How about putting everything under Bio::Lite::Taxonomy? There are several modules with Lite in the name which are generally meant to be simpler alternatives to other modules, and it sounds like your module is a simplified alternative to bioperl taxonomy modules?
On Thu, Nov 4, 2010 at 10:46 AM, Bill Ward <b...@wards.net> wrote: > 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 > -- 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
