High Level 'Type of Resource' descriptor

There are a few description systems around at the moment:
A) NCBC SoftwareOntology

- Data (Raw data, model data, textual data, etc. of various formats)
- Dissemination Vehicle (Community and User Interaction Systems, educational resources and web-services)
- Atomic (Individual, self-contained and atomic software tools or libraries that are invoked by the user on local machines or remote servers)

B) NCBC YPR WG - Definition of NCBC (Computational Biology) Resources

- Software Resources (Tools)
* Computational Algorithms (e.g., Level-sets, Bioinformatics Algorithms)
* Software Suites (e.g., Vista, geWorkbench, FEATURE, ShapeViewer, Slicer3D, Pipeline)
* Downloadable libraries (e.g., ITK, ShapeToolsLibrary)
* Locally Executable programs (e.g., Debabeler)

- (Downloadable) Data Resources
* Raw Data - acquired data, going in various SW tools (e.g., NCBI Databases, CCB IDA)
* Model Data - processed data coming out of SW tools (e.g., CCB Atlases)
* Textual Data - spread sheets, web-pages (e.g., Imaging Glossary)
* Data Types
o XML (e.g., Module Descriptions)
o JSON Objects
o Binary Data (e.g., CCB IDA)
o Comma-separated-values, .csv (e.g., California Department fo Water & Power)

- Services
* Web-services (e.g., NCBI Web-services)
* Collaborative Services (expert)
* Other Services

C) NDG/NIF

- Data Resource (neuroscience data or findings)
- Bibliographic Resource
- Software Resource
- Research Supply (access to materials)
- Portal (access to people, places or sites)

D) NITRC (V1.0)
- Information Resource
- Software Tool

Taking NCBC as the 'gold standard' for the sake of discussion, the YPR WG is a one to one mapping w/ altered names: atomic = Software; data = data resources, and dissemination = services. For NDG/NIF, software = atomic; data resource = data; bibliographic could = data or dissemination; portal = a subset of dissemination, and research supply = ???. Finally, for the current NITRC, information resource is a super-set of data and dissemination (we then split Information resources into knowledge, models and web-resources (=NCBC dissemination) and data (=NDBC data); and software = atomic. NITRC will soon be also hosting some 'hardware' resources (mock scanners, fMRI button-boxes, etc.), so we were thinking of adding a Hardware class, but this may be like what NIF calls Research Supply, eitherway, Hardware in NITRC has a questionable linkage to the NCBC high level descriptors.
So, the mapping is at least conformal, and NITRC may support an additional branch of hardware, that is orthogonal to the NCBC listing, which should also be ok. NITRC could re-split our information resources at the high level to more explicitly match the NCBC, with no loss of generality or content.

So, now that the 'community' reviewable protege version of this was available, and some definitions were added, my issue is not at all with the 3-way high level parse, but rather with the choice of the word 'atomic' for the description. Could someone tell me how the concept of atomic is not synonymous w/ the term software itself?

IE. is the following definition not equally valid?
(Individual, self-contained software tools or libraries that are invoked by the user on local machines or remote servers)
What is being gained by the use of the unconventional term 'atomic'?

So, apart from the name, and the fact that NITRC may add Hardware, I would argue that NITRC and NCBC are compliant at this level.