Re: [jats-list] I'm looking for examples of tagging molecular strucutres in the nlm 3.0 archiving tag set

["I.mulvany@xxxxxxxxxxxxxxxxx" <i.mulvany@xxxxxxxxxxxxxxxxx>]

By all means, do please correct the tagging, the only thing that I can see is
an issue with line breaks. I'm still new to nlm, so I am sure there must be
errors.

Sent from my iPad

On 8 Nov 2012, at 20:33, Wendell Piez <wapiez@xxxxxxxxxxxxxxx> wrote:

> Hi Ian,
>
> As I understand it, you are using 'alternatives' exactly correctly.
>
> I have a couple of questions about the contents as given in your
> example, but I suspect there may be transcription errors there. (Among
> other issues, it isn't valid.)
>
> In any case, the use case you describe is just what 'alternatives' is
> for, as documented in the Tag Library:
>
>
http://jats.nlm.nih.gov/publishing/tag-library/1.0/index.html?elem=alternativ
es
>
> Cheers,
> Wendell
>
> On Thu, Nov 8, 2012 at 10:17 AM, Ian Mulvany
> <i.mulvany@xxxxxxxxxxxxxxxxx> wrote:
>> Specifically would it be possible to use the <alternative> tag to
>> contain both a pointer to a local server side hosted .pdb file, and a
>> reference to a named pdb entity?
>>
>> I'm thinking of something like the following:
>>
>> <chem-struct-wrap>
>>      <caption>
>>      <p>This is the caption for the chemical structure. This tagging
>> includes reference to an
>>        image to be used in processing the XML. It also includes
>> reference to a locally hosted in-line-supplimentary data file with the
>> pdb data held locally. It also contains a reference to an external
>> link for a pdb resource. It also contains a marked up pdb named
>> entity.</p>
>>      </caption>
>>      <alternatives>
>>      <graphic xmlns:xlink="http://www.w3.org/1999/xlink";
>>      xlink:href="pq0209587032" specific-use="print"></graphic>
>>      <chem-struct>1crn</chem-struct>
>>      <inline-supplementary-material
>> xmlns:xlink="http://www.w3.org/1999/xlink";
>> xlink:title="local_pdb_file"
>> xlink:href="1crn.pdb">1crn.pdb</inline-supplementary-material>
>>      http://www.rcsb.org/pdb/explore/explore.do?structureId=1CRN
>>      <ext-link ext-link-type="pdb"
>>
xlink:href="http://dx.doi.org/elife/10.7554/eLife.00065.008";>1CRN</ext-link>
>>      </alternatives>
>> </chem-struct-wrap>
>>
>> Has anyone any experience? What am I doing wrong here (I always start
>> from the assumption that I am doing something wrong)
>>
>> - Ian
>
>
>
> --
> Wendell Piez | http://www.wendellpiez.com
> XML | XSLT | electronic publishing
> Eat Your Vegetables
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