[tdwg-guid] Embedding LSID links within Publications

Roderic Page r.page at bio.gla.ac.uk
Fri Nov 30 23:55:42 CET 2007

Dear Rich,

There are several issues here.

Personally I think we need to look way beyond the lifetime of LSIDs  
and HTTP. One reason digital library types like DOIs and Handles is  
that they serve as GUIDs independently of any protocol. They are  
printed in journal articles as bare identifiers, in the same way as  
ISSNs or ISBNs. Hence tying the LSID to a HTTP resolver strikes me as  
the quickest way to build in obsolescence.

I suspect that a betting person would put money on the paper version  
of your article outlasting any digital representation you create...

One approach is to do something like COinS (ContextObjects in Spans,  
http://ocoins.info/ ). This embeds citation metadata in HTML pages  
using OpenURL. However, it doesn't specify the OpenURL resolver. The  
user supplies this, for examples, there is a Firefox extension that  
rewrites COinS as clickable links (http://www.openly.com/ 
openurlref/ ). Here's an example of a COinS:

<span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info% 

The OpenURL syntax is horrible, but I hope you get the idea. Hence,  
what if the LSID was embedded like this:

<span class="lsid" title="urn:lsid:zoobank.org:act:1A66BAE9-9B37-4C73- 

This avoids the need to specify a resolver (at the cost of needing a  
tool to make the links clickable). However, it may help ensure long  
term survival of the identifier.

I think the focus on PDFs is misplaced. This is a binary format that  
may well be unintelligible in 10-20 years time. XML makes more sense.  
If the PDF has clickable URLs that work today, that's fine as a demo,  
but long term this stuff all needs to move to XML.

Lastly, why not simply do something like this in the text of the paper.

Chromis xus sp nov

---text goes here---

I suspect you will need to show the identifier for people to grasp  
what is going on. Yes, ultimately the GUIDs will disappear, but it  
seems that at this stage you want to show them off. You might regret  
UUIDs now ;-)



On 30 Nov 2007, at 22:07, Richard Pyle wrote:

