[ensembl-dev] taxonomy database

[Lel Eory]

Hello Developers,

Is it correct that the ncbi_taxonomy database generated via the 
Bio::EnsEMBL::Compara::PipeConfig::ImportNCBItaxonomy_conf pipeline? 
Just to get the ncbi_taxonomy database would I need to add anything to 
the ensembl-compara/scripts/taxonomy/ensembl_aliases.sql file (i.e. for 
running the ImportNCBItaxonomy_conf pipeline)?
Also, can I update the database, or do I need to drop the "old" database 
and re-run the pipeline when I want to get the most recent taxonomy 
information?

For the compara master database I need to define the 'ensembl alias 
name' and 'ensembl timetree mya' fields in ensembl_aliasese.sql file. 
Should this file only contain this information on species (and 
ancestrals) which are relevant for the compara pipelines? Will only the 
relevant information be loaded?

Is there a script I can use to get the 'ensembl timetree mya' values, or 
is it done manually from www.timetree.org?

Thank you.

Best wishes,
Lel


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