[ensembl-dev] Question about using Ensembl Perl API to fetch gene by ensembl_stable_id_version

[Matthew Laird]

Hello Tung-Han,

We only maintain the details for the current version of a feature in a 
particular release. To find information on historic version you'll want 
to look at the ArchiveStableIdAdaptor [1]. With this you'll be able to 
find what Ensembl releases a particular version of a stable id was last 
seen in.

If you want to then retrieve the record for that version of the feature, 
you'll need to connect to the specific version of Ensembl that feature 
existed in. The documentation on the Registry [2] and public facing 
databases [3] can help you with that.

If you have any further questions, please let us know.

[1] 
http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1DBSQL_1_1ArchiveStableIdAdaptor.html

[2] https://www.ensembl.org/info/docs/api/registry.html

[3] https://www.ensembl.org/info/data/mysql.html

On 04/05/18 11:43, 張東涵 wrote:
> Hi,
>
> I have a question about using Ensembl Perl API.
> I couldn't use "fetch_by_stable_id_version" to fetch gene by old 
> stable ID.
>
> For example,
> I couldn't use "fetch_by_stable_id_version" (ENSG00000167578.15) to 
> get information of gene.
>
> error message :
> Can't call method "get_all_DBEntries" on an undefined value at 
> ./test_ensembl_query line 43, <STDIN> line 60483.
> ENSG00000167578 15
>
>
> 1.How can I get information of ENSG00000167578.15(old stable id) by 
> Ensembl Perl API ?
>
> 2. How can I get ID History score about associated archived IDs for 
> this stable ID version by Ensembl Perl API?
>
> https://asia.ensembl.org/Homo_sapiens/Gene/Idhistory?g=ENSG00000167578;r=19:40778216-40796938 
> <https://asia.ensembl.org/Homo_sapiens/Gene/Idhistory?g=ENSG00000167578;r=19:40778216-40796938>
>
>
>
> Thanks
>
> =============================
> Tung-Han Chang, research student
> Institute of biomedical informatics , National Yang-Ming University
> No.155, Sec.2, Linong Street, Taipei, 112 Taiwan
> =============================
>
>
>
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-- 
Matthew Laird - Ensembl Core Developer
The European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD, United Kingdom
Tel: +44-(0)1223-494274
Fax: +44-(0)1223-494468
http://www.ebi.ac.uk/
http://www.ensembl.org/

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