[tdwg-guid] Embedding LSID links within Publications

Richard Pyle deepreef at bishopmuseum.org
Mon Dec 3 14:29:54 CET 2007

Many thanks, Robert! (And thanks also for sending the PDFs).
Besides the email addresses, the external links (to publications and
datasets) are DOIs, and within the PDF itself, are represented as clickable
links via the HTTP proxy http://dx.doi.org/ -- essentially exactly how I
would plan to embed clickable links to LSIDs.
Many thanks again!


From: tdwg-guid-bounces at lists.tdwg.org
[mailto:tdwg-guid-bounces at lists.tdwg.org] On Behalf Of Robert Huber
Sent: Monday, December 03, 2007 12:06 AM
To: tdwg-guid at lists.tdwg.org
Subject: Re: [tdwg-guid] Embedding LSID links within Publications

Dear all,

Maybe this could also help in this discussion: here is an example how data
sets are cited in an existing publication:

best regards,

2007/12/3, Robert Huber <rhuber at wdc-mare.org>: 

Dear all,

The usage of LSIDs and especially citing would be much easier if the usage
of metadata would have been more precisely defined.
Now, the recommendations allow the TDWGOntology as well as other 'well known
vocabularies' = chaos. 

We should at least decide on a small set of _obligatory_ metadata elements,
for example some dublin core fields?
For new taxon names the citation of LSIDs would be much easier, because this
metadata could then be placed somewhere in the references section such as
Pyle, R, 2007: TaxonXY, ...some other metadata..., TheLSID 

best regards, Robert

2007/12/3, Richard Pyle <  <mailto:deepreef at bishopmuseum.org>
deepreef at bishopmuseum.org>: 

Let's distinguish between the two separate places where there may be LSIDs
in the document:

1) Underneath the header for each of the five new species described in the 

2) Embedded within clicakble links scattered through the introduction, 
discussion, etc. (what I call "prose"), which are not themselves registered
nomenclatural acts; but are simply "links of convenince" to allow someone
reading the PDF to simply click on a highlighted word or symbol and be 
redirected (presumably through a web browser) to some sort of online
resource (image, video, SDD document, whatever...)

As for #1, I believe that the LSID should be displayed to the human reader
in full, and probably should *also* be a clickable link directly to the 
ZooBank record for that LSID. Displaying the full LSID here is appropriate,
because the publication itself represents the Code-governed creation event
behind that LSID. It also does not interrupt the "flow", because there is no

"flow" to the header of a new species account.

As for #2, there is "flow" here, because people are reading a normal
paragraph or text. Offsetting a clickable word in blue or underlined or with

some sort of Mouseover highlighting does not interrupt the flow -- but
inserting an LSID in parentheses within the text does interrupt the flow of

So....in this context, my current preferred way of displaying it in the 
formatted PDF is:

1) Show the LSID for the 5 new species names, as part of header for the new
species treatment (just like listing a holotype, etc.) The only question
here is whether I show only the UUID, or do I show the UUID "wrapped" within

the LSID syntax.  In order to help promote LSIDs (in keeping with the
TDWG/GBIF agenda at the moment), I'm leaning towards displaying the complete
LSID; but perhaps mentioning in the methods that the ZooBank Registration ID

is the UUID, but they are shown formatted with complete LSID resolving

2) Do not show the LSID for other clickable links within the "prose" of the
document, but embed those LSIDs in the (hidden) link URL. I'm still not sure

whether the word/name itself will be the clickable "thing", or whether I'll
add some sort of standard symbol analagous to a footnote number that the
user would click.

3) Display full URLs in an "Appendix" sort of section, at the end of the 
rest of the article, so they can be seen via the paper-printed version.

Does this make sense?  Or am I stoned...? :-)


> -----Original Message-----
> From: Paul Kirk [mailto: p.kirk at cabi.org <mailto:p.kirk at cabi.org> ]
> Sent: Sunday, December 02, 2007 10:39 PM
> To: Richard Pyle; Gregor Hagedorn; tdwg-guid at lists.tdwg.org
> Subject: RE: [tdwg-guid] Embedding LSID links within Publications 
> But Rich, the prose you refer to are the ... 'this is a
> really neat fish, just look at the video' discussion rather
> than the techie ICZN stuff ... Aus bus sp. nov ... LSID,
> Latin daignosis, holotype etc ... 
> which, at the risk of being stoned (having rocks thrown at me
> ... ;-) ... I mean) as an heretic, could perhaps be usefully
> lost in an appendix, and thus disposed would not interrupt the flow.
> Paul
> -----Original Message-----
> From: tdwg-guid-bounces at lists.tdwg.org
<mailto:tdwg-guid-bounces at lists.tdwg.org> 
> [mailto:  <mailto:tdwg-guid-bounces at lists.tdwg.org>
tdwg-guid-bounces at lists.tdwg.org] On Behalf Of Richard Pyle
> Sent: 01 December 2007 00:48
> To: 'Gregor Hagedorn'; tdwg-guid at lists.tdwg.org
> Subject: RE: [tdwg-guid] Embedding LSID links within Publications 
> Thanks, Gregor -- this is very helpful, and I pretty much agree.
> > In short: allow any normal publishing practice, consider it as a
> > special form of reference (like doi or ISBN) and observe the normal 
> > publishing practices of citing, especially avoid
> redundancies. Rich, I
> > think you are too much thinking about general rules how to always
> > handle it - but publishing practice for good reasons does 
> almost the
> > opposite (once and never again...).
> Fair enough....and I'm sure I am over-thinking this.
> However, I still see problems with your proposed approached,
> in that I do not want big, cumbersome LSIDs (even once) 
> interrupting the flow of prose.
> I think I still favor the idea of a superscript indicator
> that can be easily ignored, easily clicked, and easily used
> to refer to a printed (not hidden) set of hyperlinks 
> following the "Literature Cited" section.
> I think this strikes a resonable compromise/balance between
> how things are done in the publishing world, and how *I*
> think things *should* be done in the publishing world.... 
> :-)
> Rich
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Dr. Robert Huber,

WDC-MARE / PANGAEA - www.pangaea.de
Stratigraphy.net - www.stratigraphy.net
MARUM - Institute for Marine Environmental Sciences (location) 
University Bremen 
Leobener Strasse
POP 330 440
28359 Bremen
Phone ++49 421 218-65593, Fax ++49 421 218-65505
e-mail rhuber at wdc-mare.org 

Dr. Robert Huber,

WDC-MARE / PANGAEA - www.pangaea.de
Stratigraphy.net - www.stratigraphy.net
MARUM - Institute for Marine Environmental Sciences (location)
University Bremen
Leobener Strasse
POP 330 440
28359 Bremen
Phone ++49 421 218-65593, Fax ++49 421 218-65505
e-mail rhuber at wdc-mare.org 

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