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Re: Merging Databases

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Tue, 21 Jul 2009 20:26:39 -0400
Message-ID: <29af5e2d0907211726i1df4477jb7bb2fb69a06bdd1@mail.gmail.com>
To: Bernhard Schandl <bernhard.schandl@univie.ac.at>, Toby Inkster <tai@g5n.co.uk>
Cc: Hugh Glaser <hg@ecs.soton.ac.uk>, Amrapali Zaveri <amrapali.zaveri@gmail.com>, "public-lod@w3.org" <public-lod@w3.org>, Anja Jentzsch <anja@anjeve.de>, Susie Stephens <susie.stephens@gmail.com>
On Tue, Jul 21, 2009 at 1:23 PM, Toby Inkster<tai@g5n.co.uk> wrote:
> On Tue, 2009-07-21 at 19:52 +0300, Bernhard Schandl wrote:
>
>> > I would say: Never assert sameAs. It's just too big a hammer.
>> > Instead use a wider palette of relationships to connect entities
>> > to other ones.
>>
>> which ones would you recommend?
>
> skos:exactMatch = asserts that the two resources represent the same
> concept, but does not assert that all triples containing the first
> resource are necessarily true when the second resource is substituted
> in.

I'm having trouble parsing this one. I don't know what concepts are,
but they are an odd sort of thing if they can be the same, but can't
be substituted.

In any case, this isn't much better when the issue I point out is that
there is a specific relation between e.g. the intervention and the
drug - that relation is no where near equivalence in any form.

> skos:closeMatch = same as exact match, but slightly woolier.

Seems harmless, assuming one doesn't mind whatever one is dealing with
typed a concept.
Ditto the broader and narrower relations, which although not to my
taste  (i don't how to tell when they hold) are certainly better than
using sameAs.

> owl:equivalentProperty = if {X equivalentProperty Y} and {A X B} then
> {A Y B}. In other words, the properties can be used completely
> interchangeably. But perhaps there are other important differences
> between X and Y, such as their rdfs:label or rdfs:isDefinedBy.

Still near equivalence.

> owl:equivalentClass = if {X equivalentClass Y} then all Xs are Ys and
> vice versa. Same dealy with ´╗┐owl:equivalentProperty really.

Ditto.

> ovterms:similarTo = a general, all-purpose wimps' predicate. I use this
> extensively.

Under the principal "first do no harm", this seems to work, although I
note that the intervention (something that happens) isn't similar to
the drug used in it (something that is consumed when the intervention
happens).

seeAlso seems pretty harmless and noncommittal.

But better is probably to look more closely at what the entities are
and then choose a relationship that better expresses how they relate.
In the case of the intervention, one plausible interpretation is that
the "intervention" names a class of processes, and that there is a
subclass of such processes in which the drug participates. (the other
subclass are those in which a placebo is the participant) This can be
modeled in OWL.

(My real advice for clinical trial resource is to collaborate with the
OBI project and use terminology that is being developed for exactly
that purpose)

In my line of work I start with the OBO Relation ontology,
http://www.obofoundry.org/ro/ which provides a basic set of well
documented relations, such as the has_participant relationship.

OWL also provides some relations of beyond equivalences - subclass
relations are an option, when appropriate, as well as making
statements that classes overlap - by expressing that the intersection
of the two is not empty.

That ontology is undergoing some reform, as it should in time. Some of
the new candidate relations are documented in links from that page. In
addition it is proposed that that there be class level and instance
level versions of the relations - the class level relations might
better a modeling style that would rather avoid using OWL
restrictions, and fits well with OWL 2 which allows a name(URI) to be
used as both a class and an instance.

Finally, for those cases where there are more than one URI and they
*really* mean the same thing - why not try to get the parties who
minted them to collaborate and retire one of the URIs. If they really
mean the same thing there should be no harm in either party using the
other's URI.

-Alan

>
> --
> Toby A Inkster
> <mailto:mail@tobyinkster.co.uk>
> <http://tobyinkster.co.uk>
>
>
Received on Wednesday, 22 July 2009 00:27:34 UTC

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