[ensembl-dev] ensembl funcgen 105 homo sapiens - mysql - detailed description of table content

[Garth Ilsley]

Dear Samuele,

Thank you for your interest in the regulatory build. The mysql database 
isn’t necessarily the best or recommended place to access the output of 
the regulatory build. I assume you are using the Perl API as used in the 
tutorial you reference? There’s a fair amount of detail linked from 
there, as well as in other documentation on the Ensembl site. Details of 
the method are described in this paper: 
https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-015-0621-5.pdf?site=genomebiology.biomedcentral.com.

For your question below, Peaks are called as described here: 
http://www.ensembl.org/info/genome/funcgen/peak_calling.html. Is there 
something specific you are looking to answer?

Best wishes,
Garth

On 2021-12-15 12:01, Garda, Samuele wrote:
> Dear all,
> 
> I am writing to ask whether there is any document providing extensive
> details on the content of the mysql tables of the regulatory build
> (latest version).
> 
> I am aware of the web page with the schema description:
> 
> http://www.ensembl.org/info/docs/api/funcgen/funcgen_schema.html
> 
> but ideally there should be something more fine-grained (e.g. the
> table "external_feature" and "mirna_target_feature" have the same
> description).
> 
> The tutorial on the API :
> 
> http://www.ensembl.org/info/docs/api/funcgen/regulation_tutorial.html
> 
> seems to draw information from a source with more details, e.g.: "If a
> Peak for the same transcription factor overlaps a MotifFeature, the
> MotifFeature is classed as "experimentally validated" in that
> Epigenome", but does not provide any further reference.
> 
> Thank you in advance.
> 
> Best regards
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/