[tdwg-content] most GUIDs/URIs for names/taxon stuff not ready for prime time

Steve Baskauf steve.baskauf at vanderbilt.edu
Thu Jan 6 06:32:54 CET 2011

Well, I have continued my quest for resolvable, RDF-producing GUIDs for 
taxon/name-related stuff.  I have gotten a lot of good information from 
reading Rod Page's BMC Bioinformatics paper 
(http://dx.doi.org/10.1186/1471-2105-10-S14-S5) and from investigating 
his http://bioguid.info/ site. 

 From the standpoint of the "sec./sensu" part of a TNU/taxon concept, 
based on the recent discussion, it sounds like the DIO solution for 
publications is a good direction to go IF resolution services producing 
RDF comes into existence and IF it becomes possible to actually search 
for the DIOs of more obscure publications.  I tried using Rod's site to 
look up a journal article using the ISSN, volume, and page and the web 
interface found the DOI and generated RDF just fine.  However, an 
attempt to use the web to find the DIO of Gleason and Cronquist's Manual 
of vascular plants of Northeastern United States and adjacent Canada 
failed despite a half hour of effort (I found the UPC, the LOC call 
number, and the ISBN, but no DOI).  Maybe there just isn't a DOI for it 
but there should be a way for me to know that.  So DOIs for books and 
old journal articles are not really ready for prime time.

 From the standpoint of the "scientific name" part of a TNU/taxon 
concept, I had better luck (sort of).  Rod's "Status of biodiversity 
services" page (http://www.bioguid.info/status/) was really cool.  I saw 
resources I hadn't known about before.  I tried out several of the 
services that claimed to issue LSIDs.

Catalog of Life's LSIDs didn't work with either the 
http://www.bioguid.info/ or http://lsid.tdwg.org/ proxies with either a 
web browser or  the OpenLink RDF browser.  I only got an empty RDF 
element in response.

Index Fungorum was down.

 IPNI seemed to work.  However, I was somewhat appalled to observe that 
they seem to change the revision identifier any time that they change 
any part of the metadata.  That renders the LSID useless as a permanent 
GUID for the name and I believe is inconsistent with the design of LSIDs 
where the revision is only supposed to change if the underlying data 
itself (NOT metadata) changes.  (Catalog of Life says that they change 
the revision identifier EACH YEAR for all of their records!  That's even 
worse!)  If I'm remembering the TDWG LSID recommendations, it is not 
even recommended to use the revision part of an LSID at all in the 
biodiversity informatics context. 

ubio.org's LSIDs seemed to work properly.

[sorry - didn't try zoobank since I was looking for plants]

I don't know which (if any) of the Web sites listed on Rod's status page 
use generic HTTP URI guids (rather than LSIDs) to refer to taxon names.  
I tried out the Global Names index that Pete was mentioning.  The URI 
version of the UUIDs (e.g. 
do resolve under content negotiation, but the only useful information 
that the RDF representation seems to provide is the actual name string 
that was used to generate the UUID.  Until some other useful linked 
information is added to the RDF, there doesn't seem to be much advantage 
in pointing a semantic client to the URI over just using a string 
literal for the name. 

So the bottom line is that of the LSID services for names that I've 
tried so far, only ubio.org seems to have LSIDs for names that are 
unchanging, can work as a proxied URI,  and that produce actual useful 
RDF.  That's pretty disappointing given the apparently huge amount of 
work that's been put into building these various systems.


Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences

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