I think if you put it under Bio:: then people will naturally assume that your modules are bioperl-related. Probably a different top level name is appropriate, maybe something starting with Bio.
2010/11/4 Miguel Pignatelli <pignatelli_...@gva.es> > Dear all, > > I have written a small set of modules that have in common certain goals > with the bioperl modules Bio::DB::Taxonomy(::flatfile) and Bio::Taxon. The > main differences are: > > + No dependencies of non-standard Perl modules (VS tons of dependencies of > bioperl modules) -- This is important in certain (and convenient) > environments (like GRID or cloud systems) where you can't rely on automatic > installation of big bundles. > > + NCBI and RDP taxonomies support (VS only NCBI support of bioperl modules) > -- I plan to add support for additional taxonomies. > > + Very fast and low memory footprint (VS general poor performance of the > bioperl bundle). Orders of magnitude even for the simplest lookups. > > + Fast mapping of different identifiers (VS lack of this feature in > bioperl) > > Of course, these modules doesn't compete with Bio::DB::Taxonomy and > Bio::Taxon in completeness of methods or integration with other tools (e.g. > the rest of the bioperl bundle) but they are very handy (and actually being > used by several bioinformatics groups) for fast mapping and large datasets > analysis (frequent in bioinformatic analysis). > > The current (local) name of these modules are "Taxonomy", "Taxonomy::RDP", > "Taxonomy::NCBI", "Taxonomy::NCBI::Gi2taxid" > > I have been told to put them in CPAN. Their natural location would be under > the "Bio::" namespace. The bioperl developers don't have any problem with > this as long as i) the documentation clearly states that these modules are > not bioperl related and ii) the naming is sufficiently distinguishable from > existing (bioperl) Taxonomy modules. Bioperl already have a Bio::Taxonomy::* > (obsolete) and Bio::DB::Taxonomy::* which makes difficult the naming > decision. > > I have in mind some alternatives like: > > Bio::Taxonomy::Lite::* > Bio::DB::Taxonomy::Lite::* > Bio::TaxDB::* > Bio::TaxonomyDB::* > Bio::TaxLite::* > Bio::FastTaxonomy::* > > I don't know what is your feel about this. Any suggestion would be welcome. > > Best regards, > > M; > -- Check out my LEGO blog at http://www.brickpile.com/ View my photos at http://flickr.com/photos/billward/ Follow me at http://twitter.com/williamward
