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Re: Connecting multiple fragment selectors with individual bodies

From: Lutz Suhrbier <l.suhrbier@bgbm.org>
Date: Mon, 13 Aug 2012 17:36:25 +0200
Message-ID: <50291EF9.5090103@bgbm.org>
To: public-openannotation@w3.org
Hi Paolo,

you depicted almost everthing right. Just a few exceptions, which I did 
not have explained exactly.

Our domain specific annotation type is not specified within the general 
comment of the "meta" annotation. Therefore, one or more rdf:type 
properties of the pattern urn:guid:bgbm:annosys:typeAnnotationType 
(where AnnotationType shall represent the real type name) will be added 
to the obligatory openannotation:core:Annotation rdf:type property 
outlining the openannotation standard. For consistency, all these 
rdf:type properties will be included in both the "meta"-annotation and 
the "sub" annotations.

The general comment is just an option for the user, to leave a comment 
regarding the source XML documents, e.g. if he is not competent or 
willing to alter values or enter comments to specific XML elements (Of 
course, I am developing a user interface for that, abstracting from all 
this XML stuff). But we aim to use the format also for exchange purposes 
later on.

Maybe, I should briefly describe our initial picture of the data 
structure before I started to implement it with OA  in order to get a 
clearer view on what I intend to implement. The basic idea is, to enable 
users to annotate a domain specific XML document. So, an annotation in 
our view should collect some meta data like annotator, date and the 
source XML document being annotated. Then, the user should be enabled to 
select an specific annotation type, further indicating the kind of 
annotation he wants to create. Also, the user shall be enabled to enter 
new values and/or leave comments to any (expert users) or a predefined 
set of data elements (common users) in the source documents. Finally, an 
annotation shall be produces, which consists of the collected meta data 
and the collection of annotated elements. That's, what I am trying to 
express in OA.

I always felt that using hasSemanticTag may not be the intended means to 
express the binding between the meta annotation data, and the annotation 
elements. But alternatively, just referring to the source document as a 
whole, and then "inventing" a list of XPath expressions with new values 
and comments and implement this as a blob object in the annotation body, 
did not appear not better to me. The latter also opens the question, why 
they introduced such a powerful fragment selector mechanism for targets, 
but did not offer the possibility to relate individual bodies to them ?
In order to fastly achieve to a working prototype implementation, I 
decided to start by using that simple hasSementagTag clamp mechanism and 
to report my problem to this mailing list for discussion and to adopt to 
a final solution later. As already mentioned, I am wondering, that other 
XML related applications of OA do not share the same or similar problems ?

Regarding the usage of dctypes:Dataset in my target body resources, I 
interpreted the standard description as to indicate a general type and a 
format (mime-type) describing the general contents of the related target 
or body. The closest type matching a target XML document I found was 
Dataset with format application/xml, and I applied the same pattern to 
my application specific body implementation. But may be, I got something 
wrong or there are other type/format combination much closer to what I 
wanted to express ?

