[tdwg-guid] Embedding LSID links within Publications

Richard Pyle deepreef at bishopmuseum.org
Fri Nov 30 13:38:47 CET 2007

Thank you, Roger, for launching the next conversation I wanted to start on
this list (not to interrupt the previous conversation....but this one is
actually more pressing for me right now): 

> Would it be better to take the approach we have with LSIDs 
> where we always cite a proxied version?
> What do other people do?

As many of you already know, I'm planning to publish the description of five
new species of Chromis in Zootaxa on Jan 1 to:

- launch ZooBank
- Commemorate the 250th Anniversary of the start of Zoological Nomenclature
- Create an "exemplar" cybertaxonomy publication

I was talking this up at Bratislava, and things are still on track.  Anyone
who wants to know more about the project, let me know and I'll send a
document describing it in more detail.

For now, I'll just provide a basic synopsis: This publication will include
the first 5 zoological names proactively registered in ZooBank. As such,
there will be five ZooBank LSIDs, which I will want to include within the
publication itself (published in both paper version to comply with ICZN Code
rules; and as an online PDF version, which 99.9% of people will actually
read).  The plan is to have the PDF version marked up as much as possible,
with taXMLit & TaxonX markup files, SDD files for the character data,
ZooBank LSIDs, Images deposited in MorphBank, links to GenBank records for
Barcode sequences, links to Museum specimen databases, links to BHL for
literature cited, etc., etc.

So....this will be a document intended to show what could be possible with
all this TDWG stuff we've all be working on for all these years -- i.e., how
cybertaxonomy could/should be done in the age of the internet.

Now, the PDF file itself will be rather simple -- a standard PDF file as per
normal Zootaxa practice -- except in this document, there will be MANY
embedded links that allow point-and-click access to all sorts of online
resources -- each of which will in some way showcase TDWG and TDWG-like

A bunch of these links will be LSIDs (e.g., ZooBank LSIDs, plus maybe
others).  However, some of them may be other links (DOIs, URLs, etc.).  All
HTTP and other self-resolving links will be pretty straightforward, but I'm
not sure yet how to embed links associated with the LSIDs.

Obviously, LSIDs are not, by themselves, completely self-resolving via most
web browsers, so simply embedding the LSID as a link will not do the average
user much good.  Thus, I'm now thinking of how I can make the LSIDs
"clickable" from the PDF, to allow the cicker/user to be directed to
something meangiful.  And that has caused me to think a lot about HTTP
proxies for LSIDs.

Thus, assuming I have a ZooBank LSID that is urn:lsid:zoobank.org:act:1234,
how do I represent that as a "clickable" link?  One way to do this would be
to embed the LSID within the TDWG HTTP proxy:


However, what I'm shooting for is to have a document that can, as best as
possible, withstand the test of time, such that 250 years from now, some or
all of those embedded links will still work (I know, I know -- they won't --
but humor me....) I'm a little neverous about simply assuming that the TDWG
LSID resolver will still be around in 250 years.  Besides, 99.9% of users
will look at the returned RDF and scratch their heads.

My gut feeling is that LSIDs have a better chance of surviving the long-term
than URLs do.  And following this premise, the LSID
"urn:lsid:zoobank.org:act:1234" will only survive as long as the authority
"zoobank.org" survives (in theory), so it seems to me a slightly more
appropriate solution would be to build a custom LSID resolver at
zoobank.org, and thereby format the clickable link as:


Does this make sense to anyone?  Am I missing something fundamental here?
Is there a better way to embed clickable links to LSIDs in a PDF document?

I have a bunch of other questions to follow up with, but let's tackle this
one first.

Many thanks!!


Richard L. Pyle, PhD
Database Coordinator for Natural Sciences
  and Associate Zoologist in Ichthyology
Department of Natural Sciences, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org

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