eight genes are found in the biomart file (I grepped it, to be sure).</p>
  
  <p>I believe this is not <a href="https://www.biostars.org/p/109246/" rel="nofollow noreferrer">an issue related to databases versions</a> since I checked:</p>
  
  <pre><code>&gt;listMarts()
                 biomart               version
  1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 94
  2   ENSEMBL_MART_MOUSE      Mouse strains 94
  3     ENSEMBL_MART_SNP  Ensembl Variation 94
  4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 94
  </code></pre>
  
  <p>and:</p>
  
  <pre><code>&gt;listDatasets(ensembl)
  ...
  38 Human genes (GRCh38.p12)
  ...
  </code></pre>
  
  <p>Both are the same version used by biomart online.</p>
  
  <p>What is going on? Is it possible that biomart online is considering <a href="http://geneontology.org/page/ontology-relations" rel="nofollow noreferrer">GO relations</a> that are not specified in the R version?</p>
   1332: <p>Sorry, this was my mistake in the last question. To search down the ontology, rather than just for the specific association with a term, biomaRt needs a different filter: 'go_parent_term'.</p>
  
  <p>Try:</p>
  
  <pre><code>gene &lt;- getBM(attributes = c('external_gene_name'), filters = 'go_parent_term', values = 'GO:0030098', mart = ensembl)
  </code></pre>
  