Vocabularies with terms from other ontologies

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Vocabularies with terms from other ontologies

Stephen Ficklin-2
Hi All,

We're working on an OWL parser for Tripal.  Specifically we are trying
to load the new Relationship Ontology (RO).   This ontology includes
terms from other ontologies.  There's no problem importing these
dependent ontologies.   But, Chado does not have a direct way to include
terms from one vocabulary in another.   Here are some options I came up
with:

1) Make note of the inclusion in the cvtermprop table
2) Create a new custom cvterm_cv table to associate terms from one
vocabulary with another
3) Duplicate the term in both vocabularies.

There are issues with all 3 methods.  I don't care for option 1 as the
association isn't really a property of the term.  I also don't like
option 3 because if the term is updated in the parent vocabulary the
changes are not reflected in the copy.  My favorite option is 2 but the
fill_cvtermpath() function will not create a complete representation of
the vocabulary in the cvtermpath table. We could replace this function
with a version that can use a new cvterm_cv table.

Are there any objections to using option2?  Does anyone have other ideas
that may work?

Thanks,
Stephen

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Re: [Gmod-schema] Vocabularies with terms from other ontologies

Chris Mungall
Hi Stephen,

A couple of pointers to OWL parsers:

  - don't target the XML, this is 2 levels of abstraction too low. I can
guarantee anything you write here will likely break
  - targeting the RDF level of abstraction is better and there are RDF
parsers for every language. Still, it can be a low level way to view OWL
and there are many gotchas
  - using an OWL API is best. Unfortunately there is only the java
OWLAPI, so if you aren't in a JVM language this is harder

We may have a standard JSON/YAML that is OWL-complete in the future that
would be a better target. Having said that, a JVM language is a good
choice for a Chado ontology loader due to access to reasoners (e.g.
cvtermpath).

With the syntactic issues aside, there is still the issue of how to map
different kinds of OWL axioms to relationships. I recommend following
the same mapping we do for graph databases documented here:
https://github.com/SciCrunch/SciGraph/wiki/

As for RO, there is always the solution of tailoring the RO release for
Chado, thanks for contributing to the discussion here:
https://github.com/oborel/obo-relations/issues/68

For your solutions below, I like 2 best.

On 12 Apr 2016, at 8:48, Stephen Ficklin wrote:

> Hi All,
>
> We're working on an OWL parser for Tripal.  Specifically we are trying
> to load the new Relationship Ontology (RO).   This ontology includes
> terms from other ontologies.  There's no problem importing these
> dependent ontologies.   But, Chado does not have a direct way to
> include
> terms from one vocabulary in another.   Here are some options I came
> up
> with:
>
> 1) Make note of the inclusion in the cvtermprop table
> 2) Create a new custom cvterm_cv table to associate terms from one
> vocabulary with another
> 3) Duplicate the term in both vocabularies.
>
> There are issues with all 3 methods.  I don't care for option 1 as the
> association isn't really a property of the term.  I also don't like
> option 3 because if the term is updated in the parent vocabulary the
> changes are not reflected in the copy.  My favorite option is 2 but
> the
> fill_cvtermpath() function will not create a complete representation
> of
> the vocabulary in the cvtermpath table. We could replace this function
> with a version that can use a new cvterm_cv table.
>
> Are there any objections to using option2?  Does anyone have other
> ideas
> that may work?
>
> Thanks,
> Stephen
>
> ------------------------------------------------------------------------------
> Find and fix application performance issues faster with Applications
> Manager
> Applications Manager provides deep performance insights into multiple
> tiers of
> your business applications. It resolves application problems quickly
> and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

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