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From Mario Gazzo <mario.ga...@gmail.com>
Subject Re: Approach for keeping track of formatting associated with text views
Date Sat, 14 Mar 2015 13:49:00 GMT
No problem. You can contact me anytime in case you have additional questions.

> On 14 Mar 2015, at 14:34 , Peter Klügl <pkluegl@uni-wuerzburg.de> wrote:
> Hi,
> thanks for the issue and sorry for the delayed response. I did not yet find the time
to look into it, but I will the next days.
> Best,
> Peter
> Am 13.03.2015 um 23:51 schrieb Mario Gazzo:
>> The issue has now been created:
>> https://issues.apache.org/jira/browse/UIMA-4286 <https://issues.apache.org/jira/browse/UIMA-4286>
>>> On 11 Mar 2015, at 14:47 , Mario Gazzo <mario.gazzo@gmail.com> wrote:
>>> Thanks, I understand the choices now. I would also probably prefer to use the
document annotation if no text content is associated with the tag. However, ideally I would
prefer that tag annotations get the offsets of content that is within their scope but otherwise
get offsets of content within their closest shared ancestor element. Ultimately this could
end up being the document annotation. E.g.
>>> <journal-meta>
>>>    <journal-id journal-id-type="nlm-ta">Environ Health Perspect</journal-id>
>>>    <journal-title>Environmental Health Perspectives</journal-title>
>>>    <issn pub-type="ppub">0091-6765</issn>
>>>    <publisher>
>>>        <publisher-name>National Institute of Environmental Health Sciences</publisher-name>
>>>    </publisher>
>>> </journal-meta>
>>> I would here expect journal-meta to have the offsets of all content within its
scope, which in the converted view of my experiments gets combined to the following “Environ
Health PerspectEnvironmental Health Perspectives0091-6765National Institute of Environmental
Health Sciences”. This works as expected when I just disable the “inBody”-flag of the
HtmlConverterVisitor except that there is no clear separation between the content elements
any longer, which is why I would like to have a sentence separator like “. ” between them
so that I instead get: “Environ Health Perspect. Environmental Health Perspectives. 0091-6765.
National Institute of Environmental Health Sciences.”. The dot separators should then of
course not be included in the converters offsets since they are not part of the original text.
>>> Additionally there might be a case where a meta tag doesn’t have any content
within its scope but it contains attribute values:
>>> <Parent>
>>> 	<Child1 attribute=“someValue” />
>>> 	<Child2/>Some content.</Child2>
>>> </Parent>
>>> In this case I would prefer that Child1 has the same offsets as Child2 since
the tag is most closely related to that content. In case there is no content within the scope
of its parent then I would find the first ancestor that contains content within its scope
and use that offset although this choice is questionable. I haven’t a good example of this
case though so I presume they are in reality rare.
>>> That said, the latter is more complicated to implement, so I would be happy if
I could just easily turn off the “inBody”-test in the HtmlConverterVisitor and have some
way to add content separation between tags outside body without resorting to code modifications.
>>> Hope this feedback was helpful.
>>> Your time is much appreciated, thanks.
>>>> On 09 Mar 2015, at 16:56 , Jens Grivolla <j+asf@grivolla.net> wrote:
>>>> Hi Peter, while I don't think I will be using the HtmlConverter right away,
>>>> I would vote for using the length of the document annotation for
>>>> annotations that relate to the whole document (such as metadata).  That
>>>> makes them show up nicely in the CasEditor/Viewer and you could maintain
>>>> in all segments when you split a CAS (e.g. with something based on the
>>>> SimpleTextSegmenter example).
>>>> -- Jens
>>>> On Sat, Mar 7, 2015 at 5:33 PM, Peter Klügl <pkluegl@uni-wuerzburg.de>
>>>> wrote:
>>>>> Hi,
>>>>> there is no way yet to customize this behavior. The HtmlConverter only
>>>>> retains annotation of a length > 0 since annoations with length ==
0 are
>>>>> rather problematic and should be avoided.
