<div dir="ltr">OK thanks.<div><br></div><div>Another question please:</div><div><br></div><div>Going back to my perl subroutine for getting xref for ensembl IDs:</div><div><br></div><div>use warnings;</div><div><div>sub print_DBEntries</div>
<div>{</div><div><span class="" style="white-space:pre"> </span>my $db_entries = shift;</div><div><span class="" style="white-space:pre"> </span>foreach my $dbe ( @{$db_entries} ) {</div><div><span class="" style="white-space:pre"> </span>printf "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n", $dbe->dbname(), $dbe->display_id(), $dbe->description(), $dbe->db_display_name(), $dbe->info_text(), $dbe->info_type(), $dbe->primary_id(), join(", ",@{$dbe->get_all_synonyms()}) , $dbe->version();</div>
<div><span class="" style="white-space:pre"> </span>}</div><div>}</div></div><div><br></div><div>I found that some values are not returned for some databases. For example using ENSG00000151067:</div><div><br></div><div><div>
#Use of uninitialized value in printf at ./<a href="http://fetch_ensembl_genes_v2.pl">fetch_ensembl_genes_v2.pl</a> line 47.</div><div>OTTG<span class="" style="white-space:pre"> </span>OTTHUMG00000150243<span class="" style="white-space:pre"> </span>Havana gene<span class="" style="white-space:pre"> </span>NONE<span class="" style="white-space:pre"> </span>OTTHUMG00000150243<span class="" style="white-space:pre"> </span>7</div>
<div>#Use of uninitialized value in printf at ./<a href="http://fetch_ensembl_genes_v2.pl">fetch_ensembl_genes_v2.pl</a> line 47.</div><div>ENS_LRG_gene<span class="" style="white-space:pre"> </span>LRG_334<span class="" style="white-space:pre"> </span>LRG display in Ensembl<span class="" style="white-space:pre"> </span>NONE<span class="" style="white-space:pre"> </span>LRG_334<span class="" style="white-space:pre"> </span>0</div>
<div>LRG<span class="" style="white-space:pre"> </span>LRG_334<span class="" style="white-space:pre"> </span>Locus Reference Genomic record for CACNA1C<span class="" style="white-space:pre"> </span>Locus Reference Genomic<span class="" style="white-space:pre"> </span>DIRECT<span class="" style="white-space:pre"> </span>LRG_334<span class="" style="white-space:pre"> </span>0</div>
<div>ArrayExpress<span class="" style="white-space:pre"> </span>ENSG00000151067<span class="" style="white-space:pre"> </span>ArrayExpress<span class="" style="white-space:pre"> </span>DIRECT<span class="" style="white-space:pre"> </span>ENSG00000151067<span class="" style="white-space:pre"> </span>0</div>
<div>EntrezGene<span class="" style="white-space:pre"> </span>CACNA1C<span class="" style="white-space:pre"> </span>calcium channel, voltage-dependent, L type, alpha 1C subunit<span class="" style="white-space:pre"> </span>EntrezGene<span class="" style="white-space:pre"> </span>DEPENDENT<span class="" style="white-space:pre"> </span>775<span class="" style="white-space:pre"> </span>CACH2, CACN2, CACNL1A1, CaV1.2, CCHL1A1, LQT8, TS<span class="" style="white-space:pre"> </span>0</div>
<div>HGNC<span class="" style="white-space:pre"> </span>CACNA1C<span class="" style="white-space:pre"> </span>calcium channel, voltage-dependent, L type, alpha 1C subunit<span class="" style="white-space:pre"> </span>HGNC Symbol<span class="" style="white-space:pre"> </span>Generated via ensembl_manual<span class="" style="white-space:pre"> </span>DIRECT<span class="" style="white-space:pre"> </span>1390<span class="" style="white-space:pre"> </span>CACH2, CACN2, CACNL1A1, Cav1.2, CCHL1A1, LQT8, TS<span class="" style="white-space:pre"> </span>0</div>
<div>MIM_GENE<span class="" style="white-space:pre"> </span> CALCIUM CHANNEL, VOLTAGE-DEPENDENT [*114205]<span class="" style="white-space:pre"> </span> CALCIUM CHANNEL, VOLTAGE-DEPENDENT, L TYPE, ALPHA-1C SUBUNIT; CACNA1C<span class="" style="white-space:pre"> </span>MIM gene<span class="" style="white-space:pre"> </span>DEPENDENT<span class="" style="white-space:pre"> </span>114205<span class="" style="white-space:pre"> </span>0</div>
