[Owl-devel] suggestions for updating the package structure in OWL

Henning Stehr stehr at molgen.mpg.de
Fri Mar 19 10:09:44 EDT 2010

> OWL also stands for 'Web Ontology Language' (a so-called dyslexic acronym).

Good to know. We didn't really check other people's claims for the name OWL.
Even though we have much better arguments to use the name in a
non-dyslexic way :)
Of course, the java convention would be to use
org.bifx.owl.proteinstructure as the package name. I had
thought that we could avoid that but maybe we have to think about it
one more time before fixing anything.


On Fri, Mar 19, 2010 at 2:57 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
> biology are written in the OBO format, however, there is a push to
> move towards the more standard OWL format for biological ontologies.
> For this reason 'owl.protein' may not be the best name for your
> package.
> Just something to consider - it may not be an issue at all.
> All the best,
> Dan.
> On 19 March 2010 10:13, Henning Stehr <stehr at molgen.mpg.de> wrote:
>> Dear developers,
>> since we are currently rearranging some stuff in OWL which always
>> makes it necessary to
>> update imports and calls in other projects, maybe its a good time to
>> think about the package
>> structure in general to make OWL fit for the future.
>> So here are some suggestions for changes to the package structure in OWL:
>> Minor changes:
>> - move all SomethingRunner classes from owl.proteinstructure and
>> owl.sequence to owl.runners
>> - create a subpackage owl.runners.blast and move all Blast related stuff there
>> - move owl.tinker to owl.runners.tinker and create owl.runners.gromacs
>> for gromacs stuff
>> - create a subpackage proteinstructure.graphs and move all RIG and AIG
>> related stuff there
>> - maybe create proteinstructure.graphs.rigs and proteinstructure.graphs.aigs
>> Major changes:
>> - make a root package 'owl' and move everything there, i.e.
>> owl.proteinstructure, owl.sequence, ...
>>  this would be clearer and prevent name conflicts with other
>> libraries which may also contain e.g. a 'sequence' package
>> - currently there are two types of packages:
>>  1. those containing collections of basic classes such as sequence,
>> proteinstructure, features, connections, runners and
>>  2. those containing essentially independent projects such as casp,
>> deltaRank, embed, sadp.
>>  Suggestion: Create a package owl.core and move all packages from 1.
>> there. The basic idea would be that 'core' should
>> be stuff that is used by many projects and 2. stuff that is more for a
>> specific usecase
>> - if we do the above, owl.proteinstructure.decoyScoring should be
>> moved to owl.decoyScoring
>> As you can see some of these are more long term plans but maybe it's
>> less painfull to do it all together so that hopefully
>> the package structure can remain stable for a while.
>> For the moment, I won't do anything, but what do you think about these
>> changes? We can dicuss later when would be
>> a good time to actually do it.
>> Henning
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