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Re: [ontolog-forum] Namespaces for ontologies

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Duane Nickull <dnickull@xxxxxxxxx>
Date: Mon, 27 Apr 2009 04:28:15 -0700
Message-id: <C61AE4DF.3E91%dnickull@xxxxxxxxx>
John:    (01)

My comments inline:
On 4/26/09 5:34 PM, "John Graybeal" <graybeal@xxxxxxxxx> wrote:    (02)

> Hi Duane,
> On Apr 22, 2009, at 3:09 PM, Duane Nickull wrote:
>> The problem is that there are no namespace qualifications for these so I want
>> to introduce that into my work.  I was planning on just using the root URLıs
>> for each work however there are versions possible in some of the work.
>> I would like this to be in the firm of
>> <upper_ontology_identifier>+<version_or_instance>+<uuid> as a classifier
>> followed by the term label such as ³transitive².  I will probably use URIıs
>> for the UUID.
>> Question:
>> Has anyone ever come across a similar problem and if so, how did they solve
>> it?
> We came across two similar problems, I think.  We are republishing
> vocabularies, so it is I believe analogous.  Some questions for you that you
> have, I imagine, thought about, then my own contributions.
DN: I don't think that is quite the same.  Vocabularies are terms while
mapping terms to concepts is the work I am pursuing within a metadata
> 1) I am not sure what your '+' means -- I assume it is a literal? And what
> does 'as a classifier' mean -- everything that comes before the 'term label'?
> More specifics would be helpful here, unless everyone else understands
> already.
DN: Sorry - I may have not been clear.  It is meant as a logical
concatenation operator.  What I would like to have is something like this:    (03)

SUMO:Version1:104379243    (04)

This corresponds to a specific concept in a specific version of SUMO.  This
work has currently been done for one ontology via wordnet
http://sigma.ontologyportal.org:4010/sigma/WordNet.jsp?word=table&POS=1    (05)

My goal is to map the terms from multiple languages and contexts to multiple
upper ontologies.    (06)

> 2) By 'uuid' I assume you mean the UUID for the original term. Is it definite
> that all the ontologies have a clearly usable UUID for each of their terms?
> (For example, if the UUID is constructed with a fragment syntax ('#'), your
> URL will get a bit weird, won't it?  And I *think* some references to URLs
> within URLs (whether URL#1 is your UUID) can require some ugly expansions in
> some http circumstances, but I haven't had to master that myself yet.    (07)

DN: Not quite but close.  The UUID for the concept rather than the term.
This could be encoded as a URL however that would likely lead to
dependencies which I would not want to introduce.  Notice how elegant the
wordnet concept<->word mapping is without URL's.
> 3) I am a little lost as to the value of adding the label, if it is the label
> of the term identified by the UUID.  This makes me worry I may have
> misunderstood your goal.
> My thoughts in response:
> In one of our scenarios we had to deal with people who want URNs instead of
> URLs, while we always wanted to have a URL for all our terms.  A
> quasi-solution we found is to embed the URN, as a sort of literal code, inside
> the URL, so that part of your model seems at least consistent with what we
> came up with.
DN: Since I am doing this project largely on my own, I have the luxury of
making up all the rules ;-)  In true REST fashion, each concept would have a
> In our whole world of use cases we had to deal with versioning. While in
> theory we could have supported any style of version, we ended up making an
> ISO8601 look-alike, that goes into as much detail (days, hours, milliseconds
> (!)) as required to ensure uniqueness from previous submissions.  This
> provided useful visual context and avoided considering weird versioning labels
> that might have been URL- or user-unfriendly. So the notion of the version is
> consistent too.
> The one thing about versions is that they are pretty consistent if you can
> align them with the moment a resource is submitted. But if you are trying to
> capture the version of an external resource, you'll have to decide what you
> mean by 'version' of that resource, considering (a) they may not version, (b)
> you may not have the ability to inspect their version transitions -- either
> when they happen or what the change was, and (c) you'll have to decide what
> relation you want between uniqueness and version ID (different term guarantees
> different version, vice-versa, or both?). Ick.
DN: I agree.  Ick!  There is probably no one-size-fits-all solution here.
> Details are buried in various documents associated with our semantic framework
> [1], I can provide specific pointers to our URL construction notions (or you
> can search on the site) if you want them.
> Hope this helps.
DN: it definitely helps.  Thank you for the resource link.    (08)

> John
> [1] MMI Semantic Framework: http://marinemetadata.org/semanticframework
> --------------
> John Graybeal   <mailto:graybeal@xxxxxxxxx>  -- 831-775-1956
> Monterey Bay Aquarium Research Institute
> Marine Metadata Interoperability Project: http://marinemetadata.org
>     (09)

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