> Ricardo's email prompted me to launch into the next round of questions
> concerning the implementation of LSIDs in real-world taxonomy.  His  
> comment
> was this:
>> In short, the document
>> recommends that you use the LSID in its pure form as
>> the link text and the proxy version as the link URL.
> I have long believed that GUIDs (and especially LSIDs) were meant  
> for use by
> computers, not humans.  As such, I am generally opposed to the idea of
> printing or displaying LSIDs in a way intended for humans to read  
> them.
> They should be hidden, behind the scenes, enebling the cross-links.
> In the case of the five new species of Chromis, I think it's  
> appropriate to
> display the ID's in the human-readable parts of the document,  
> because these
> are technically the ZooBank Registration IDs for the nomencatural  
> acts.
> However, here is where the first question comes in.  As I've described
> previously, my strategy with ZooBank is to assign UUIDs to the  
> records, and
> then use the UUIDs as the "ObjectID" part of the LSID, such as:
> urn:lsid:zoobank.org:act:20889795-7EC7-42F3-A4C3-D1D97704A609
> The idea behind using UUIDs is to "hedge my bets" agaisnt the possible
> demise of the LSID standard.  In this sense, the LSID syntaxt is  
> really just
> a wrapper representing a resolution protocol for the "real" GUID,  
> which in
> this case is the UUID.
> So....if I am to print/display the "ZooBank Registration ID", what  
> should it
> be?  The full LSID (which is placing a bet that LSIDs will still be
> recognizable/resolvable 250 years from now); or just the UUID  
> (which is the
> "true" GUID for the ZooBank record, independent of the mechanism  
> used to
> resolve it)?
> Let's assume, based on the other thread discussion, that I will be  
> wrapping
> the LSID within an HTTP proxy to make it clickable for the URL part  
> of the
> hyperlink.  The question is, what do I show the human reader?   
> Options are:
> <a
> href="http://zoobank.org/urn:lsid:zoobank.org:act: 
> 20889795-7EC7-42F3-A4C3-D1
> D97704A609">20889795-7EC7-42F3-A4C3-D1D97704A609</a>
> OR:
> <a
> href="http://zoobank.org/urn:lsid:zoobank.org:act: 
> 20889795-7EC7-42F3-A4C3-D1
> D97704A609">urn:lsid:zoobank.org:act:20889795-7EC7-42F3-A4C3- 
> D1D97704A609</a
>> <a href="http://lsids.sourceforge.net/"><img
> src="http://zoobank.bishopmuseum.org/images/lsidlogo.jpg"></a>
> ...the main difference being whether the human sees the "ZooBank
> Registration ID" (UUID), or sees the "ZooBank LSID" (=ZooBank  
> RegistrationID
> wrapped in LSID syntax)?
> I'm torn on this -- part of me wants to keep it to just the UUID  
> (which
> makes the publication look slightly less stupid 250 years from now,  
> in the
> event that LSIDs do not last more than a few years); but the other  
> part of
> me wants to trumpet the notion of LSIDs to support the general TDWG  
> cause,
> and hence set an example of representing ZooBank Ids as LSIDs,  
> rather than
> stripped-down UUIDs.
> Thoughts?
> This also sets me up for the next related question:
> Though I can see the justification for displaying, in human  
> readable form,
> an LSID/UUID that serves as a "ZooBank Registration ID" within the  
> context
> of the actual pblication that "creates" the identified nomenclatural
> act....I'm not expecially inclined to sprinkle such cumbersome  
> LSIDs in
> human-readible form throughout the entire document.
> For example, consider this sentence from the Introduction of the  
> Chromis MS:
> "The pomacentrid genus Chromis Cuvier 1814 (type species Sparus  
> chromis
> Linnaeus 1758) is the largest genus of the family, with 86 valid  
> species."
> One way to mark this up would be as follows:
> "The pomacentrid genus <i><a
> href="http://zoobank.org/ 
> urn:lsid:zoobank.org:act:B8F9F80D-5798-4342-810D-D8
> 274164F8F1">Chromis</a></i> Cuvier 1814 (type species <i><a
> href="http://zoobank.org/urn:lsid:zoobank.org:act: 
> 1A66BAE9-9B37-4C73-A560-BF
> 63D0345F04">Sparus</a></i> <i><a
> href="http://zoobank.org/urn:lsid:zoobank.org:act: 
> 8F966156-68DE-4147-953D-74
> E1B3724F5F">chromis</a></i> Linnaeus 1758) is the largest genus of the
> family, with 86 valid species."
> This would appear to the user exactly the same as the above quote,  
> except
> the three taxon names would be clickable links to the repsective  
> ZooBank
> records.
> The alternative would be to do something like this:
> "The pomacentrid genus <i>Chromis</i> [<a
> href="http://zoobank.org/ 
> urn:lsid:zoobank.org:act:B8F9F80D-5798-4342-810D-D8
