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From Mario Gazzo <mario.ga...@gmail.com>
Subject Re: Approach for keeping track of formatting associated with text views
Date Wed, 11 Mar 2015 13:47:19 GMT
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-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-name>National Institute of Environmental Health Sciences</publisher-name>

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:

	<Child1 attribute=“someValue” />
	<Child2/>Some content.</Child2>

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 it
> 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 the
>> 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 to
>>> only convert tag annotations that surround or are inside the body tag.
>>> Metadata elements like citations are ignored. The only way to get around
>>> this seems to be by forking and modifying the codebase, which I like to
>>> 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 this
>>> behaviour without code modifications?
>>> Your input is appreciated, thanks.
>>> On 18 Feb 2015, at 23:03 , Mario Gazzo <mario.gazzo@gmail.com> wrote:
>>>> 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 also
>>>>> 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 article
>>>>>> 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
>>>>>> 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
>>>>>> 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
>>>>>> approach with more experienced users since this is the first application
>>>>>> are building with UIMA.
>>>>>> In the first step we would annotate every important element of the
>>>>>> 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
>>>>>> initially hoped would be necessary. We haven’t been able to find
>>>>>> examples of how this is usually done and the UIMA docs are vague
>>>>>> managing this kind of relationships across views. We would therefore
>>>>>> like to know if there is a simpler and better approach.
>>>>>> Any feedback is greatly appreciated. Thanks.

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