Comments for JATS standing committee

[Klortho]

While working on the paper, I found a couple of areas where I think the JATS tag library (documentation) could be improved. Most were pretty minor, and I've gone ahead and made those comments myself (568, 569, 570).

Here are some others that I'd like to submit on behalf of the group, but might need a little bit of discussion. Please give thumbs up or thumbs down, or suggest changes.

Comment D - Suggestions for the @assigning-authority page.

In this page: http://jats.nlm.nih.gov/publishing/tag-library/1.1d2/attribute/assigning-authority.html.

When “GenBank” and “PDB” appear in quotes, they should be lowercase --
isn't it an established convention that these attribute values should be lowercase?
In this page, the values are given in monospace font, implying that they are the actual
values that would appear in XML.

Also, the last sentence of the remarks says, "but was assigned to <ext-link> to handle
those rare cases where an external link, which is a link by definition, codes an
identifier, such as a DOI." This seems to imply that it's okay to use <ext-link> to
tag a DOI, independent of where that appears. But, isn't it true that, inside citations,
it's always better to use <pub-id> for any identifier, including DOI?

We'd like to suggest rewording this to make it clear that this covers the case where
<ext-link> must be used for an identifier because the content model doesn't allow for
<pub-id>. Something like this:

The attribute makes more semantic sense for a publication identifier, but was assigned
to <ext-link> to handle cases of external links that appear in places in
the document where <pub-id> is not allowed, and that code identifiers, such
as, for example, DOIs.

Comment E - Add some info about @assigning-authority to the @pub-id-type and @ext-link-type pages

Refer to comment #538.

We'd like to suggest to add some verbiage to both
@pub-id-type and
@ext-link-type
pages to include information about the assigning-authority attribute. The new text should
reflect the Standing Committee recommendations from that comment.

Comment F - Example for @publication-type

The second example for @publication-type
(http://jats.nlm.nih.gov/publishing/tag-library/1.1d2/attribute/publication-type.html) is:

<mixed-citation publication-type="data">Di Stefano B, Collombet S, Graf T. 
  <source>Figshare</source>
  <ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.6084/m9.figshare.939408">
    http://dx.doi.org/10.6084/m9.figshare.939408</ext-link> 
  (<year iso-8601-date="2014">2014</year>).</mixed-citation>

Wouldn't it be better if the DOI were given with the <pub-id> element? We'd like to suggest
changing this to:

<mixed-citation publication-type="data">Di Stefano B, Collombet S, Graf T. 
  <source>Figshare</source>
  <pub-id pub-id-type="doi" 
    assigning-authority="figshare">10.6084/m9.figshare.939408</pub-id> 
  (<year iso-8601-date="2014">2014</year>).</mixed-citation>