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Re: Best Practices - Semantic Tagging

From: Bob Morris <morris.bob@gmail.com>
Date: Sun, 3 Mar 2013 00:26:49 -0500
Message-ID: <CADUi7O5M7e2dC8gFXVGvY7mka9kfhEbLKJCwJV3GwzBxG_QaCg@mail.gmail.com>
To: Paolo Ciccarese <paolo.ciccarese@gmail.com>
Cc: "Timothy W. Cook" <timothywayne.cook@gmail.com>, public-openannotation <public-openannotation@w3.org>
Ah, Tim's case is somewhat akin to one of our important use cases for
actionable annotations on mutable data, which resonated for a few
others in the Chicago meeting.

Although more general than what I write here, one use case amounts to
making an annotation that is intended to assert something like "Given
a query expressible as Q, the application of which in\any context in
which it can be applied and provide data returns of the form R, we
need to assert that R should always have some particular relation to
something R0 in the body."  Conversationally, we tend to think of this
as annotating the query, but it seems more like annotating a schema.
We use it in data quality control annotations.  It's sort of using
annotations to assert that a rule applies to a context, rather than to
a SpecificResource.   Another example is an annotation whose body is
something like "For all manuscripts in this project, the appropriate
contraction of "do not" is "don't"  ".   In essence, these are
annotations on Targets that are classes of Resources (In fact, just
yesterday we were wondering if OA needs an oa:GeneralResource...but I
digress), as is Tim's.  It seems to me that OA already sometimes has
to tiptoe around this issue with Styles, States, and perhaps other
such things whose presence (or absence) intends to convey that the
Body applies, potentially, to lots of stuff, whether presently an
extant digital resource or not.

We are rewriting a manuscript about data annotation at the moment, and
in the next week or so I might have some more specific OA examples of
how we handle these not-so-specific resources.

