[Bioperl-l] Bio::Species validate_species_name

Stefan Kirov skirov at utk.edu
Wed Sep 21 08:46:05 EDT 2005

Thanks for the great answer Hilmar!
I would prefer to have some kind of a check if the user wishes so. For 
example Entrezgene file contains some HTML tags in some entries species 
names which is good to know.
I will put an option -validate_species in the constructor to turn the 
check on and off. Maybe a species filter can be of some use as well. 
though you can just select the correct file from the NCBI site....
Thanks again!

Hilmar Lapp wrote:

> Sure this is even likely once Entrez Gene comprises of as many species 
> as e.g. UniProt does - which is not imminent AFAIK but may be the case 
> one day.
> I like to take the position that throwing an exception is always 
> better than silently making a mistake, but in the case of stream 
> parsers typically for most users an exception isn't helpful because 1) 
> they can't fix the datasource, 2) often they can't fix the responsible 
> Bioperl code either, and 3) most often they don't care about the 
> fringe species anyway and would have screened out that record anyway.
> You could throw a warning if the species name doesn't look like it 
> fits your expected pattern, but even detecting that isn't easy.
>     -hilmar
> On Sep 20, 2005, at 10:06 AM, Stefan Kirov wrote:
>> Hilmar,
>> Before I modify entrezgene to override the classification 
>> verification I have a question - what's the reason to do that? What 
>> about the danger of inconsistencies down the road? One can imagine a 
>> situation, where the parser having passed a bad classification 
>> creates invalid binomial name, which then breaks the user's code (for 
>> example database queries, file structure, etc.).
>> Thanks!
>> Stefan
>> Hilmar Lapp wrote:
>>> If you set the classification array and pass a second argument that 
>>> eval's to true validation is turned off. See 
>>> Bio::Species::classification. This is what the SeqIO parsers do (or 
>>> should do).
>>>     -hilmar
>>> On Sep 19, 2005, at 6:56 AM, Stefan Kirov wrote:
>>>> NCBI and Bio::Species have very different views on what is the 
>>>> format of a species field. Is it possible to relax a bit the 
>>>> species regular expression? For example, 'Rhizophidium sp. 136' is 
>>>> a valid NCBI species name, but this is not the case in bioperl 
>>>> (species name in this case is starting with a number). There are 
>>>> other collisions as well, such as special characters found in the 
>>>> species name: ()'/
>>>> Any thoughts?
>>>> Stefan
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at portal.open-bio.org
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>> -

Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

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