[Taxacom] ZooBank Progress

Richard Pyle deepreef at bishopmuseum.org
Sat Apr 27 14:57:54 CDT 2013

Many thanks, Francisco!

> In 2003 we applied to the German Science Foundation to do link on page
> level the Linnean names with the original sources. They allowed is to
> AnimalBase, but denied our request for a page level linking, arguing that
> old literature is not of any interest any more today...
> 10 years later you are doing exactly this and the results looks great! I
> really happy that you finally did it. This is very useful.

Good to know!  The intention of GNA is to build these cross-links very
broadly, and in a way that's very easy to access -- either by downloading a
copy of the cross-link index, or by using simple services to access it in
real time.  Back in the earliest days of ZooBank I wanted to establish a few
examples of this sort of cross-linking functionality, and one of the
cross-links I established was with AnimalBase. For example, if you go to the
record for Linnaeus 1758 (which is a bit slow to load, because there are
nearly 5000 names that are loaded for this publication), you can see the
list of icons under the ZooBank LSID for all the cross-links:
One of them is the record for AnimalBase.

What I would *love* to do is establish all the cross-links between
AnimalBase Authors, literature and names (I think you and I discussed this
once -- I believe we were on the Tube in London at the time....)  That way,
any link to BHL that is made via ZooBank, would simultaneously be made for
AnimalBase.  Thus, you could either have a copy of the cross-linked index on
your server that allows a page-link to BHL to appear on AnimalBase whenever
someone establishes one on ZooBank; or we could make a simple service on
GNUB (where the cross-links actually reside) such that your page could call
the service for a given record of yours, and get back all the cross-links to
other databases that GNUB knows about (including BHL, and others).  For
example, if you passed in your AnimalBase reference identifier "4" to this
service (as well as an indication that the "4" applies to an AnimalBase
Reference identifier), then the service would give you back something that
looks like this:

Domain:	Amphibian Species of the World References
Identifier:	2794
Link:		URL:
Domain:	AnimalBase References
Identifier:	4
Domain:	Biodiversity Heritage Library Title
Identifier:	542
Link:		http://www.biodiversitylibrary.org/bibliography/542 
Domain:	Botanicus
Identifier:	b12066783
Link:		http://www.botanicus.org/bibliography/b12066783 
Domain:	Digital Object Identifier	
Identifier:	10.5962/bhl.title.542
Link:		http://dx.doi.org/10.5962/bhl.title.542 
Domain:	Eschmeyer References	
Identifier:	2787
Domain:	FishBase - References	
Identifier:	1652
Link:		http://www.fishbase.org/References/FBRefSummary.php?id=1652 
Domain:	Gallica
Identifier:	ark:/12148/bpt6k99004c
Link:		http://gallica.bnf.fr/ark:/12148/bpt6k99004c 
Domain:	Google Books
Identifier:	yZM5AAAAcAAJ
Link:		http://books.google.com/books?id=yZM5AAAAcAAJ 
Domain:	Hymenoptera Online - References
Identifier:	978
Link:		http://hol.osu.edu/reference-full.html?id=978 
Domain:	International Plant Names Index - Publications
Identifier:	14210-2
Link:		http://www.ipni.org/ipni/idPublicationSearch.do?id=14210-2 
Domain:	Internet Archive Text Records
Identifier:	mobot31753000798865
Link:		http://archive.org/details/mobot31753000798865 
Domain:	Library of Congress Control Number
Identifier:	6017147
Link:		http://lccn.loc.gov/06017147 
Domain:	Tropicos Reference Records
Identifier:	1254
Link:		http://www.tropicos.org/Publication/1254 
Domain:	World Registry of Marine Species - Reference
Identifier:	8
Link:		http://www.marinespecies.org/aphia.php?p=sourcedetails&id=8 
Domain:	ZooBank Publication

Obviously, we could include a whole bunch of other metadata as well (such as
a link to the icon, more information about the Domain, etc.)

The nice thing is that there is no limit to the number of cross-links we can
establish using this system.  It's just a matter of building those links --
which involves a process that can be partially automated, but also involves
a lot of manual proofing.  This is where the "crowd sourcing" concept comes
into play.  

In any case, Francisco -- it' you're interested in building these crosslinks
for AnimalBase, please contact me off-list and I can describe the process
for doing this.  We have some online tools that are designed to make this
process as painless as possible (for example, Donat Agosti cross-linked all
800 journals from Hymenoptera Name Server in a few days using these tools).
This, of course, applies to anyone on Taxacom who has a dataset with
resolvable identifiers that would like to be cross-linked.  Even if you
don't have resolvable identifiers, it's still worth building the cross-links
so that your system can cross-link your records to all these other records
and build links to them from your web pages.

> 1 - Sometimes you have incorrect names in your database. How can we
> correct them?

ZooBank already allows for editing records.  There was a ZooBank Users
Policy that was circulated to this list a while ago that explains who can
edit what sorts of content. That Policy is in the final stages of
ratification, but in brief, people with self-created (unverified) user
accounts can edit their own records; verified users (someone has confirmed
that you are who you say you are) can also edit records that he or she is an
author of (even if that person didn't create the record); "Editors" can edit
all content.

> 2 - Sometimes more than 1 page represent the original source, but 2 pages,
> which need 2 separate page links. In rare cases even 3 (I know some of
> cases in Swainson 1840).

Yes, I've given this a lot of thought.  Of course, there is absolutely
nothing preventing us from linking to multiple pages -- that's easy.
However, there seems to be a general consensus among the GNA-folk that one
page should be selected as the specific page on which a name comes into
existence.  Paul Kirk: this is your cure to chime in on this topic.  

> An example with both case at once is here:
> http://zoobank.org/NomenclaturalActs/668885BB-153E-4A55-A65E-BA4EFA302618
> ZooBank says Buprestis gnita, correct would be Buprestis ignita Linnæus,
> 1758.
> Page numbers: 408, 824, both are important and should be linked.

Ah!  Good catch, and good point!  Question to Paul Kirk:  How would you deal
with this sort of situation?

For now, I added the second page link, I corrected the spelling of the name,
and I made a note about the pagination (go to the link above to see how I
dealt with it).  For now, I think we'll keep the ZooBank webpage to only
allow one page link to be made, and then I'll manage these exceptional cases
for now.  We can always update the web page interface later, if we decide
this is something that happens more often.

Here's a question for people on this list:  In such cases, should both pages
be displayed as thumbnails?  Is there an upper limit to how many pages can
be displayed for a single name?  Is there a clear policy for what situations
call for linking to multiple pages?  Should it include all pages that the
name appears on, or just ones that have nomenclatural relevance?  In the
latter case, how would "nomenclatural relevance" be defined?  These are the
kinds of questions that the community should address.  My hope/dream/vision
is that GNUB will become a resource of the taxonomic community, owned and
maintained by the taxonomic community, and perpetuated for the taxonomic
community (to paraphrase one of the more well-known former U.S. presidents).
Thus, the taxonomic community should be the ones discussing these sorts of

In any case, I'll try to find the time to make similar corrections to all
the names that appear on page 824.

> Here you can see a list with human-corrected Linnean 1758 new names:

Now, that's a link that I (and ZooBank) already knew about! (see above)

Thanks again for your very helpful feedback!


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