> 274164F8F1">ZooBank: B8F9F80D-5798-4342-810D-D8274164F8F1</a>]  
> Cuvier 1814
> (type species <i>Sparus</i> [<a
> href="http://zoobank.org/urn:lsid:zoobank.org:act: 
> 1A66BAE9-9B37-4C73-A560-BF
> 63D0345F04">ZooBank: 1A66BAE9-9B37-4C73-A560-BF63D0345F04</a>]
> <i>chromis</i> [<a
> href="http://zoobank.org/urn:lsid:zoobank.org:act: 
> 8F966156-68DE-4147-953D-74
> E1B3724F5F">ZooBank: 8F966156-68DE-4147-953D-74E1B3724F5F</a>]  
> Linnaeus
> 1758) is the largest genus of the family, with 86 valid species."
> To the human reader, this would appear as follows:
> "The pomacentrid genus Chromis [ZooBank:
> B8F9F80D-5798-4342-810D-D8274164F8F1] Cuvier 1814 (type species Sparus
> [ZooBank: 1A66BAE9-9B37-4C73-A560-BF63D0345F04] chromis [ZooBank:
> 8F966156-68DE-4147-953D-74E1B3724F5F] Linnaeus 1758) is the largest  
> genus of
> the family, with 86 valid species."
> Kinda klunky, if you ask me -- even moreso if the full LSID syntax is
> included -- and more klunky still if I add the little "LSID" icon  
> logos to
> each one.
> My preference would be to go with the first option, and simply make  
> the text
> of the names the clickable part, and have the UUID/LSID hidden from  
> the user
> (but still visible to the computer) via the embedded HTTP proxy link.
> But if I go that route this leads to another problem:
> Because ICZN still requires paper-based publication for the new  
> names to be
> available, there will also be a paper version published concurrently
> (standatd Zootaxa practice).  If the GUIDs are not visible to the  
> human in
> the PDF, they will not be visible at all in the paper copy.
> So....I'm now considering adding an extra section to the published  
> version
> of the article (both paper and PDF), that comes after the  
> "Literature Cited"
> section, and represents a series of "end notes", indexed from the  
> text via
> superscript numbers, that display in human readible form the  
> complete URL of
> the link.
> For example, something along the lines of the following:
> "The pomacentrid genus <i>Chromis </i> <sup><a
> href="http://zoobank.org/ 
> urn:lsid:zoobank.org:act:B8F9F80D-5798-4342-810D-D8
> 274164F8F1">1</a></sup> Cuvier 1814 (type species <i>Sparus</i>  
> <sup><a
> href="http://zoobank.org/urn:lsid:zoobank.org:act: 
> 1A66BAE9-9B37-4C73-A560-BF
> 63D0345F04">2</a></sup> <i>chromis</i> <sup><a
> href="http://zoobank.org/urn:lsid:zoobank.org:act: 
> 8F966156-68DE-4147-953D-74
> E1B3724F5F">chromis</a></sup> Linnaeus 1758) is the largest genus  
> of the
> family, with 86 valid species."
> Which would appear to the user simply as:
> "The pomacentrid genus Chromis^1 Cuvier 1814 (type species Sparus^2
> chromis^3 Linnaeus 1758) is the largest genus of the family, with  
> 86 valid
> species."
> (where "^" indicates superscripted character)
> The "1", "2" and "3" would be the clickale links to the online  
> resources,
> but at the end of the article there would ba a section called "Linked
> Resources" or something, along the lines of the following:
> Linked Resources:
> 1.
> http://zoobank.org/urn:lsid:zoobank.org:act:B8F9F80D-5798-4342-810D- 
> D8274164
> F8F1
> 2.
> http://zoobank.org/urn:lsid:zoobank.org:act:1A66BAE9-9B37-4C73-A560- 
> BF63D034
> 5F04
> 3.
> http://zoobank.org/urn:lsid:zoobank.org:act: 
> 8F966156-68DE-4147-953D-74E1B372
> 4F5F
> That way, the reader of the paper copy of the publication could, if  
> they
> wanted to, manually type the various links into a browser.
> This seems like the best compromise solution to me; but there is one
> problem:
> If the superscript "1", "2", "3" etc are the clicable links, that  
> makes for
> a very small tarket.  People not so dexterous with the mouse  
> control might
> be annoyed trying to click on the tiny little number.  So I'm  
> thinking maybe
> a little Icon similar to the LSID icon
> (http://zoobank.bishopmuseum.org/images/lsidlogo.jpg), except  
> numbered.
> That would make for an easier mouse target to click on, and also would
> distinguish it from other superscript numbers (footnotes, etc.).
> Alternatively, I could simply make the superscript hyperlinked text  
> be:
> "Link: 1", "Link: 2" and so on.
> Well... That's probably enough for now.  I still want to respond to  
> Chuck's
> email, but I have to get to a meeting now.
> Aloha,
> Rich
> P.S. Later today I'll create a web version of this, so make it a  
> bit more
> intelligible.
> 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
> http://hbs.bishopmuseum.org/staff/pylerichard.html
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