Added hierarchy of ontology module types

[cmungall]

if the owldiff is hard to read, I added classes in the 8x range:

. BFO:0000031
 % IAO:0000030 ! information content entity
  % IAO:0000027 ! data item
   % IAO:0000102 ! data about an ontology part
    % IAO:8000000 ! ontology module * 
     % IAO:8000014 ! generated ontology module
      % IAO:8000015 ! template generated ontology module
     % IAO:8000002 ! editors ontology module
     % IAO:8000013 ! reasoned ontology subset module
     % IAO:8000001 ! component ontology module
     % IAO:8000004 ! bridge ontology module
      % IAO:8000016 ! taxonomic bridge ontology module
     % IAO:8000003 ! main release ontology module
     % IAO:8000006 ! subset ontology module
      % IAO:8000005 ! import ontology module
       % IAO:8000011 ! external import ontology module
      % IAO:8000007 ! curation subset ontology module
      % IAO:8000009 ! single layer subset ontology module
      % IAO:8000008 ! analysis subset ontology module
      % IAO:8000010 ! exclusion subset ontology module
      % IAO:8000012 ! species subset ontology module

@zhengj2007 I took 8x onwards, how do I claim an IAO range? See #35

Comments welcome @jamesaoverton @balhoff @alanruttenberg @mcourtot @dosumis @drseb @matentzn @rctauber @simonjupp

See also

• Atomic (base) module proposal INCATools/ontology-development-kit#50
• Create PROV metadata graph describing operation flow for robot commands ontodev/robot#6
• https://github.com/balhoff/ultimate-ontology-makefile

I would like to axiomatize the above (this would not be intended for use in the actual ontologies that use these, more as a documentation feature). What do we think of using PROV-O here?

[zhengj2007]

@cmungall current ID ranges are indicated in the IAO ontology comments, like:
comment: IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999
comment: IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999
see: http://www.ontobee.org/ontology/IAO

I think we'd use a better way than it. But I have no idea how.

[cmungall]

I think we'd use a better way than it. But I have no idea how

https://github.com/INCATools/ontology-starter-kit/

https://github.com/INCATools/ontology-starter-kit/blob/master/template/src/ontology/README-editors.md#id-ranges

IAO presents a challenge as IDs split across 2 repos

[cmungall]

I have also added a new class for representing "obo basic" subsets, see http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2

[jamesaoverton]

It's a good idea. The proposed terms make sense. There are some that I can't imagine using myself. Tools such as ROBOT will be able to automatically annotate some of these terms, but some will require manual assertion.

I'm fine with the proposed definitions, but not all the proposed terms have definitions. 'ontology module' is undefined, for one.

Minor point: there's alternation between 'subset ontology module' and 'ontology subset module', but I don't understand what the difference could be.

[cmungall]

Should be consistently subset ontology now

There are some notes on ontology module. We have to think about the semantics. There are problems in DL with an ontology instantiating this. I would opt for this being a simple descriptive hierarchy that is associated to an ontology using dcterms:type or similar.