<div>MIM_MORBID<span class="" style="white-space:pre"> </span> TIMOTHY SYNDROME [#601005]<span class="" style="white-space:pre"> </span> TIMOTHY SYNDROME; TS<span class="" style="white-space:pre"> </span>MIM disease<span class="" style="white-space:pre"> </span>DEPENDENT<span class="" style="white-space:pre"> </span>601005<span class="" style="white-space:pre"> </span>0</div>
<div>MIM_MORBID<span class="" style="white-space:pre"> </span> BRUGADA SYNDROME 3 [#611875]<span class="" style="white-space:pre"> </span> BRUGADA SYNDROME 3; BRGDA3<span class="" style="white-space:pre"> </span>MIM disease<span class="" style="white-space:pre"> </span>DEPENDENT<span class="" style="white-space:pre"> </span>611875<span class="" style="white-space:pre"> </span>0</div>
<div>UniGene<span class="" style="white-space:pre"> </span>Hs.690010<span class="" style="white-space:pre"> </span>Voltage-dependent L-type Ca2+ channel alpha 1 subunit (CACNA1C) mRNA, exon 1a and partial cds<span class="" style="white-space:pre"> </span>UniGene<span class="" style="white-space:pre"> </span>SEQUENCE_MATCH<span class="" style="white-space:pre"> </span>Hs.690010<span class="" style="white-space:pre"> </span>0</div>
<div>UniGene<span class="" style="white-space:pre"> </span>Hs.697137<span class="" style="white-space:pre"> </span>Transcribed locus, weakly similar to XP_416388.3 PREDICTED: voltage-dependent L-type calcium channel subunit alpha-1C [Gallus gallus]<span class="" style="white-space:pre"> </span>UniGene<span class="" style="white-space:pre"> </span>SEQUENCE_MATCH<span class="" style="white-space:pre"> </span>Hs.697137<span class="" style="white-space:pre"> </span>0</div>
<div>Uniprot_gn<span class="" style="white-space:pre"> </span>CACNA1C<span class="" style="white-space:pre"> </span>UniProtKB Gene Name<span class="" style="white-space:pre"> </span>DEPENDENT<span class="" style="white-space:pre"> </span>CACNA1C<span class="" style="white-space:pre"> </span>CACH2, CACN2, CACNL1A1, CCHL1A1<span class="" style="white-space:pre"> </span>0</div>
<div>WikiGene<span class="" style="white-space:pre"> </span>CACNA1C<span class="" style="white-space:pre"> </span>calcium channel, voltage-dependent, L type, alpha 1C subunit<span class="" style="white-space:pre"> </span>WikiGene<span class="" style="white-space:pre"> </span>DEPENDENT<span class="" style="white-space:pre"> </span>775<span class="" style="white-space:pre"> </span>0</div>
</div><div><br></div><div>I would expect for missing value to be empty string. Am I missing anything?</div><div><br></div><div>On a related note, this code runs very slowly (takes 6 mns for 100 genes). From an earlier post, it seems that connecting to the database is the bottleneck. Connecting to <a href="http://useastdb.ensembl.org">useastdb.ensembl.org</a> instead of <a href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a> is not much better. So I was wondering whether there is a way to turn off lazy loading for the purpose of debugging?</div>
<div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 27 February 2014 14:43, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Genomeo,<br>
<br>
Taking the last entry as example:<br>
Hs.743764 refers to
<a href="http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=5947187&TAXID=9606&SEARCH=Hs.743764" target="_blank">http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=5947187&TAXID=9606&SEARCH=Hs.743764</a><br>
This is a human locus.<br>
The description means that this locus is similar to a gene in rat,
as it has not been fully annotated in human.<br>
<br>
I agree the description can be misleading, but it is imported
directly from NCBI as is, so there is not much we can do about it.<br>
<br>
<br>
Regards,<br>
Magali<div><div class="h5"><br>
<br>
<div>On 27/02/2014 14:37, Genomeo Dev wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Thanks very much Magali for pointing that out.
