[ensembl-dev] question on external_db_name CORE database
nconte at ebi.ac.uk
nconte at ebi.ac.uk
Tue Jul 16 17:27:20 BST 2013
thanks a lot for this Andy!
Nathalie
> Hi Nathalie,
>
> The values for $external_db_name can be found in the external_db table.
>
> select db_name from external_db;
>
> To find those which are involved in an external reference you can use the
> following query
>
> select distinct db_name from external_db join xref using (external_db_id)
> order by db_name;
>
> When run on human from release 72 this gives the following rows:
>
> ------------------------------------
> | db_name |
> ------------------------------------
> | ArrayExpress |
> ------------------------------------
> | CCDS |
> ------------------------------------
> | Clone_based_ensembl_gene |
> ------------------------------------
> | Clone_based_ensembl_transcript |
> ------------------------------------
> | Clone_based_vega_gene |
> ------------------------------------
> | Clone_based_vega_transcript |
> ------------------------------------
> | DBASS3 |
> ------------------------------------
> | EMBL |
> ------------------------------------
> | Ens_Hs_gene |
> ------------------------------------
> | Ens_Hs_transcript |
> ------------------------------------
> | Ens_Hs_translation |
> ------------------------------------
> | ENS_LRG_gene |
> ------------------------------------
> | ENS_LRG_transcript |
> ------------------------------------
> | EntrezGene |
> ------------------------------------
> | GO |
> ------------------------------------
> | goslim_goa |
> ------------------------------------
> | HGNC |
> ------------------------------------
> | HGNC_transcript_name |
> ------------------------------------
> | HPA |
> ------------------------------------
> | Interpro |
> ------------------------------------
> | LRG |
> ------------------------------------
> | MEROPS |
> ------------------------------------
> | MIM_GENE |
> ------------------------------------
> | MIM_MORBID |
> ------------------------------------
> | miRBase |
> ------------------------------------
> | miRBase_transcript_name |
> ------------------------------------
> | Orphanet |
> ------------------------------------
> | OTTG |
> ------------------------------------
> | OTTT |
> ------------------------------------
> | PDB |
> ------------------------------------
> | protein_id |
> ------------------------------------
> | RefSeq_mRNA |
> ------------------------------------
> | RefSeq_mRNA_predicted |
> ------------------------------------
> | RefSeq_ncRNA |
> ------------------------------------
> | RefSeq_ncRNA_predicted |
> ------------------------------------
> | RefSeq_peptide |
> ------------------------------------
> | RefSeq_peptide_predicted |
> ------------------------------------
> | RFAM |
> ------------------------------------
> | RFAM_transcript_name |
> ------------------------------------
> | shares_CDS_and_UTR_with_OTTT |
> ------------------------------------
> | shares_CDS_with_OTTT |
> ------------------------------------
> | UCSC |
> ------------------------------------
> | UniGene |
> ------------------------------------
> | UniParc |
> ------------------------------------
> | Uniprot/SPTREMBL |
> ------------------------------------
> | Uniprot/SWISSPROT |
> ------------------------------------
> | Uniprot_genename |
> ------------------------------------
> | Uniprot_genename_transcript_name |
> ------------------------------------
> | Vega_transcript |
> ------------------------------------
> | Vega_translation |
> ------------------------------------
> | WikiGene |
> ------------------------------------
>
> Using direct SQL statements is the only way to extract this list.
>
> Best regards,
>
> Andy
>
> Andrew Yates Ensembl Core Software Project Leader
> EMBL-EBI Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK http://www.ensembl.org/
>
> On 16 Jul 2013, at 17:10, Nathalie Conte <nconte at ebi.ac.uk> wrote:
>
>>
>>
>>
>>
>>
>> HI, I am looking for $external_db_name list, I want to use this method
>> and put a database name in my script.
>> thanks
>> Nathaie
>>
>>
>> public Listref
>> Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_all_by_external_name
>> (
>> )
>> Arg [1] : String $external_name The external identifier for the gene to
>> be obtained Arg [2] : (optional) String $external_db_name The name of
>> the external database from which the identifier originates. Arg [3] :
>> Boolean override. Force SQL regex matching for users who really do want
>> to find all 'NM%' Example :
>>
>> --
>> Nathalie Conte, PhD
>> Bioinformatician BMB (WP3, WP7)
>> Functional Genomics group
>> EMBL-EBI,UK
>> 01223 492562
>>
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>
>
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