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Hi Fin Swimmer,<br>
<br>
<br>
<div class="moz-cite-prefix">On 24/02/2016 10:12, Fin Swimmer wrote:<br>
</div>
<blockquote
cite="mid:0bea6ed97c17cf2d305698d23ba7c825@tobiasklare.de"
type="cite">Hello Magali,
<br>
thanks for your quick answer.
<br>
<br>
Am 23.02.2016 17:45, schrieb mag:
<br>
<blockquote type="cite">1. As long as our default assembly is
GRCh38, the sequence for a
<br>
specific region will be stable.
<br>
</blockquote>
Fine.
<br>
<br>
<blockquote type="cite">2. Disease information like Orphanet or
MIM morbid are better accessed
<br>
via the Phenotype tab on the gene page
<br>
for example:
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000139618;r=13:32315474-32400266">http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000139618;r=13:32315474-32400266</a>
<br>
We are currently figuring out the best way to retrieve and
display
<br>
this data, hence some links might be missing.
<br>
MIM gene links will remain accessible from the external
references tab.
<br>
</blockquote>
Ok, thanks for this hint. But it doesn't explain why for some
genes the MIM morbid links are missing.
<br>
</blockquote>
The data in OMIM is not always straightforward to retrieve
programmatically.<br>
As a result, we often miss out some subtleties resulting in unmapped
entries.<br>
We are currently working on improving these links.<br>
<blockquote
cite="mid:0bea6ed97c17cf2d305698d23ba7c825@tobiasklare.de"
type="cite">
<br>
<blockquote type="cite">3. The /overlap endpoint can return most
Ensembl features overlapping
<br>
your region or feature of choice.
<br>
This includes karyotype band information.
<br>
You can input a gene id, or a whole chromosomal region.
<br>
For example:
<br>
<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/overlap/id/ENSG00000157764?feature=gene;content-type=text/xml;feature=band">http://rest.ensembl.org/overlap/id/ENSG00000157764?feature=gene;content-type=text/xml;feature=band</a>
<br>
or
<br>
<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/overlap/region/human/7:140424943-140624564?feature=gene;feature=band;content-type=text/xml">http://rest.ensembl.org/overlap/region/human/7:140424943-140624564?feature=gene;feature=band;content-type=text/xml</a>
<br>
</blockquote>
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.<br>
</blockquote>
Our general approach regarding REST documentation is as follows:<br>
- search for generic terms on the main page, to select the endpoint
which seems appropriate to your use case<br>
For example, I could search for gene, which would select the
following description<br>
'Retrieves features (e.g. genes, transcripts, variants and more)
that overlap a region defined by the given identifier.'<br>
- click on the endpoint, which lists available options and
parameters for that endpoint<br>
<a class="moz-txt-link-freetext" href="http://rest.ensembl.org/documentation/info/overlap_id">http://rest.ensembl.org/documentation/info/overlap_id</a><br>
Here you can see that band is listed in the feature types that can
be specified<br>
<br>
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.<br>
I agree though that it is not always easy to find exactly what you
are looking for.<br>
Please let us know if you have any suggestions, we are always
looking for ways to improve the service.<br>
<meta charset="utf-8">
<blockquote
cite="mid:0bea6ed97c17cf2d305698d23ba7c825@tobiasklare.de"
type="cite">
<br>
<blockquote type="cite">4. This is a bug we only recently
uncovered, apologies about the inconvenience.
<br>
Luckily, it is now fixed and will be rolled out with our new
release,
<br>
84, scheduled for early March.
<br>
</blockquote>
That sounds very good.
<br>
<br>
Bye,
<br>
fin swimmer<br>
</blockquote>
<br>
Regards,<br>
Magali<br>
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