[ensembl-dev] Create local ensembl SQL database for new organism

[Luke Goodsell]

Hi Albert,

Unfortunately, there isn't any documentation (that I know of) for the creation of the tables for a new species, probably because it's quite a varied process depending on the origin of the data. If you want to pursue this approach, I'd suggest studying the schema documentation (http://www.ensembl.org/info/docs/api/core/core_schema.html) and trying to replicate the structure for your new species, using one of the simpler species' architecture as a template. This would be a time-consuming task, though.

Kind regards,
Luke

-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Zhou Albert
Sent: 14 August 2015 11:11
To: Ensembl developers list
Subject: Re: [ensembl-dev] Create local ensembl SQL database for new organism

Hi Luke,

Many thanks for the response! 

Yes I have read these pages. However what I would like to do is creating a new SQL database in core schema that contains new organism’s genome data (currently in GFF and FASTA), so that it can be recognized and used in the web code. I’m looking for the proper tool to fulfill this task. 

best wishes,
Albert


> 在 2015年8月14日，上午10:15，Luke Goodsell <Luke.Goodsell at ogt.com> 写道：
> 
> Hi again, Albert,
> 
> This section might also be useful: http://www.ensembl.org/info/docs/webcode/custom/index.html
> 
> And more generally: http://www.ensembl.org/info/docs/webcode/index.html
> 
> Kind regards,
> Luke
> 
> -----Original Message-----
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Luke Goodsell
> Sent: 14 August 2015 09:30
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] Create local ensembl SQL database for new organism
> 
> Dear Albert
> 
> Have you seen this section of the EnsEMBL website: http://www.ensembl.org/info/docs/webcode/mirror/index.html
> 
> Kind regards,
> Luke
> 
> -----Original Message-----
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Zhou Albert
> Sent: 12 August 2015 13:16
> To: dev at ensembl.org
> Subject: [ensembl-dev] Create local ensembl SQL database for new organism
> 
> Dear all,
> 
> I'm currently working on building a local ensembl database web server, within which we would like to include our own genome data from a new organism. However after googling this subject, I still can't find any documents explaining how this can be happened. 
> 
> Could someone please show me where can I find such document / guide, or perhaps the ensembl simply does not provide such function?
> 
> Many thanks!
> 
> Albert
> 
> 
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