[ensembl-dev] where can I find the consequence_type terminology correspondence between term_types?

[Laurent Gil]

Hi Pablo,

You can find this information in the online variation documentation:
http://www.ensembl.org/info/docs/variation/predicted_data.html#consequences

Cheers,

Laurent


On 22/03/2012 22:12, Pablo Marin-Garcia wrote:
>
> hello,
>
> I would like to obtain a table with the correspondences between the 
> consequence_types used by the different term_types? Is there such a 
> table around?
>
> From the pdocs I see that ensembl can use 4 different term_types: 
> Ensembl display terms, label, Sequence Ontology and NCBI
>
> --------------------
> Bio::EnsEMBL::Variation::VariationFeature::consequence_type     
> (         )
>
>   Arg [1]    : (optional) String $term_type
>   Description: Get a list of all the unique consequence terms of this
>                VariationFeature. By default returns Ensembl display terms
>                (e.g. 'NON_SYNONYMOUS_CODING'). $term_type can also be 
> 'label'
>                (e.g. 'Non-synonymous coding'), 'SO' (Sequence 
> Ontology, e.g.
>                'non_synonymous_codon') or 'NCBI' (e.g. 'missense')
>   Returntype : listref of strings
>   Exceptions : none
>   Status     : At Risk
>
> ---------------------------
>
> Thanks.
>