>>>>> I can add a configuration parameter for keeping these annoations if you
>>>>> want (best open an issue for it). What should be the offsets of the
>>>>> annotations for elements in the head of the html document? 0, those of
>>>>> first token or those of the document annotation?
>>>>> Best,
>>>>> Peter
>>>>> Am 06.03.2015 um 14:00 schrieb Mario Gazzo:
>>>>> We conducted some experiments with both the HtmlAnnotator and the
>>>>>> HtmlConverter but we ran into an issue with the converter. It appears
>>>>>> only convert tag annotations that surround or are inside the body
>>>>>> Metadata elements like citations are ignored. The only way to get
>>>>>> this seems to be by forking and modifying the codebase, which I like
>>>>>> avoid. Both modules seem otherwise very useful to us but I am looking
for a
>>>>>> better approach to solve this issue. Is there some way to customise
>>>>>> behaviour without code modifications?
>>>>>> Your input is appreciated, thanks.
>>>>>> On 18 Feb 2015, at 23:03 , Mario Gazzo <mario.gazzo@gmail.com>
>>>>>>> Thanks. Looks interesting, seems that it could fit our use case.
We will
>>>>>>> have a closer look at it.
>>>>>>> On 18 Feb 2015, at 21:58 , Peter Klügl <pkluegl@uni-wuerzburg.de>
>>>>>>>> wrote:
>>>>>>>> Hi,
>>>>>>>> you might want to take a look at two analysis engines of
UIMA Ruta:
>>>>>>>> HtmlAnnotator and HtmlConverter [1]
>>>>>>>> The former one creates annotations for html element and therefore
>>>>>>>> for xml tags. The latter one creates a new view with only
the plain text
>>>>>>>> and adds existing annotations while adapting their offsets
to the new
>>>>>>>> document.
>>>>>>>> Best,
>>>>>>>> Peter
>>>>>>>> [1] http://uima.apache.org/d/ruta-current/tools.ruta.book.html#
>>>>>>>> ugr.tools.ruta.ae.html
>>>>>>>> Am 18.02.2015 um 21:46 schrieb Mario Gazzo:
>>>>>>>>> We are starting to use the UIMA framework for NL processing
>>>>>>>>> text, which is usually stored with metadata in some XML
format. We need to
>>>>>>>>> extract text elements to be processed by various NL analysis
engines that
>>>>>>>>> only work with pure text but we also need to keep track
of the formatting
>>>>>>>>> information related to the processed text. It is in general
also valuable
>>>>>>>>> for us to be able to track every annotation back to the
original XML to
>>>>>>>>> maintain provenance. Before embarking on this I like
to validate our
>>>>>>>>> approach with more experienced users since this is the
first application we
>>>>>>>>> are building with UIMA.
>>>>>>>>> In the first step we would annotate every important element
of the XML
>>>>>>>>> including formatting elements in the body. We maintain
some DOM-like
>>>>>>>>> relationships between the body text and formatting annotations
so that text
>>>>>>>>> formatting can be reproduced later with NLP annotations
in some article
>>>>>>>>> viewer.
>>>>>>>>> Next we would in another AE produce a pure text view
of the text
>>>>>>>>> annotations in the XML view that need to be NL analysed.
In this new text
>>>>>>>>> view we would annotate the different text elements with
references back to
>>>>>>>>> their counterpart in the original XML view so that we
can trace back
>>>>>>>>> positions in the original XML and the formatting relations.
This of course
>>>>>>>>> will require mapping NLP annotation offsets in the text
view back to the
>>>>>>>>> XML view but the information should then be there to
make this possible.
>>>>>>>>> This approach requires somewhat more handcrafted book
keeping than we
>>>>>>>>> initially hoped would be necessary. We haven’t been
able to find any
>>>>>>>>> examples of how this is usually done and the UIMA docs
are vague regarding
>>>>>>>>> managing this kind of relationships across views. We
would therefore really
>>>>>>>>> like to know if there is a simpler and better approach.
>>>>>>>>> Any feedback is greatly appreciated. Thanks.

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