<div><br>
</div>
<div>If understand you correctly db_type and species are
therefore attributes of the query gene IDs not the returned
cross-reference ids. For my query IDs I see I define that
here:</div>
<div><br>
</div>
<div>my $gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor(
"human", "core", "gene" );<br>
</div>
<div><br>
</div>
<div>I have tried to lookup about 5000 human ensembl IDs and
found that for 256 I get cross mapping to other organisms. It
only happens for UniGene. For example for ENSG00000010244:</div>
<div><br>
</div>
<div>display_id<span style="white-space:pre-wrap"> </span>dbname<span style="white-space:pre-wrap"> </span>ensembl_start<span style="white-space:pre-wrap"> </span>xref_start<span style="white-space:pre-wrap"> </span>display_id<span style="white-space:pre-wrap"> </span>score<span style="white-space:pre-wrap"> </span>db_display_name<span style="white-space:pre-wrap"> </span>xref_end<span style="white-space:pre-wrap"> </span>evalue<span style="white-space:pre-wrap"> </span>info_text<span style="white-space:pre-wrap"> </span>info_type<span style="white-space:pre-wrap"> </span>ensembl_end<span style="white-space:pre-wrap"> </span>primary_id<span style="white-space:pre-wrap"> </span>ensembl_identity<span style="white-space:pre-wrap"> </span>synonyms<span style="white-space:pre-wrap"> </span>version<span style="white-space:pre-wrap"> </span>cigar_line<span style="white-space:pre-wrap"> </span>xref_identity<span style="white-space:pre-wrap"> </span>dbname<span style="white-space:pre-wrap"> </span>description<br>
</div>
<div>
<div>ENSG00000010244<span style="white-space:pre-wrap"> </span>ensembl<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>Hs.500775<span style="white-space:pre-wrap"> </span>23313<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>4672<span style="white-space:pre-wrap"> </span>SEQUENCE_MATCH<span style="white-space:pre-wrap"> </span>4672<span style="white-space:pre-wrap"> </span>Hs.500775<span style="white-space:pre-wrap"> </span>99<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>1631M1D1592M1I1448M<span style="white-space:pre-wrap"> </span>99<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>Zinc finger protein 207</div>
<div>ENSG00000010244<span style="white-space:pre-wrap"> </span>ensembl<span style="white-space:pre-wrap"> </span>5667<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>Hs.612377<span style="white-space:pre-wrap"> </span>1200<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>249<span style="white-space:pre-wrap"> </span>SEQUENCE_MATCH<span style="white-space:pre-wrap"> </span>5417<span style="white-space:pre-wrap"> </span>Hs.612377<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>249M<span style="white-space:pre-wrap"> </span>97<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>Transcribed locus</div>
<div>ENSG00000010244<span style="white-space:pre-wrap"> </span>ensembl<span style="white-space:pre-wrap"> </span>12853<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>Hs.636112<span style="white-space:pre-wrap"> </span>2260<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>452<span style="white-space:pre-wrap"> </span>SEQUENCE_MATCH<span style="white-space:pre-wrap"> </span>12400<span style="white-space:pre-wrap"> </span>Hs.636112<span style="white-space:pre-wrap"> </span>3<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>452M<span style="white-space:pre-wrap"> </span>100<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>Transcribed locus</div>
<div>ENSG00000010244<span style="white-space:pre-wrap"> </span>ensembl<span style="white-space:pre-wrap"> </span>5213<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>Hs.658344<span style="white-space:pre-wrap"> </span>3230<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>684<span style="white-space:pre-wrap"> </span>SEQUENCE_MATCH<span style="white-space:pre-wrap"> </span>4526<span style="white-space:pre-wrap"> </span>Hs.658344<span style="white-space:pre-wrap"> </span>4<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>615M1I8M1D3M1D34M1D13M1D5M1I4M<span style="white-space:pre-wrap"> </span>91<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>Transcribed locus</div>
<div>ENSG00000010244<span style="white-space:pre-wrap"> </span>ensembl<span style="white-space:pre-wrap"> </span>3014<span style="white-space:pre-wrap"> </span>23<span style="white-space:pre-wrap"> </span>Hs.670238<span style="white-space:pre-wrap"> </span>1995<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>427<span style="white-space:pre-wrap"> </span>SEQUENCE_MATCH<span style="white-space:pre-wrap"> </span>2607<span style="white-space:pre-wrap"> </span>Hs.670238<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>399M1D6M<span style="white-space:pre-wrap"> </span>94<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>Transcribed locus</div>
