[ensembl-dev] question on external_db_name CORE database

[Andy Yates]

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
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/