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

[mag]

Hi Fin Swimmer,


On 24/02/2016 10:12, Fin Swimmer wrote:
> Hello Magali,
> thanks for your quick answer.
>
> Am 23.02.2016 17:45, schrieb mag:
>> 1. As long as our default assembly is GRCh38, the sequence for a
>> specific region will be stable.
> Fine.
>
>> 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.
> Ok, thanks for this hint. But it doesn't explain why for some genes 
> the MIM morbid links are missing.
The data in OMIM is not always straightforward to retrieve programmatically.
As a result, we often miss out some subtleties resulting in unmapped 
entries.
We are currently working on improving these links.
>
>> 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 
>>
> Nice. Where can I fnd out more about which features are available? So 
> the "band" feature isn't mentioned in the doc of the API.
Our general approach regarding REST documentation is as follows:
- search for generic terms on the main page, to select the endpoint 
which seems appropriate to your use case
For example, I could search for gene, which would select the following 
description
'Retrieves features (e.g. genes, transcripts, variants and more) that 
overlap a region defined by the given identifier.'
- click on the endpoint, which lists available options and parameters 
for that endpoint
http://rest.ensembl.org/documentation/info/overlap_id
Here you can see that band is listed in the feature types that can be 
specified

We are trying to provide a useful description that remains succint in 
the main page, so information does not get lost in too much detail.
I agree though that it is not always easy to find exactly what you are 
looking for.
Please let us know if you have any suggestions, we are always looking 
for ways to improve the service.
>
>> 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.
> That sounds very good.
>
> Bye,
> fin swimmer

Regards,
Magali
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