<div>ENSG00000010244<span style="white-space:pre-wrap"> </span>ensembl<span style="white-space:pre-wrap"> </span>11505<span style="white-space:pre-wrap"> </span>2<span style="white-space:pre-wrap"> </span>Hs.694378<span style="white-space:pre-wrap"> </span>3063<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>628<span style="white-space:pre-wrap"> </span>SEQUENCE_MATCH<span style="white-space:pre-wrap"> </span>12131<span style="white-space:pre-wrap"> </span>Hs.694378<span style="white-space:pre-wrap"> </span>4<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>627M<span style="white-space:pre-wrap"> </span>98<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>Transcribed locus</div>
<div>ENSG00000010244<span style="white-space:pre-wrap"> </span>ensembl<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>Hs.716993<span style="white-space:pre-wrap"> </span>1971<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>396<span style="white-space:pre-wrap"> </span>SEQUENCE_MATCH<span style="white-space:pre-wrap"> </span>396<span style="white-space:pre-wrap"> </span>Hs.716993<span style="white-space:pre-wrap"> </span>99<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>396M<span style="white-space:pre-wrap"> </span>99<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>Transcribed locus,
strongly similar to NP_001034109.1 Zfp207 gene product
[Rattus norvegicus]</div>
<div>ENSG00000010244<span style="white-space:pre-wrap"> </span>ensembl<span style="white-space:pre-wrap"> </span>50<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>Hs.743764<span style="white-space:pre-wrap"> </span>3472<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>791<span style="white-space:pre-wrap"> </span>SEQUENCE_MATCH<span style="white-space:pre-wrap"> </span>841<span style="white-space:pre-wrap"> </span>Hs.743764<span style="white-space:pre-wrap"> </span>5<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>716M1D75M<span style="white-space:pre-wrap"> </span>91<span style="white-space:pre-wrap"> </span>UniGene<span style="white-space:pre-wrap"> </span>Transcribed locus,
moderately similar to NP_001034109.1 Zfp207 gene product
[Rattus norvegicus]</div>
</div>
<div><br>
</div>
<div class="gmail_extra">(obtained from Rest)</div>
<div class="gmail_extra"><br>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 27 February 2014 14:00, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi Genomeo,<br>
<br>
To find which attributes are available, the Ensembl
Doxygen documentation usually covers everything you
need.<br>
Looking at
<a href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Gene.html" target="_blank">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Gene.html</a><br>
will tell you that you can obtain the following from a
gene:<br>
<br>
$gene->source()<br>
$gene->analysis->logic_name()<br>
$gene->description()<br>
$gene->external_name()<br>
$gene->biotype()<br>
$gene->seq_region_start()<br>
$gene->seq_region_end()<br>
$gene->seq_region_name()<br>
$gene->seq_region_strand()<br>
$gene->display_id()<br>
<br>
When using the API, you should always know what
object_type you are using, as it allows you to use the
correct attributes.<br>
In this example, if you are using a Bio::EnsEMBL::Gene,
object_type is 'gene'<br>
<br>
For species and db_type as well, you need to know those
beforehand when using directly the perl API.<br>
They are the ones which will allow you to connect to the
correct database based on the data you are looking for.<br>
<br>
Regarding cross references to other organisms, do you
have any examples?<br>
Generally, we should be only mapping to other resources
for the same organism.<br>
For example, for pig, we will only assign cross
references to Uniprot pig proteins.<br>
<br>
The main exceptions I can think of are:<br>
- HGNC names<br>
Typically, if the coverage for a species is low (ie, not
all 20 odd thousand proteins have been submitted to
Uniprot or RefSeq), we will use HGNC names to fill in
the gaps.<br>
Where no name can be found and there is a homolog in
human, we use the same name as in human.<br>
- Ensembl translations<br>
For some low coverage species, annotations was provided
by projecting human annotation via a whole genome
alignment.<br>
For these models, we add an external reference to the
human translation which was used to build the model.<br>
<br>
<br>
Hope this helps,<br>
Magali
<div>
<div><br>
<div><br>
</div>
<div>On 27/02/2014 13:41, Genomeo Dev wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Thanks very much for the useful
answer.