Bob

On Sat, Mar 2, 2013 at 1:12 PM, Paolo Ciccarese
<paolo.ciccarese@gmail.com> wrote:
> Dear Tim,
> Apologize, I sent the email by mistake and I was still in the process of
> editing.
>
> I just wanted to add that I don't recall any discussion close to what you
> are asking.
> So what I expressed was purely my personal first reaction to your problem.
>
> Also the use of oa:SemanticTag to fit into XMLSchema has to be thought
> through as I think that is far from what the term has been conceived for.
> <xs:appinfo> is very permissive but we are still in the XML realm.
>
> Best,
> Paolo
>
>
> On Sat, Mar 2, 2013 at 1:04 PM, Paolo Ciccarese <paolo.ciccarese@gmail.com>
> wrote:
>>
>> Dear Tim,
>> in general, the OA model is meant to be used for achieving
>> interoperability (between systems).
>> Also it is normally used for defining instances of data and not for
>> meta-modelling.
>>
>> In other words, as we are in the realm of XMLSchema and as your annotation
>> is not going to be reproduced in instances of data I would *personally* not
>> bother too much with the OA concept of annotation.
>>
>> I would probably  do something similar to what you did or I would find
>> some other term that clearly states that the value is 'of topic' that
>> specific URI (some sort of range).
>>
>> Alternative would be:
>> <xs:annotation>
>>       <xs:appinfo>
>>                <oa:semanticTag>
>>
>> is a bit of a stretch.
>>
>> Best,
>> Paolo
>>
>>
>>
>>
>>
>>
>> On Sat, Mar 2, 2013 at 9:23 AM, Timothy W. Cook
>> <timothywayne.cook@gmail.com> wrote:
>>>
>>> HI All,
>>>
>>> Though I have read virtually everything I can find related to this
>>> subject; including:
>>>
>>> http://lists.w3.org/Archives/Public/public-openannotation/2013Feb/0051.html
>>>
>>> I really don't see the answer to my question.
>>>
>>> First of all this is a "green field" area.  I do not have to be
>>> concerned with existing documents and how it has been done in the
>>> past.
>>>
>>> I just want to get this right, the first time. Given all the
>>> experience from people here.
>>>
>>> Scenario:
>>>
>>> I have XML Schemas that define data instance structures (as usual).
>>> These schemas use a lot of complexTypes that are restrictions from a
>>> base schema.  Since each base schema complexType can be represented in
>>> a schema multiple times with different restrictions, I use a UUID
>>> based name. For example:
>>>
>>>   <xs:complexType name="ct-f6c5ea6e-6458-4799-874d-7f3d365d260d">
>>>         <xs:complexContent>
>>>             <xs:restriction base="mlhim2:DvQuantityType">
>>>                 <xs:sequence>
>>>
>>> ...
>>>
>>> These complexTypes are almost always definable via a controlled
>>> vocabulary, ex. SNOMED-CT
>>>
>>> In order to add semantics to the complexType definition my current
>>> thought is to use:
>>>
>>>   <xs:complexType name="ct-f6c5ea6e-6458-4799-874d-7f3d365d260d">
>>>     <xs:annotation>
>>>       <xs:appinfo>
>>>         <rdfs:isDefinedBy
>>> rdfs:resource="http://purl.bioontology.org/ontology/SNOMEDCT/365761000"/>
>>>       </xs:appinfo>
>>>     </xs:annotation>
>>>         <xs:complexContent>
>>>             <xs:restriction base="mlhim2:DvQuantityType">
>>>                 <xs:sequence>
>>> ...
>>>
>>> Which will identify this complexType as a Sodium level finding
>>> according to SNOMED-CT.
>>>
>>> My first question is:
>>> 1) is it correct to make the assumption that the annotation applies to
>>> the enclosing complexType without using an rdf:about (or similar)
>>> definition?
>>>
>>> 2) is rdfs:isDefinedBy the "tag" to use, or is something like
>>> oa:SemanticTag a better choice?
>>>
>>> Realizing that these annotations will not be reproduced in the
>>> instance data.  The eco-system around this says that to determine the
>>> full semantics you must have the schema associated with any instance
>>> data.
>>>
>>> Thoughts?
>>>
>>> Cheers,
>>> Tim
>>>
>>>
>>>
>>> --
>>> ============================================
>>> Timothy Cook, MSc           +55 21 94711995
>>> MLHIM http://www.mlhim.org
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>>> Circle us on G+: http://goo.gl/44EV5
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>>> LinkedIn Profile:http://www.linkedin.com/in/timothywaynecook
>>>
>>
>>
>>
>> --
>> Dr. Paolo Ciccarese
>> http://www.paolociccarese.info/
>> Biomedical Informatics Research & Development
>> Instructor of Neurology at Harvard Medical School
>> Assistant in Neuroscience at Mass General Hospital
>> Member of the MGH Biomedical Informatics Core
>> +1-857-366-1524 (mobile)   +1-617-768-8744 (office)
>>
>> CONFIDENTIALITY NOTICE: This message is intended only for the
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>
>
>
>
> --
> Dr. Paolo Ciccarese
> http://www.paolociccarese.info/
> Biomedical Informatics Research & Development
> Instructor of Neurology at Harvard Medical School
> Assistant in Neuroscience at Mass General Hospital
> Member of the MGH Biomedical Informatics Core
> +1-857-366-1524 (mobile)   +1-617-768-8744 (office)
>
> CONFIDENTIALITY NOTICE: This message is intended only for the addressee(s),
> may contain information that is considered
> to be sensitive or confidential and may not be forwarded or disclosed to any
> other party without the permission of the sender.
> If you have received this message in error, please notify the sender
> immediately.



-- 
Robert A. Morris

Emeritus Professor  of Computer Science
UMASS-Boston
100 Morrissey Blvd
Boston, MA 02125-3390

IT Staff
Filtered Push Project
Harvard University Herbaria
Harvard University

email: morris.bob@gmail.com
web: http://efg.cs.umb.edu/
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http://www.cs.umb.edu/~ram
===
The content of this communication is made entirely on my
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Received on Sunday, 3 March 2013 05:27:17 GMT

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