[Bioc-devel] 2 candidates for BiocGenerics

[Laurent Gatto]

On 16 March 2015 21:45, Hervé Pagès wrote:

> Hi Laurent,
>
> On 03/10/2015 07:28 AM, Laurent Gatto wrote:
>>
>> Dear all,
>>
>> Two possible candidates for BiocGenerics:
>>
>>> GenomeInfoDb::species
>> standardGeneric for "species" defined from package "GenomeInfoDb"
>>
>> function (x)
>> standardGeneric("species")
>> <environment: 0x7278130>
>> Methods may be defined for arguments: x
>> Use  showMethods("species")  for currently available ones.
>>> AnnotationDbi::species
>> standardGeneric for "species" defined from package "AnnotationDbi"
>>
>> function (x)
>> standardGeneric("species")
>> <environment: 0x89feb18>
>> Methods may be defined for arguments: x
>> Use  showMethods("species")  for currently available ones.
>>
>>
>> and
>>
>>> annotate::organism
>> standardGeneric for "organism" defined from package "annotate"
>>
>> function (object)
>> standardGeneric("organism")
>> <environment: 0x8771908>
>> Methods may be defined for arguments: object
>> Use  showMethods("organism")  for currently available ones.
>>> GenomeInfoDb::organism
>> standardGeneric for "organism" defined from package "GenomeInfoDb"
>>
>> function (x)
>> standardGeneric("organism")
>> <environment: 0x8232da0>
>> Methods may be defined for arguments: x
>> Use  showMethods("organism")  for currently available ones.
>
> The situation is actually worse than that: we have 5 organism
> generics, 4 `organism<-` generics, 7 species generics, and 2
> `species<-` generics, defined across all software packages.
>
> The various "species" methods sometimes return the genus
> and species, and sometimes return the Genbank common name
> (e.g. Human or Mouse) which I've heard can upset some biologists
> (but note that UCSC has been doing this forever
> http://genome.ucsc.edu/FAQ/FAQreleases.html#release1)
>
> Anyway, given that:
>
>    (1) The NCBI Assembly pages have an "Organism name" field that
>        contains the genus and species:
>
>          http://www.ncbi.nlm.nih.gov/assembly/883148
>
>    (2) On our website, all the views under "Organism" are
>        of the form "Genus_species" (note the underscore):
>
>          http://bioconductor.org/packages/devel/BiocViews.html#___Organism
>
>    (3) Almost all our annotation packages have an organism field
>        that contains the genus and species.
>
> it seems that maybe we should just keep using organism() the way
> it's used (i.e. for genus and species). Then the question is
> what to do with species(): the methods that return the genus and
> species are redundant with organism() and those that return the
> common name just seem wrong. Suggestions?
>
> When I move the organism() and species() generics to BiocGenerics
> I'll add a man page for them. This will be a good place (and the
> perfect time) to clarify what they're supposed to return. Having some
> agreement on that will make it easier to develop tools that search
> the ocean of annotations (900 annotation packages + 18992 records
> on AnnotationHub).

I think your suggestions are fine. As organism and genus_species is what
is used throughout the Bioc organism annotations, I guess that should be
the suggested option.

Thanks!

Laurent

> Thanks,
> H.
>
>>
>>
>> Best wishes,
>>
>> Laurent
>>
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