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Hi,<br>
<br>
I am using REST API for my Java application, however I am stuck with
a problem:<br>
I have a list of transcript IDs (ENSMUST....) from which, I want to
gather gene IDs. So I have decided to use following endpoint:<br>
<a class="moz-txt-link-freetext" href="http://beta.rest.ensembl.org">http://beta.rest.ensembl.org</a><b>/feature/id/ENSMUST00000163188</b><b>?feature=gene</b>;content-type=text/xml<br>
as you can see that this returns 2 IDs:<br>
<br>
<div class="line" style="color: rgb(0, 0, 0); font-family:
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class="webkit-html-tag"><opt></span></div>
<div class="collapsible-content" style="margin-left: 1em; color:
rgb(0, 0, 0); font-family: monospace; font-size: 13px; font-style:
normal; font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span
class="text"></span>
<div class="line"><span class="webkit-html-tag"><data<span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">ID</span>="<span
class="webkit-html-attribute-value">ENSMUSG00000035835</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">biotype</span>="<span
class="webkit-html-attribute-value">protein_coding</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">description</span>="<span
class="webkit-html-attribute-value">cDNA sequence BC005764
[Source:MGI Symbol;Acc:MGI:2388640]</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">end</span>="<span
class="webkit-html-attribute-value">79874634</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">external_name</span>="<span
class="webkit-html-attribute-value">BC005764</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">feature_type</span>="<span
class="webkit-html-attribute-value">gene</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">logic_name</span>="<span
class="webkit-html-attribute-value">ensembl_havana_gene</span>"</span><span
class="webkit-html-attribute"><span
class="webkit-html-attribute-name">seq_region_name</span>="<span
class="webkit-html-attribute-value">10</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">source</span>="<span
class="webkit-html-attribute-value">ensembl_havana</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">start</span>="<span
class="webkit-html-attribute-value">79860475</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">strand</span>="<span
class="webkit-html-attribute-value">-1</span>"</span>/></span></div>
<span class="text"></span>
<div class="line"><span class="webkit-html-tag"><data<span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">ID</span>="<span
class="webkit-html-attribute-value">ENSMUSG00000057729</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">biotype</span>="<span
class="webkit-html-attribute-value">protein_coding</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">description</span>="<span
class="webkit-html-attribute-value">proteinase 3
[Source:MGI Symbol;Acc:MGI:893580]</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">end</span>="<span
class="webkit-html-attribute-value">79883174</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">external_name</span>="<span
class="webkit-html-attribute-value">Prtn3</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">feature_type</span>="<span
class="webkit-html-attribute-value">gene</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">logic_name</span>="<span
class="webkit-html-attribute-value">ensembl_havana_gene</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">seq_region_name</span>="<span
class="webkit-html-attribute-value">10</span>"</span><span
class="webkit-html-attribute"><span
class="webkit-html-attribute-name">source</span>="<span
class="webkit-html-attribute-value">ensembl_havana</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">start</span>="<span
class="webkit-html-attribute-value">79874476</span>"</span><span
class="webkit-html-attribute"><span
class="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">strand</span>="<span
class="webkit-html-attribute-value">1</span>"</span>/></span></div>
<span class="text"></span></div>
<div class="line" style="color: rgb(0, 0, 0); font-family:
monospace; font-size: 13px; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: auto; text-align: start; text-indent: 0px;
text-transform: none; white-space: normal; widows: auto;
word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span
class="webkit-html-tag"></opt></span></div>
<br>
When queried from Ensembl website I "only" get one result:<br>
<a
href="http://www.ensembl.org/Mus_musculus/Transcript/Summary?db=core;g=ENSMUSG00000057729;r=10:79874476-79883041;t=ENSMUST00000163188">http://www.ensembl.org/Mus_musculus/Transcript/Summary?db=core;g=ENSMUSG00000057729;r=10:79874476-79883041;t=ENSMUST00000163188</a><br>
<br>
My idea, when I first ran into this problem was to use logic_name as
an indicator, as this problem is even more frequent with ncrna, etc.
However both results here have same logic_name.<br>
Correct results would be "according to my dataset" the second one.
Am I using a wrong approach here or should I include more parameters
in my query?<br>
<br>
As an example here are more queries with multiple results:<br>
<a
href="http://beta.rest.ensembl.org/feature/id/ENSMUST00000040746?feature=gene;content-type=text/xml">http://beta.rest.ensembl.org/feature/id/ENSMUST00000040746?feature=gene;content-type=text/xml</a><br>
<a
href="http://beta.rest.ensembl.org/feature/id/ENSMUST00000075162?feature=gene;content-type=text/xml">http://beta.rest.ensembl.org/feature/id/ENSMUST00000075162?feature=gene;content-type=text/xml</a><br>
<a
href="http://beta.rest.ensembl.org/feature/id/ENSMUST00000080673?feature=gene;content-type=text/xml">http://beta.rest.ensembl.org/feature/id/ENSMUST00000080673?feature=gene;content-type=text/xml</a><br>
<a
href="http://beta.rest.ensembl.org/feature/id/ENSMUST00000118639?feature=gene;content-type=text/xml">http://beta.rest.ensembl.org/feature/id/ENSMUST00000118639?feature=gene;content-type=text/xml</a><br>
<br>
Cheers,<br>
Saren<br>
<br>
<div class="moz-signature">-- <br>
Saren Tasciyan<br>
<br>
Master Student & IT Technician at Karl Kuchler Group<br>
Room: 2.107<br>
<br>
Max F. Perutz Laboratories GmbH<br>
Dr. Bohr-Gasse 9<br>
A-1030 Wien<br>
<br>
T: +43-1-4277- 61812<br>
E: <a class="moz-txt-link-abbreviated" href="mailto:saren.tasciyan@univie.ac.at">saren.tasciyan@univie.ac.at</a></div>
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