<div><br>
</div>
<div>I noticed that cross ref also maps to genes
from organisms other than that of the query
gene ID. Any comment on that?<br>
<div><br>
</div>
<div>Related to the previous question, I use
the following Rest python code to do id
lookup for particular Ensembl IDs:</div>
<div><br>
</div>
<div>
<div>pref= "/lookup/id/"</div>
<div>ext = "?"</div>
<div><br>
</div>
<div>for line in inputfile1:</div>
<div> geneid= line.rstrip('\n')</div>
<div><br>
</div>
<div> resp, content =
http.request(server+pref+geneid+ext,
method="GET",
headers={"Content-Type":"application/json"})</div>
<div><br>
</div>
<div> if not resp.status == 200:</div>
<div> print "%s\t%s\t%s" %
(geneid, "Invalid response:",
resp.status)</div>
<div> continue</div>
<div> #sys.exit()</div>
<div> print "%s\t%s" %
(geneid,content)</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>And I get this output:</div>
<div><br>
</div>
<div>
<div>ENSG00000223972<span style="white-space:pre-wrap"> </span>{"source":"ensembl_havana","object_type":"Gene","logic_name":"ensembl_havana_gene","species":"homo_sapiens","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box helicase 11 like
1 [Source:HGNC
Symbol;Acc:37102]","display_name":"DDX11L1","biotype":"pseudogene","end":14412,"seq_region_name":"1","db_type":"core","strand":1,"id":"ENSG00000223972","start":11869}</div>
</div>
<div><br>
</div>
<div>What would be the classes/attributes to
use under the Perl API to get that? i.e:</div>
<div><br>
</div>
<div>source</div>
<div>object_type</div>
<div>logic_name</div>
<div>species</div>
<div>description</div>
<div>display_name</div>
<div>biotype</div>
<div>end</div>
<div>seq_region_name<br>
</div>
<div>db_type</div>
<div>strand</div>
<div>id</div>
<div>start</div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>G.</div>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 27 February 2014
11:39, mag <span dir="ltr"><<a href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi
Genomeo,<br>
<br>
The REST server only display the
current/latest release.<br>
The release version can be found with this
endpoint:<br>
<a href="http://beta.rest.ensembl.org/documentation/info/software" target="_blank">http://beta.rest.ensembl.org/documentation/info/software</a><br>
<br>
To get more details with the Ensembl API,
you only need to update the
print_DBEntries method to display all the
attributes you are looking for.<br>
Compared to the output from REST, we have
the following:<br>
- display_id is $dbe->display_id()<br>
- primary_id is $dbe->primary_id()<br>
- version is $dbe->version()<br>
- description is $dbe->description()<br>
- dbname is $dbe->dbname()<br>
- synonyms is $dbe->get_all_synonyms()<br>
- info_type is $dbe->info_type()<br>
- info_text is $dbe->info_text()<br>
- db_display_name is
$dbe->db_display_name()<br>
<br>
You can chose what format the REST will
output.<br>
Details of all formats can be found in our
user guide:<br>
<a href="http://beta.rest.ensembl.org/documentation/user_guide" target="_blank">http://beta.rest.ensembl.org/documentation/user_guide</a><br>
For tab-delimited output,
content_type=text/x-gff3 is used, but it
is only available for the /feature
endpoint.<br>
<br>
There is no file in the Ensembl ftp dumps
that contains all the external references
produced.<br>
<br>
<br>
Regards,<br>
Magali
<div>
<div><br>
<br>
<div>On 27/02/2014 11:20, Genomeo Dev
wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<div dir="ltr">
<div><font color="#000000" face="arial, helvetica,
sans-serif"><span style="line-height:18px;white-space:pre-wrap">Hi,</span></font></div>
<div><font color="#000000" face="arial, helvetica,
sans-serif"><span style="line-height:18px;white-space:pre-wrap"><br>
</span></font></div>
