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

[Will McLaren]

Hi Pablo,

This table should help you:

http://www.ensembl.org/info/docs/variation/predicted_data.html

Cheers

Will

On 22 March 2012 22:12, Pablo Marin-Garcia <pablo.marin at uv.es> 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.
>
> --
> =============================================================
> Pablo Marin-Garcia, PhD
> UNIDAD DE GENOTIPADO Y DIAGNOSTICO GENETICO
> FUNDACIÓN INVESTIGACIÓN CLÍNICO DE VALENCIA-INCLIVA
> Avda. BLASCO IBAÑEZ Nº 17
> 46010 VALENCIA
> SPAIN
>
> TELF. 963864976
> FAX. 963987860
> e-mail: pablo.marin at uv.es
>
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