[ensembl-dev] question about compara in plants

[Arnaud Kerhornou]

Hi Eduardo,

As for the fetch_by_method_link_type_species_set_name method, it can not 
be used as it appears that there is no data in species_set_tag table. So 
for the next release we will populate this table, to let users query EPO 
data using this method.

As for the broken API links, someone is working on them, and they should get fixed today

All the best,
Arnaud


On 26/03/2012 16:13, Eduardo Andrés León wrote:
> Dear all,
> 	I usually got  some alignments in mammals using the method_link_species_set :
>
> 	my $method_link_species_set = $method_link_species_set_adaptor->fetch_by_method_link_type_species_set_name("EPO", "mammals");
>
> Now I,m working in a new project to do something similar but in Arabidopsis thaliana.
>
> The EPO and mammals words,  I know that they come from the name field, in the table method_link_species_set  :
>
> mysql>  use ensembl_compara_66
> mysql>  select name from method_link_species_set where name like '%mammals%';
> +--------------------------------------------------+
> | name                                             |
> +--------------------------------------------------+
> | 12 eutherian mammals EPO                         |
> | 35 eutherian mammals EPO_LOW_COVERAGE            |
> | Gerp Constrained Elements (35 eutherian mammals) |
> | Gerp Conservation Scores (35 eutherian mammals)  |
> +--------------------------------------------------+
> 4 rows in set (0.00 sec)
>
> But in plants the thing is quite different :
>
> mysql>  use ensembl_compara_plants_13_66 -A
> mysql>  select name from method_link_species_set where name like '%orthologues%';
> +-----------------------+
> | name                  |
> +-----------------------+
> | 1245-1173 orthologues |
> | 1505-1245 orthologues |
> | 1505-1173 orthologues |
> | 1505-1506 orthologues |
> | 1245-1506 orthologues |
> | 1173-1506 orthologues |
> | 1505-1537 orthologues |
> | 1245-1537 orthologues |
> | 1173-1537 orthologues |
>
> .....
>
> So what do I have to use in order to get the alignments from the arabidopsis taxa ? http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=3701&lvl=3&p=mapview&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=5&unlock
> What are those numbers in the name description ?
>
> by the way , the documentations for the API's in plants are not working :
>
>
> http://plants.ensembl.org/info/docs/Doxygen/compara-api/index.html
> http://plants.ensembl.org/info/docs/Doxygen/core-api/index.html
>
> Thanks in advance !!!
>
>
> ===================================================
> Eduardo Andrés León
> Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 5054)
> e-mail: eandres at cnio.es        Fax: (+34) 91 224 69 76
> Unidad de Bioinformática       Bioinformatics Unit
> Centro Nacional de Investigaciones Oncológicas
> C.P.: 28029                Zip Code: 28029
> C/. Melchor Fernández Almagro, 3    Madrid (Spain)
> http://bioinfo.cnio.es	http://bioinfo.cnio.es/people/eandres
> ===================================================
>
>
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