[Taxacom] Data query

Richard Pyle deepreef at bishopmuseum.org
Tue Jun 25 15:48:57 CDT 2013

Yes, Stephen has just explained, in more complicated terms, what GNUB does
using Identifier Domains!


[CouldnÂ’t resist



From: Stephen Thorpe [mailto:stephen_thorpe at yahoo.co.nz] 
Sent: Tuesday, June 25, 2013 10:23 AM
To: Dr Brian Taylor; Richard Pyle; Tony.Rees at csiro.au; Bob Mesibov
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] Data query


Hi Brian,

That is a slightly different problem, which is fairly easily solved, i.e.,
by using a template instead of links hard written into every page. Then, if
things change, you just change the template, and all the pages follow
automatically. This is what Wikispecies does (mostly). The bigger issue
still to me is why you should have to manually find, for every name, the
corresponding arbitrary identifier in the database which you want to link
to. If you could link using the actual taxon name, then the links could be
generated automatically at your end ...




From: Dr Brian Taylor <dr.brian.taylor at ntlworld.com>
To: Richard Pyle <deepreef at bishopmuseum.org>; 'Stephen Thorpe'
<stephen_thorpe at yahoo.co.nz>; Tony.Rees at csiro.au; Bob Mesibov
<mesibov at southcom.com.au> 
Cc: taxacom at mailman.nhm.ku.edu 
Sent: Tuesday, 25 June 2013 10:39 PM
Subject: Re: [Taxacom] Data query

A little point but critical to the ongoing discussion.  On each taxonomic
page of my website "Ants of Africa", I painstakingly gave a link to the
Hymenoptera Name Server.

The link for several years has been on

Suddenly the location (server, I assume) has changed to


So all my 2000 or so pages have a non-operational link.

So, I might argue, what was the point of my spending time giving links?


On 25/06/2013 07:55, "Richard Pyle" <deepreef at bishopmuseum.org> wrote:

> I slogged through this discussion, and found many things I agreed with,
> many things I disagreed with, from all of the major contributors to the
> thread.  However, I did want to call attention to one point raised by
> several different people, that I STRONGLY agree with, and that I would
> to see amplified repeatedly  and very loudly:
> Tony Rees said it this way:
>> What we really need to aspire to is a network of linked systems
>> whereby changes and new content entered once can propagate
>> automatically elsewhere as needed rather than requiring manual input
> And again this way:
>> Perhaps it is time to move the discussion on to related matters
>> such as how to possibly chain these systems together in the future
>> so that updates may more readily flow from the point of entry to
>> potentially multiple points of re-use...
> And then Stephen followed with this gem:
>> Well, one thing that stands out here is that the only honourable
>> thing to do, but is rarely done, is to provide links from a taxon
>> page in one project to the corresponding taxon pages in other
>> projects which may have better and more complete data on
>> that taxon, so as to give the user a chance of finding what
>> they want to know even if the project they have visited
>> doesn't have the data. Conversely, doing so will also highlight
>> how good the visited project is, if the linked projects have
>> less data, so it is win-win, really!
> YES!  YES! YES!!
> About two years ago, it became very clear to me that a small feature I
> to my Taxonomer database back in the 1990's, and included in the first
> version of ZooBank back in 2008 (cross-linking identifiers) will almost
> certainly come to be known as one of the most important (if not *the* most
> important) contributions from GNUB/ZooBank to our community; which is a
> generic mechanism for cross-linking records to each other.
> It's an incredibly simple data structure, and is now built in to the
> website for Authors, References and Taxon Names (but it can easily be
> applied to any record in any table of the database).  When you're logged
> to ZooBank and have access to a particular record for editing, you'll see
> small link next to the "Edit" button for "add external identifier". Click
> this and you get a pop-up form that lets you create cross-links to other
> external databases.  Just for fun, I went to my old trusty example:
> http://zoobank.org/8BDC0735-FEA4-4298-83FA-D04F67C3FBEC
> and added a link to the Wikispecies page (Identifier Doimain =
> Page"; Identifier = "Chromis_abyssus"), and voilĂ !  A link from the
> record to the WikiSpecies page is born!
> Now... a few caveats...  there is a buglet that prevents the closing of
> pop-up form after you create such a link (just refresh the page to make it
> go away).  Also, it's only visible if you have edit access to a particular
> record in ZooBank.  Once we fix the buglet and beef up the protection code
> (to minimize bogus entries), we'll make this feature available to anyone
> with a login account for applying to any record (whether or not the user
> edit access to the record).
> Our plan is to develop a generic service around this cross-linking
> such that anyone can harvest the cross-links for any record, and display
> them on their local page.  The REALLY cool part is this:  Once I link the
> ZooBank record to the Wikispecies page, the WoRMS page, the FishBase page,
> and so on....I've not only linked ZooBank to these other sources, we've
> linked these other sources TO EACH OTHER. In the example I gave above
> (Chromis abyssus), I didn't just link ZooBank to WikiSpecies; I also
> WikiSpecies to BOLD, Bill Eschmeyer's Catalog of Fishes, Digimorph, EoL,
> FishBase, MorphBank, NCBI/GenBank, and WoRMS.  And, I've linked each of
> these databases to WikiSpecies (as well as each other).  The idea for the
> generic service would be for WoRMS to fire off its identifier (in this
> 345844) to the service and get back the links to all the other databases.
> As Stephen says, the honorable data managers will see this as a no-brainer
> win-win.
> I'll post more on this service once we get it functional.
> Aloha,
> Rich
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