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George Peter

Subject: CSV DOC to XML CONVERSION
Author: George Peter
Date: 01 Jul 2009 09:53 AM

Hi I am now testing the trial version and I am trying to convert a .doc file into the standard Medline XML (pubmed). Is it possible to generate the xml automatically? Also, how can I map a csv to the standart pubmed xml?

EXAMPLE
I need to generate something like this:

<ref-list>
<ref id="R1"><label>1</label><nlm-citation citation-type="journal"><person-group person-group-type="author"><name><surname>Oosterlinck
</surname><given-names>O</given-names></name><name><surname>van der Meijden</surname><given-names>A</given-names></name></person-group>
<source>Guidelines on TaT1 (Non-muscle invasive) Bladder Cancer. European Association of Urology Guidelines</source><year>2007</year><fpage>1</fpage>
<lpage>17</lpage></nlm-citation></ref> </ref-list>

(Deleted User)

Subject: CSV DOC to XML CONVERSION
Author: (Deleted User)
Date: 07 Jul 2009 04:59 AM

Hi George,
usually when converting from CSV to XML you use the XML Converter functionality of Stylus Studio, then design an XSLT stylesheet using Mapper to build the desired output structure.
For instance, create a new XSLT stylesheet, go to the Mapper tab, click on the "Add source document" button, select the CSV file in the Open File Dialog, check the "Open with XML Converter" check box and press OK; in the following dialog select the Comma Separated Values entry on the left and press OK.
In Mapper click on the "Set Target Document" button and select either the PubMed schema or an XML instance of such a schema.
Now you are ready to connect the element on the left schema to the ones on the right.

If the CSV data is stored inside a Word document, you will have to extract it to a separate file, e.g. by running another XSLT stylesheet against an XML version of the document

Hope this helps,
Alberto

George Peter

Subject: CSV DOC to XML CONVERSION
Author: George Peter
Date: 08 Jul 2009 06:36 AM

Hi Alberto

Thank you very munch for your feed back. I did everything you suggested and now I have the desired structure. The question is now how can I actually import the values from the csv over this structure in order to generate the complete xml with values.

(Deleted User)

Subject: CSV DOC to XML CONVERSION
Author: (Deleted User)
Date: 08 Jul 2009 08:41 AM

Hi George,
could you attach an example of the data, and what you wrote? I don't understand what you mean by "importing the values from csv over this structure".

Alberto

George Peter

Subject: CSV DOC to XML CONVERSION
Author: George Peter
Date: 10 Jul 2009 06:16 AM

Hi Alberto,
Sorry for not beeing so clear the first time
I need a csv like the one I attached to go into this kind of structure. It doesn't need to be a csv it can be also a flat file (.txt or .doc).

<ref-list>
<ref id="R1"><label>1</label><nlm-citation citation-type="journal"><person-group person-group-type="author"><name><surname>Oosterlinck
</surname><given-names>O</given-names></name><name><surname>van der Meijden</surname><given-names>A</given-names></name></person-group>
<source>Guidelines on TaT1 (Non-muscle invasive) Bladder Cancer. European Association of Urology Guidelines</source><year>2007</year><fpage>1</fpage>
<lpage>17</lpage></nlm-citation></ref>
<ref id="R2"><label>2</label><nlm-citation citation-type="journal"><person-group person-group-type="author"><name><surname>Loidl</surname><given-names>
W</given-names></name><name><surname>Schmidbauer</surname><given-names>J</given-names></name><name><surname>Susani</surname><given-names>M</given-names>
</name></person-group><article-title>Flexible Cystoscopy assisted by Hexaminolevulinate Induced Fluorescence: A New Approach for Bladder Cancer Detection
and Surveillance?</article-title><source>Eur Urol</source><year>2005</year><volume>47</volume><fpage>323</fpage><lpage>326</lpage></nlm-citation></ref>
<ref-list>

Book2.csv

2.doc
this is how we recieve the references

(Deleted User)

Subject: CSV DOC to XML CONVERSION
Author: (Deleted User)
Date: 10 Jul 2009 06:50 AM

Hi George,
in the attached picture you can see how I mapped the CSV structure to the XML structure you provided. To run them, just place the other files in the same directory and run the stylesheet.

Hope this helps,
Alberto

mapper(2).JPG
Screenshot of XSLT Mapper

ref-list.xsl
XSLT stylesheet

ref-list.xml
XML structure

Book2(1).csv
CSV source

George Peter

Subject: CSV DOC to XML CONVERSION
Author: George Peter
Date: 10 Jul 2009 09:40 AM

Hi Alberto,

Thank you so much. This is almost what i needed. I think my problem was that the csv file was not in the same folder as the xsl and the xml.

Two more questions please:

1. How can we make the tag <ref id="1"> </ref> auto increment for all the iterations?
i.e. <ref id="1"> </ref>
<ref id="2"> </ref> and so on
2. How can we write automatically inside a tag?
i.e <nlm-citation citation-type="journal"> </nlm-citation> - this can be wither journal, either book
<person-group person-group-type="author"> </person-group> - this is unchangeble

Thank you
George

(Deleted User)

Subject: CSV DOC to XML CONVERSION
Author: (Deleted User)
Date: 10 Jul 2009 09:55 AM

Hi George,
to specify a fixed value for an element, you right click in the target schema node and select Set Text Value.
For the "id" attribute of the "ref" element you should enter {position()} so that the current row number is entered; for "person-group-type" you enter author. For the "citation-type", you will have to come up with some code to decide whether the issue is a journal or a book...

Alberto

George Peter

Subject: CSV DOC to XML CONVERSION
Author: George Peter
Date: 10 Jul 2009 10:49 AM

Hi Alberto
I took your advice but it does not write inside the begining tag
i.e <ref id="1"> . It writes between the tags i.e: <ref> aaaa</ref>.
Is there something I am missing?

10x
George

(Deleted User)

Subject: CSV DOC to XML CONVERSION
Author: (Deleted User)
Date: 10 Jul 2009 12:13 PM

Hi George,
you must have invoked the Set Text Value on the "ref" element instead of its "id" attribute.

Alberto

George Peter

Subject: CSV DOC to XML CONVERSION
Author: George Peter
Date: 13 Jul 2009 08:31 AM

Hi Alberto,
Thank you so much. You were right . I did not have an id attribute. Now it is working perfect. Once again thank you so much for all the help.

Best regards,
George

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