[ensembl-dev] Ensembl IDs versus HGNC

[Genomeo Dev]

Thanks Magali for the response.

1) I don't quite understand these two points:

'..As each entry is manually curated, not all ensembl mappings are
necessarily available..'

Is this due to the non-practicality of manually working with large ensembl
IDs?

'.. What can also happen is that our ensembl stable ID changes between
releases due to massive changes in the underlying sequence..We then feed
those cases back to HGNC for them to update their records if they agree
with the replacement.'

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?

2) Based on the rest of your email, let me reiterate back my understanding
and let me know if that is correct:

- 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.

- 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.

If this understanding is correct, I don't see how this will lead to Ensembl
having greater coverage than HGNC.

G.





On 20 February 2014 16:18, mag <mr6 at ebi.ac.uk> wrote:

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