<div><span style="line-height:18px;white-space:pre-wrap;font-family:arial,helvetica,sans-serif">I
am interested in getting wide
cross references to ensembl
gene IDs. I found two
programmatic ways to do that
which give consistent results
but different amount of
details. Using ENSG00000223972
as an example:</span><br>
</div>
<div><font color="#000000" face="arial, helvetica,
sans-serif"><span style="line-height:18px;white-space:pre-wrap">(1)</span></font></div>
<div><font color="#000000" face="arial, helvetica,
sans-serif"><span style="line-height:18px;white-space:pre-wrap">Using
this rest API Endpoint
python code (<a href="http://beta.rest.ensembl.org/documentation/info/xref_id" target="_blank">http://beta.rest.ensembl.org/documentation/info/xref_id</a>)</span></font></div>
<div><br>
</div>
<ol>
<li style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,136)">import</span><span style="color:rgb(0,0,0)">
httplib2</span><span style="color:rgb(102,102,0)">,</span><span style="color:rgb(0,0,0)">
sys</span></li>
<li style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,0)"> </span></li>
<li style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,0)">http
</span><span style="color:rgb(102,102,0)">=</span><span style="color:rgb(0,0,0)">
httplib2</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(102,0,102)">Http</span><span style="color:rgb(102,102,0)">(</span><span style="color:rgb(0,136,0)">".cache"</span><span style="color:rgb(102,102,0)">)</span></li>
<li style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,0)"> </span></li>
<li style="line-height:18px;color:rgb(190,190,197);list-style-type:decimal;padding-left:12px"><span style="color:rgb(0,0,0)">server
</span><span style="color:rgb(102,102,0)">=</span><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(0,136,0)">"<a href="http://beta.rest.ensembl.org" target="_blank">http://beta.rest.ensembl.org</a>"</span></li>
<li style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,0)">ext
</span><span style="color:rgb(102,102,0)">=</span><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(0,136,0)">"/xrefs/id/ENSG00000157764?"</span></li>
<li style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,0)">resp</span><span style="color:rgb(102,102,0)">,</span><span style="color:rgb(0,0,0)">
content </span><span style="color:rgb(102,102,0)">=</span><span style="color:rgb(0,0,0)">
http</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">request</span><span style="color:rgb(102,102,0)">(</span><span style="color:rgb(0,0,0)">server</span><span style="color:rgb(102,102,0)">+</span><span style="color:rgb(0,0,0)">ext</span><span style="color:rgb(102,102,0)">,</span><span style="color:rgb(0,0,0)">
method</span><span style="color:rgb(102,102,0)">=</span><span style="color:rgb(0,136,0)">"GET"</span><span style="color:rgb(102,102,0)">,</span><span style="color:rgb(0,0,0)">
headers</span><span style="color:rgb(102,102,0)">={</span><span style="color:rgb(0,136,0)">"Content-Type"</span><span style="color:rgb(102,102,0)">:</span><span style="color:rgb(0,136,0)">"application/json"</span><span style="color:rgb(102,102,0)">})</span></li>
<li style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,0)"> </span></li>
<li style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,136)">if</span><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(0,0,136)">not</span><span style="color:rgb(0,0,0)">
resp</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">status
</span><span style="color:rgb(102,102,0)">==</span><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(0,102,102)">200</span><span style="color:rgb(102,102,0)">:</span></li>
