[ensembl-dev] Use of Coelomata in NCBI Taxonomy

[Moretti Sébastien]

Hi Matthieu

We will try to follow this.

At the same times it looks that NCBI has removed the Coelomata term from 
its taxonomy.

Regards

> I don't know exactly how you apply the filter, but yes, it probably
> needs to be updated (like using "Coelomata" instead of "Bilateria")
>
> There are also ways of filtering homologies / tree nodes automatically.
> For example, the NCBITaxon adaptor allows you to:
>   - fetch taxon objects from their scientific names (fetch_node_by_name)
>   - fetch the last common ancestor of a list of taxa
> (fetch_first_shared_ancestor_indexed)
> Any NCBITaxon object has the has_ancestor($anc) that returns a boolean
> if $anc is an ancestor of the current object.
>
> You can combine these methods to check, for any homology, whether it is
> under the Bilateria node, and even better: "Bilateria" can be defined by
> a list of species. The script should then be able to cope with other
> taxon changes (if any)
>
> Matthieu
>
> On 18/12/12 14:59, Moretti Sébastien wrote:
>> It means we cannot, in ensembl compara, make a filtering on Bilateria
>> anymore. We need to use Coelomata as Vertebrate/Nematoda/Arthropoda
>> root ?
>>
>>> Hi Sébastien
>>>
>>> By default, the gene-tree pipeline is building a species tree from the
>>> NCBI taxonomy. This stands for Ensembl (vertebrates) and some
>>> divisions of Ensembl Genomes (for other divisions, the feature is
>>> overridden by a custom species tree).
>>>
>>> The NCBI has recently updated the taxonomy at the base of the animal
>>> kingdom between e68 and e69. The tree now looks like:
>>> (Metazoa > ... > Bilateria > ) Coelomata
>>>    > Deuterostomia ( > Chordata > ... > Homo sapiens)
>>>    > Protostomia > Ecdysozoa
>>>             > Panarthropoda ( > ... > Drosophila melanogaster)
>>>             > Nematoda ( > ... > Caenorhabditis elegans)
>>> instead of:
>>> (Metazoa > ... >) Bilateria
>>>    > Pseudocoelomata > Nematoda ( > ... > Caenorhabditis elegans)
>>>    > Coelomata
>>>             > Protostomia ( > Panarthropoda > ... > Drosophila
>>> melanogaster)
>>>             > Deuterostomia ( > Chordata > ... > Homo sapiens)
>>>
>>> In the e69 Compara database, you can see homologies linked to
>>> "Coelomata" and "Ecdysozoa", but not to "Metazoa" or "Bilateria". In
>>> Ensembl Genomes, the change has also been included between versions 15
>>> and 16, but there are more species covering this part of the tree of
>>> life. As a result, you can still find homologies linked to
>>> "Bilateria", "Metazoa", etc.
>>>
>>> We thought about publishing a blog post about that, but did not find
>>> any exciting consequence
>>>
>>> Best regards,
>>> Matthieu
>>>
>>> On 17/12/12 13:55, Moretti Sébastien wrote:
>>>> Hi
>>>>
>>>> The documentation links towards
>>>> http://www.phylowidget.org/full/index.html?tree=http://tinyurl.com/ensembltree&useBranchLengths=true&minTextSize=7,
>>>>
>>>>
>>>> but this does not seem to be the tree used. You seem to be using the
>>>> NCBI Taxonomy.
>>>>
>>>> Moreover, NCBI taxonomy includes Bilateria and Metazoa, which we do not
>>>> find in Ensembl Vertebrata. We do find them in Ensembl Metazoa.
>>>>
>>>> Could you please clarify these points for Ensembl Compara users?

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/