<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Saren,<br>
<br>
The feature look up will return all features of the given object
type that overlap your queried region.<br>
<br>
In your example, the region is the input gene and two transcripts
overlap this region.<br>
<br>
To retrieve the gene linked to a transcript, I would recommend using
'feature=transcript' instead<br>
Among the fields returned, there is a 'Parent' field that will
specify which gene the transcript belongs to.<br>
<br>
<a class="moz-txt-link-freetext" href="http://beta.rest.ensembl.org/feature/id/ENSMUST00000163188?feature=transcript;content-type=text/xml">http://beta.rest.ensembl.org/feature/id/ENSMUST00000163188?feature=transcript;content-type=text/xml</a><br>
<meta charset="utf-8">
<span style="color: rgb(136, 18, 128); 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; display: inline
!important; float: none;"><data</span><span
class="webkit-html-attribute" style="color: rgb(136, 18, 128);
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="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">ID</span>="<span
class="webkit-html-attribute-value">ENSMUST00000163188</span>"</span><span
class="webkit-html-attribute" style="color: rgb(136, 18, 128);
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="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">Parent</span>="<span
class="webkit-html-attribute-value">ENSMUSG00000057729</span>"</span><span
class="webkit-html-attribute" style="color: rgb(136, 18, 128);
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="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">biotype</span>="<span
class="webkit-html-attribute-value">processed_transcript</span>"</span><span
class="webkit-html-attribute" style="color: rgb(136, 18, 128);
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="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">description</span>="<span
class="webkit-html-attribute-value"></span>"</span><span
class="webkit-html-attribute" style="color: rgb(136, 18, 128);
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="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">end</span>="<span
class="webkit-html-attribute-value">79883041</span>"</span><span
class="webkit-html-attribute" style="color: rgb(136, 18, 128);
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="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">external_name</span>="<span
class="webkit-html-attribute-value">Prtn3-004</span>"</span><span
class="webkit-html-attribute" style="color: rgb(136, 18, 128);
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="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">feature_type</span>="<span
class="webkit-html-attribute-value">transcript</span>"</span><span
class="webkit-html-attribute" style="color: rgb(136, 18, 128);
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="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">logic_name</span>="<span
class="webkit-html-attribute-value">havana</span>"</span><span
class="webkit-html-attribute" style="color: rgb(136, 18, 128);
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-attribute-name">seq_region_name</span>="<span
class="webkit-html-attribute-value">10</span>"</span><span
class="webkit-html-attribute" style="color: rgb(136, 18, 128);
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="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" style="color: rgb(136, 18, 128);
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="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" style="color: rgb(136, 18, 128);
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="Apple-converted-space"> </span><span
class="webkit-html-attribute-name">strand</span>="<span
class="webkit-html-attribute-value">1</span>"</span><span
style="color: rgb(136, 18, 128); 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; display: inline
!important; float: none;">/><br>
<br>
</span>This will still return more transcripts than your input, but
you will be able to uniquely associate each transcript to its gene.<br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 19/05/2014 10:00, Saren Tasciyan
wrote:<br>
</div>
<blockquote cite="mid:5379C840.7070801@univie.ac.at" type="cite">
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
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 moz-do-not-send="true" 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:
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>
<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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true" class="moz-txt-link-abbreviated"
href="mailto:saren.tasciyan@univie.ac.at">saren.tasciyan@univie.ac.at</a></div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>