IAO individuals are annotation properties in RO

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IAO's ontology-metadata.owl has individuals that are usually used as the object 
of the 'has curation status' property such as 'ready for release', 'pending 
final vetting', 'requires discussion', etc. 

For some reason, these are showing up as annotation properties in RO core. This 
causes problems.

Original issue reported on code.google.com by rlwalls2...@gmail.com on 14 Mar 2015 at 1:58

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I believe that Ramona's list of problem terms is complete. I see three of them: 
'ready for release', 'pending final vetting', 'requires discussion'.

They were introduced to annotations.owl in r428:

https://code.google.com/p/obo-relations/source/detail?r=428

I think this is just a mistake. Chris: can I go ahead and change these to 
individuals?

Original comment by ja...@overton.ca on 16 Mar 2015 at 3:42

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You're right, this is a mistake. Go ahead and fix. Or can we now go ahead and 
safely import iao metadata in toto?

Original comment by cmung...@gmail.com on 18 Mar 2015 at 12:29

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If RO core included IAO's ontology-metadata.owl, I would not have to import it 
separately and could just get it from RO. 

Original comment by rlwalls2...@gmail.com on 18 Mar 2015 at 1:36

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I took a quick look at 
<http://purl.obolibrary.org/obo/iao/2015-02-23/ontology-metadata.owl>. I think 
it will be fine. It doesn't use any object properties, and the only overlapping 
class is BFO_0000031 'generically dependent continuant'.

I'll experiment with it tomorrow and report back.

Original comment by ja...@overton.ca on 18 Mar 2015 at 2:03

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Sorry for the delay.

The RO annotations.owl file contains terms from:

- IAO (a bunch)
- Dublin Core
  - 'contributor'
  - 'creator'
  - 'publisher'
  - 'source'
  - 'title'
- FOAF (Friend of a Friend)
  - 'homepage'
  - 'page'
- OBO in OWL:
  - 'shorthand'
- RO:
  - 'temporal interpretation'
  - 'axiom holds for all times'
  - 'relation has no temporal argument'

The IAO ontology-metadata.owl only contains IAO terms. So RO's annotations.owl 
can't be replaced, but it could import ontology-metadata.owl. I experimented 
with this and it worked properly.

Things we can do:

1. import IAO ontology-metadata.owl into annotations.owl (and remove IAO axioms 
from annotations.owl)
2. import the DC terms from 
<http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl> into 
annotations.owl (and remove DC axioms from annotations.owl); we do this in OBI 
and IAO
3. import FOAF from <http://xmlns.com/foaf/spec/index.rdf> into 
annotations.owl; since we only use two terms without any further annotations on 
them, this probably doesn't make sense
4. clean up annotation property axioms from ro-edit.owl

I've tested 1,2,3 but I'm not confident that I can do 4 without breaking 
something.

Original comment by ja...@overton.ca on 25 Mar 2015 at 2:05

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I think 1 makes sense.

Original comment by cmung...@gmail.com on 3 Apr 2015 at 3:03

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Arg, now I can't decide. Importing ontology-metadata.owl into annotations.owl 
works fine, but it includes 'information content entity', 'data item', and some 
child classes. They look kind of ugly when they appear in 
bfo-classes-minimal.owl and core.owl.

I've attached an edited file. Please try it out and let me know whether we want 
to go ahead with the import, or forget about the import and just make the 
minimal fixes to annotations.owl.

Original comment by ja...@overton.ca on 7 Apr 2015 at 1:47

Attachments:

• annotations.owl

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This issue was closed by revision r449.

Original comment by ja...@overton.ca on 9 Apr 2015 at 7:30

• Changed state: Fixed

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This was taking way too long (entirely my fault) so I just made the minimal 
fix. I'll open a new issue about using IAO ontology-metadata.owl.

Original comment by ja...@overton.ca on 9 Apr 2015 at 7:31

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Thanks James!

Original comment by rlwalls2...@gmail.com on 9 Apr 2015 at 7:54