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

[Wendell Piez <wapiez@xxxxxxxxxxxxxxx>]

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=alternatives

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
>



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