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Hi Genomeo,<br>
<br>
HGNC data is manually curated, so HGNC curators check a locus and
assign the corresponding ensembl entry.<br>
As each entry is manually curated, not all ensembl mappings are
necessarily available.<br>
It does mean though that HGNC can be updated in permanence.<br>
<br>
In Ensembl, we typically update those mappings every release, as the
human gene set is updated every release.<br>
We assign HGNC IDs using direct mappings from HGNC.<br>
These are complemented by indirect mappings, via Uniprot or RefSeq.<br>
If a Uniprot entry is mapped to an ensembl entry and that same
Uniprot entry is mapped in HGNC to an HGNC symbol, the HGNC symbol
is assigned to the ensembl entry.<br>
<br>
So there are more HGNC-ensembl ID links in Ensembl than they are in
HGNC.<br>
<br>
What can also happen is that our ensembl stable ID changes between
releases due to massive changes in the underlying sequence.<br>
For those cases, we will not be able to get the direct mapping from
HGNC.<br>
We might still be able to keep the same name for the gene thanks to
the two-step mappings via RefSeq or Uniprot.<br>
We then feed those cases back to HGNC for them to update their
records if they agree with the replacement.<br>
<br>
I am unsure on how NCBI assigns mappings to Ensembl, they could be
importing the mappings from us directly or generate their own
mappings.<br>
<br>
I hope this answers most of your questions.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 20/02/2014 11:43, Genomeo Dev wrote:<br>
</div>
<blockquote
cite="mid:CAKry3c0JgFPJQ0_L2PDsp1MoS-Dym_f-d3f3pDgUpPRmJMmtZg@mail.gmail.com"
type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>I have a set of ~ 6000 Ensembl IDs which I want to map to
HGNC IDs. I am faced with the following situation:</div>
<div><br>
</div>
<div>Based on Ensembl Biomart or Ensembl Rest, there are ~ 4000
of these that have HGNC IDs.</div>
<div><br>
</div>
<div>Based on HGNC biomart, there are ~ 3000 which have HGNC
IDs. HGNC DB mention that themselves use mapping supplied by
Ensembl.</div>
<div><br>
</div>
<div>The IDs mapped from each of these sources are not always
the same.</div>
<div><br>
</div>
<div>Questions:</div>
<div><br>
</div>
<div>- What is causing the different level of coverage?</div>
<div>- What is causing the differences in specific mapping if
all of it is done by Esembl?</div>
<div>- How often does this mapping change at any of these
sources?</div>
<div>- How do other sources like NCBI assign Ensembl IDs to
their Entrez IDs?</div>
<div>- What is the best way of getting HGNC IDs for Ensembl IDs?
from Ensembl or HGNC DB?</div>
<div><br>
</div>
<div>Thanks!<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">G.</div>
</div>
</div>
<br>
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