[jats-list] Linking to Accession Numbers and other Database links

["Haber, David dhaber@xxxxxxxxxx" <jats-list-service@xxxxxxxxxxxxxxxxxxxxxx>]

Hi,

For the past few years, we have been attempting to link to various different
accession number database (pdb, nucleotide, eupath, etc.) using JATs 1.1
(journal publishing). These links are found both in the PDF and HTML when the
XML is approved for delivery, which means we are including tagging and linking
early in the production process. We have tried two different ways of tagging
these numbers.

Method 1

Using an @ext-link-type, which would hold the database. For example:

 <ext-link ext-link-type="DDBJ/EMBL/GenBank"
          xlink:href="EU008541">EU008541</ext-link>]

This works well except that we make multiple deliveries to different vendors,
and each vendor uses its own ext-link-type to construct the html links. So,
for example GenBank could be "gen" for one vendor and "DDBJ/EMBL/GenBank".
What this means that links that may work on one platform, and then fail on
another.

Method 2

Using an @ext-link-type that is set equal to "uri" and points directly to a
specific website. For example:
<ext-link ext-link-type="uri"
xlink:href="https://www.ncbi.nlm.nih.gov/nuccore/MWKW00000000";>MWKW00000000</
ext-link>

Although this keeps the links functional across vendors in the short-term, as
organizations merge and databases move to new platforms, links will die over
time.

So what we were wondering if others had experience working around this sort of
issue?

Ideally, we would include both the database name and the hard link so we would
have a record of both so that content housed by different vendors would not
have dead links, while at the same time, allowing us to maintain a record of
the specific database name in case it was swallowed by another organization.

But that does not seem possible in JATS right now (I believe we tried some
sort of nested specific use tagging). Anybody have other ideas?

Thanks.

David