On Fri, Nov 14, 2003 at 03:23:29PM +0100, Perl Authors Upload Server wrote: > > The following module was proposed for inclusion in the Module List: > > modid: Prospect > DSLIP: bdpOo > description: I'face to Prospect protein threading package > userid: REECE (Reece Hart) > chapterid: 24 (Commercial_Software_Interfaces) > communities: > SourceForge (project pending) > > similar: > none similar; related: Bio:: and CompBio:: trees > > rationale: > > Rationale for the module ------------------------ There are no > existing perl interfaces to the Prospect package; this module is > unique. We have endeavored to use other packages where possible > (e.g., Bio:: (aka bioperl)). > > Rationale for the namespace --------------------------- The major > reason for choosing Prospect:: over a package name within the Bio:: > or CompBio:: trees is that those are to be broad names assigned to > small groups of individuals. In particular, Bio:: is a big chunk of > namespace assigned to a group with enforced coding guidelines. > bioperl would probably not accept any package which doesn't adhere > to their coding guidelines.
That doesn't mean you can't create modules in the Bio:: namespace. Your module does not have to become part of the bioperl project. But couldn't you work within their guidelines anyway? > I like ontologies and organization. If you can think of an > appropriate place to stick this module (be nice) then I'm happy to > discuss it. One possibility is to start a new tree with a designed > hierarchy and that is not owned by a single group. As far as I'm aware the bioperl group do not 'own' the Bio:: namespace. > E.g., Biology:: > Entities:: Sequence Structure Gene Protein Alignment ... GUI:: ... > Tools:: Prospect:: BLAST:: > > I know that there has been discussion on the bioperl mailing list > regarding breaking Bio:: up into subtrees in order to address this > issue, but I'm not aware of any progress on this yet. Meanwhile I think you can use Bio:: (or CompBio::). In general frameworks of related modules seeking to 'own' a namespace should invent a top-level namespace that acts as a 'brand name' for the framework (eg Tangram::*). Top level names that relate directly to a topic (like Bio::) are viewed as the natural home for other modules related to that topic. Tim.
