<div dir="ltr">Thanks Magali for the response. <div><br></div><div>1) I don't quite understand these two points:</div><div><br></div><div>'..<span style="font-family:arial,sans-serif;font-size:13px">As each entry is manually curated, not all ensembl mappings are necessarily available..'</span></div>
<div><br></div><div>Is this due to the non-practicality of manually working with large ensembl IDs?</div><div><br></div><div><span style="font-family:arial,sans-serif;font-size:13px">'.. What can also happen is that our ensembl stable ID changes between releases due to massive changes in the underlying sequence..</span><span style="font-family:arial,sans-serif;font-size:13px">We then feed those cases back to HGNC for them to update their records if they agree with the replacement.'</span><br>
</div><div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div>But if the sequence changes, it will change for both Ensembl and HGNC because they both refer to the same reference genome right? so why HGNC needs to agree?</div>
<div><br></div><div>2) Based on the rest of your email, let me reiterate back my understanding and let me know if that is correct:<div><br></div><div>- Ensembl doesn't assign any of its IDs to HGNC IDs on its own judgement, rather it uses the manual assignments of HGNC DB and assignments done by Uniprot and RefSeq.<br>
</div><div><br></div><div>- Because A) Ensembl updates these assignment each release and not more frequently, B) HGNC keep making more manual assignments continuously, and C) Ensembl IDs can change between releases, all these factors lead to differences between what is in Ensembl and HGNC in terms of mapping.</div>
<div><br></div><div>If this understanding is correct, I don't see how this will lead to Ensembl having greater coverage than HGNC.</div><div><br></div><div>G.</div><div><br><div><br></div><div><br></div></div></div></div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On 20 February 2014 16:18, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
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<div><div class="h5"><br>
<br>
<div>On 20/02/2014 11:43, Genomeo Dev wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<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>
<fieldset></fieldset>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">G.</div>
</div>