[ensembl-dev] Some general questions about ensembl's data and REST-Api

[mag]

Hi Fin,

1. As long as our default assembly is GRCh38, the sequence for a 
specific region will be stable.
There might be minor assembly changes, which result in regions being 
added, like alternative sequences.
The already existing regions remain unchanged though.

2. Disease information like Orphanet or MIM morbid are better accessed 
via the Phenotype tab on the gene page
for example: 
http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000139618;r=13:32315474-32400266
We are currently figuring out the best way to retrieve and display this 
data, hence some links might be missing.
MIM gene links will remain accessible from the external references tab.

3. The /overlap endpoint can return most Ensembl features overlapping 
your region or feature of choice.
This includes karyotype band information.
You can input a gene id, or a whole chromosomal region.
For example:
http://rest.ensembl.org/overlap/id/ENSG00000157764?feature=gene;content-type=text/xml;feature=band
or
http://rest.ensembl.org/overlap/region/human/7:140424943-140624564?feature=gene;feature=band;content-type=text/xml

4. This is a bug we only recently uncovered, apologies about the 
inconvenience.
Luckily, it is now fixed and will be rolled out with our new release, 
84, scheduled for early March.


Regards,
Magali

On 23/02/2016 10:05, Fin Swimmer wrote:
> Hello,
> i have some general questions about ensembl's data and some concerning 
> the REST-Api.
>
> 1. The human sequences in ensembl are based on GRCh38. So can I be 
> sure, that the sequence for a specific region will be stable as long 
> as ensembl uses GRCh38? Or can there be minor changes in sequence or 
> counting the position over the time?
> 2. I found out that for some genes there are no entries under external 
> references for the diseases linked to gene to omim ("MIM morbid"). 
> E.g. BRCA2 or FBN1. Why?
> 3. Is there a way via REST-Api to find out on which arm of the 
> chromosome a gene is located? I fear not, because I cannot find this 
> information on the ensembl webpage as well.
> 4. Is there a reason why I cannot receive information about the 
> translation, if I use the lookup/id endpoint for a transcript id, but 
> for a gene id I can?
>
> Thanks for a reply.
>
> fin swimmer
>
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