<li style="line-height:18px;background-color:rgb(238,238,238);color:rgb(190,190,197);list-style-type:decimal;padding-left:12px"><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(0,0,136)">print</span><span style="color:rgb(0,0,0)"> </span><span style="color:rgb(0,136,0)">"Invalid
response: "</span><span style="color:rgb(102,102,0)">,</span><span style="color:rgb(0,0,0)">
resp</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">status</span></li>
<li style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,0)">
sys</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,136)">exit</span><span style="color:rgb(102,102,0)">()</span></li>
<li style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,136)">import</span><span style="color:rgb(0,0,0)">
json</span></li>
<li style="line-height:18px;list-style-type:decimal;color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,0)"> </span></li>
<li style="line-height:18px;list-style-type:decimal;background-color:rgb(238,238,238);color:rgb(190,190,197);padding-left:12px"><span style="color:rgb(0,0,0)">decoded
</span><span style="color:rgb(102,102,0)">=</span><span style="color:rgb(0,0,0)">
json</span><span style="color:rgb(102,102,0)">.</span><span style="color:rgb(0,0,0)">loads</span><span style="color:rgb(102,102,0)">(</span><span style="color:rgb(0,0,0)">content</span><span style="color:rgb(102,102,0)">)</span></li>
<li style="line-height:18px;color:rgb(190,190,197);list-style-type:decimal;padding-left:12px"><span style="color:rgb(0,0,136)">print</span><span style="color:rgb(0,0,0)">
repr</span><span style="color:rgb(102,102,0)">(</span><span style="color:rgb(0,0,0)">decoded</span><span style="color:rgb(102,102,0)">)</span></li>
</ol>
<div><br>
</div>
<div>I get:</div>
<div><br>
</div>
<div>
<div>{"display_id":"OTTHUMG00000000961","primary_id":"OTTHUMG00000000961","version":"2","description":null,"dbname":"OTTG","synonyms":[],"info_type":"NONE","info_text":"","db_display_name":"Havana
gene"}</div>
<div><br>
</div>
<div>{"primary_id":"Hs.714157","dbname":"UniGene","ensembl_identity":98,"synonyms":[],"ensembl_start":6,"xref_start":1,"xref_end":1639,"db_display_name":"UniGene","display_id":"Hs.714157","ensembl_end":1657,"version":"0","score":8055,"cigar_line":"1200M1D299M12D140M","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box
helicase 11 like
1","xref_identity":97,"evalue":null,"info_text":"","info_type":"SEQUENCE_MATCH"}</div>
<div><br>
</div>
<div>{"primary_id":"Hs.618434","dbname":"UniGene","ensembl_identity":58,"synonyms":[],"ensembl_start":669,"xref_start":1,"xref_end":974,"db_display_name":"UniGene","display_id":"Hs.618434","ensembl_end":1655,"version":"0","score":4757,"cigar_line":"537M1D299M12D138M","description":"Similar
to DEAD/H
(Asp-Glu-Ala-Asp/His) box
polypeptide 11 isoform 1, mRNA
(cDNA clone
IMAGE:6103207)","xref_identity":96,"evalue":null,"info_text":"","info_type":"SEQUENCE_MATCH"}</div>
<div><br>
</div>
<div>{"display_id":"DDX11L1","primary_id":"37102","version":"0","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box
helicase 11 like
1","dbname":"HGNC","synonyms":[],"info_type":"DIRECT","info_text":"Generated
via
ensembl_manual","db_display_name":"HGNC
Symbol"}</div>
<div><br>
</div>
<div>{"display_id":"DDX11L5","primary_id":"100287596","version":"0","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box
helicase 11 like
5","dbname":"EntrezGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"EntrezGene"}</div>
<div><br>
</div>
<div>{"display_id":"DDX11L1","primary_id":"100287102","version":"0","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box
helicase 11 like
1","dbname":"EntrezGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"EntrezGene"}</div>
<div><br>
</div>