best regards

> Hi Lutz,
> I tried to depict your example. I stripped out those details that I 
> thought where not relevant in regards to what you call the 
> 'meta-annotation' and I copied some n3 in the pictures to be brief.
> I am trying to interpret what you are doing but I am not sure on what 
> you mean. Let me give you an example so you can tell me how close or 
> far I am. I look at a resource and I create a general comment saying 
> 'there are several typos'. Then I create some other annotations - what 
> you call sub-annotations - that, for instance, are detailing all the 
> typos in the document. All the sub-annotations point to a fragment of 
> the document and also point to the general comment as you consider 
> them parts of that.
> Is this similar to what you are trying to do? The use of 
> oax:hasSemanticTag is certainly very far from what we created it for.
> Rob and Kevin, I am wondering if the oax:basedOn would work here. In 
> other words I have a general comment 'there are several typos' and 
> then through the relationship oax:basedOn I point to the 
> sub-annotations that help me supporting the general comment.
> Also, Lutz, I am not completely sure on your use of dctypes:Dataset. 
> Could you tell me more about it?
> On Mon, Aug 13, 2012 at 9:00 AM, Lutz Suhrbier <l.suhrbier@bgbm.org 
> <mailto:l.suhrbier@bgbm.org>> wrote:
>     Hi Leyla and Paolo,
>     please find attached the export of the very simple model from my
>     Annotation JUnit-Test in rdf-xml and N3.
>     It simply creates two types of Agents and Institutions, serving as
>     annotator and generator of a single "meta" annotation, which
>     include a single "sub" annotion which
>     The annotation is about a source target with the URI
>     "urn:guid:BGBM:Bridel+Herbar:Bridel-1-12:1344860699609:http%3A%2F%2Fwww.tdwg.org
>     <http://2Fwww.tdwg.org>%2Fschemas%2Fabcd%2F2.06".
>     The "meta" - annotation URI is
>     urn:guid:bgbm:annosys:1344860701104:1344860701104.
>     The "sub"annotation outlining the XPath within the source target
>     XML document is urn:guid:bgbm:annosys:1344860701292:1344860701292,
>     and uses the hasSemantic Tag pointing at the enclosing
>     "meta"-annotation.
>     The specific Target describing the XML Element within source
>     target is urn:guid:bgbm:annosys:1344860701296:1344860701296.
>     Furthermore, I introduced a XPath selector called <oax:xpath>,
>     which simply includes an XPath expression to describe the XML
>     element to be annotated.
>     The body of each "sub" annotation (XML Element annotation) may
>     comprise a new value and/or a comment related to the annotated XML
>     element.
>     I hope, my explication is not too complicated. If you have any
>     questions, please come back to me.
>     BTW. As I am quite new to RDF, what tool are you using to
>     visualise all the RDF graphs in your documentation ? Protegé ?
> All the figures you see in the documentation are actually manually 
> created with Omnigraffle.
> Best,
> Paolo
>>     Hi Lutz,
>>     On Wed, Aug 8, 2012 at 2:53 PM, Lutz Suhrbier
>>     <l.suhrbier@bgbm.org <mailto:l.suhrbier@bgbm.org>> wrote:
>>         Hi,
>>         I am currently trying to adopt OA to an application scenario,
>>         which I actually didn't found described here.
>>         The plan is to annotate XML documents in a way that the
>>         annotation relates one or more XML element values(let's call
>>         them subannotations), which can be given a domain specific
>>         annotation type.
>>     So, if I understand well, you have one annotation A1 and another
>>     one A2 and you want to create an annotation to relate them? Are
>>     you using predefined relations? or will you allow people to
>>     define the relation on the fly? for instance, using the body of
>>     the annotation as the suggested name for the relation.
>>     We have worked on a similar scenario but it is not yet compatible
>>     with OA. Anyway, if you provide some more information, maybe as
>>     Paolo suggests an example, it would make easier to understand
>>     better your scenario.
>>     cheers,
>>     Leyla
>>         As the target selection of subannotations(XML Elements) can
>>         be realised by the usage of multiple specific targets in
>>         combination with fragment selectors, there is no obvious and
>>         standard conform way of assigning individual annotated
>>         values(bodies) to the selected targets.
>>         Currently, I implemented a workaround by applicating the
>>         oax:hasSemanticTag predicate to each subannotation "pointing"
>>         at an embracing "meta" annotation.
>>         Even though that workaround appears to be doing its job, I am
>>         wondering
>>         1) if that is the intended way of using hasSemanticTag ?
>>         2) if there is no other standard conform method reflecting
>>         that scenario which can actually reflect those requirements ?
>>         With regard to a potential approach to be integrated within
>>         the standard, simply allowing multiple targets and multiple
>>         bodies does not appear to solve that question adequately, as
>>         the relationship between the specific target and the body
>>         (subannotation) would not be reflected. As the crucial point
>>         is the relationship between target and body, a target
>>         predicate like "hasBody" would be a better approach, at least
>>         from my perspective. One may even think about moving the
>>         "hasBody" predicate from oa:annotation to oa:target, as I see
>>         no relevant application of having annotations just consisting
>>         of a body without any target ?
>>         Anyway, doing so should not hinder any otherwise possible
>>         logical construction of annotations, or does it ? Also, it
>>         does not preclude annotations having targets pointing at the
>>         same body, nor does it preclude targets having multiple
>>         bodies if the discussion shows that this is somewhat useful.
>>         I have to mention, that this is my first project using RDF or
>>         OA, so may be I am in some topic completely misleaded. But I
>>         would appreciate if my point could be somehow discussed and
>>         reflected in an upcoming release of the standard.
>>         best regards
>>         Lutz Suhrbier
> -- 
> 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
> +1-857-366-1524 (mobile)   +1-617-768-8744 (office)
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Received on Monday, 13 August 2012 15:36:52 UTC

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