<div>{"display_id":"ENSG00000223972","primary_id":"ENSG00000223972","version":"0","description":"","dbname":"ArrayExpress","synonyms":[],"info_type":"DIRECT","info_text":"","db_display_name":"ArrayExpress"}</div>
<div><br>
</div>
<div>{"display_id":"DDX11L5","primary_id":"100287596","version":"0","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box
helicase 11 like
5","dbname":"WikiGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"WikiGene"}</div>
<div><br>
</div>
<div>{"display_id":"DDX11L1","primary_id":"100287102","version":"0","description":"DEAD/H
(Asp-Glu-Ala-Asp/His) box
helicase 11 like
1","dbname":"WikiGene","synonyms":[],"info_type":"DEPENDENT","info_text":"","db_display_name":"WikiGene"}]</div>
<div><br>
</div>
</div>
<div>(2)</div>
<div><br>
</div>
<div>Using this perl API code
(based on <a href="http://www.ensembl.org/info/docs/api/core/core_tutorial.html" target="_blank">http://www.ensembl.org/info/docs/api/core/core_tutorial.html</a>):</div>
<div><br>
</div>
<div>
<pre style="margin-top:0px;margin-bottom:16px;border:1px solid rgb(204,204,204);background-color:rgb(240,240,240);padding:8px!important"><font color="#555555" face="courier new, monospace"><span style="line-height:16px"># Define a helper subroutine to print DBEntries
sub print_DBEntries
{
my $db_entries = shift;
foreach my $dbe ( @{$db_entries} ) {
printf "\tXREF %s (%s)\n", $dbe->display_id(), $dbe->dbname();
}
}
my $genes = $gene_adaptor->fetch_all_by_stable_id_list([@gene_list]);</span></font></pre>
<pre style="margin-top:0px;margin-bottom:16px;border:1px solid rgb(204,204,204);background-color:rgb(240,240,240);line-height:16px;color:rgb(85,85,85);padding:8px!important"><font face="courier new, monospace">
...</font></pre>
<pre style="margin-top:0px;margin-bottom:16px;border:1px solid rgb(204,204,204);background-color:rgb(240,240,240);line-height:16px;color:rgb(85,85,85);padding:8px!important"><font face="courier new, monospace">
print "GENE ", $gene->stable_id(), "\n";
print_DBEntries( $gene->get_all_DBEntries() );</font></pre>
</div>
<div>
<div><span style="white-space:pre-wrap">I
get:</span></div>
<div><span style="white-space:pre-wrap">
</span></div>
<div>XREF OTTHUMG00000000961
(OTTG)</div>
<div>XREF ENSG00000223972
(ArrayExpress)</div>
<div>XREF DDX11L1 (EntrezGene)</div>
<div>XREF DDX11L5 (EntrezGene)</div>
<div>XREF DDX11L1 (HGNC)</div>
<div>XREF Hs.618434 (UniGene)</div>
<div>XREF Hs.714157 (UniGene)</div>
<div> XREF DDX11L1 (WikiGene)</div>
<div>XREF DDX11L5 (WikiGene)</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Questions:</div>
<div><br>
</div>
<div>1. am I correct in saying
that the Rest code uses the
latest Ensembl release while the
API code uses the Ensembl
release currently installed as
part of the VM (I am using
release 74)?</div>
<div><br>
</div>
<div>2. Rest code gives more
extensive details (which I like)
compared to the perl API code.
Could you suggest a simple way
to use the API to get the same
details?</div>
<div><br>
</div>
<div>3. The Rest code output
format. Is tab separated text
supported?<br>
</div>
<div><br>
</div>
<div>4. Is there a file in the
Ensembl ftp area which contains
pre generated detailed cross ref
mappings for all current Ensembl
genes?</div>
--
<div><br>
</div>
<div>Thanks,</div>
<div><br>
<div dir="ltr"> G.</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
</div>
</div>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe
info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">G.</div>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</div>
</div>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">G.</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</div></div></div>
<br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">G.</div>
</div>