[Tdwg-guid] Zoobank LSID Service
peter.hollas at thomson.com
peter.hollas at thomson.com
Fri Sep 22 15:13:31 CEST 2006
Rod and Sally,
Thanks for your posts, they are very helpful!
I agree that for ZooBank it's probably best to just return metadata
instead of data, as at the moment we don't have any useful such as
holotype photos. Indeed I thought that we could just link to them using
an RDF resource anyway.
Our decision to go with TCS/RDF was largely based on the flexibility it
offers. Often we don't have any information about a name other than the
name itself and classification (such as a higher taxa like "animalia").
TCS doesn't impose restrictions on which fields must be included, and
seems to fit much better to the datasets we have. I'm sure that we'll be
including Dublic Core where possible too.
Once I get something up and running I'll post some example endpoints for
From: tdwg-guid-bounces at mailman.nhm.ku.edu
[mailto:tdwg-guid-bounces at mailman.nhm.ku.edu] On Behalf Of Roderic Page
Sent: 22 September 2006 13:18
To: <tdwg-guid at mailman.nhm.ku.edu> <tdwg-guid at mailman.nhm.ku.edu>
Subject: Re: [Tdwg-guid] Zoobank LSID Service
Here are some thoughts.
On 22 Sep 2006, at 11:42, <peter.hollas at thomson.com> wrote:
> Hi everyone,
> I am in the process of putting together the LSID service component of
> Zoobank.org, after a few initial hiccups and difficulties I have a
> service up and running in the development environment.
> Now I have arrived at the contentious issue of what data/metadata to
> return and in which flavour.
> I have a few questions...
> 1. What format should I return the metadata response in? From
> discussions with Roger it seems appropriate to go with RDF/TCS for the
> metadata reponse. Would this be a good way to go, and does anyone have
> any static examples of such a response?
I think TCS is a bit limited as it currently stands. For example, I'd
strongly encourage linking to publications via GUIDs where ever
possible, including DOIs. Including bibliographic information simply as
text seems retrograde to me. This is particularly an issue for ZooBank,
because you potentially could serve LSIDs for all the zoological
literature indexed in Zoological Record (as well as DOIs where ever
they have been assigned).
> 2. If a Data service were implemented, should the response simply be
> LSID or the taxon name as we don't currently hold any holotype photos
I'm not sure you have any "data" as such. I would treat names and/or
concepts as metadata. If you wanted to include other items, such as
publications or images, then I would include these by linking them in
the metadata, using rdf:resource attributes. Let's say you have a tag
"holotypeImage" (I'm not advocating you have such a tag), then
<holotypeImage rdf:resource="urn:lsid:zoobank.org:image:156545" />
would do the trick. For an image, I think you do have data (namely the
stream of bytes corresponding to the image file, in other words, if the
image is a TIFF file the data is that file). For example, we serve
images from SID (http://sid.zoology.gla.ac.uk/) as data. To see an
example of RDF metadata for an image, try
http://lsidres.org/urn:lsid:sid.zoology.gla.ac.uk:id:2000. If you use
LSID LaunchPad, you should be able to get the actual image from this
I'm also guessing that Zoobank won't itself actually have many (any?)
holotype images, as these will be stored by other sites, so most times
you'll want to link to the database that actually curates the images.
In the same way, presumably you'd link to an external provider's
information on the holotype specimen, rather than duplicate that
This may provoke a fire storm, but I think the data/metadata
distinction is in most cases overblown.
> 2. Is there any standard scheme for LSID discovery? i.e. Would it be a
> good/bad idea to extend the LSID service to allow machine queries of
> LSIDs by taxon name rather than discovering them through the web
I think it would be a bad idea to extend LSIDs as such, but absolutely
vital to add a search interface. My vote is OpenSearch, which is
simple, open, and supported. See
for some links on this topic. You could have a simple service that
returned a list of LSIDs that matched a query. The other advantage of
OpenSearch is that you can display the search results using news feed
readers, which means you kill two birds with one stone -- a human
readable display and a computer readable format.
> Any comments and suggestions are very welcome!
> Regards, Peter.
> Peter Hollas MSc BSc(hons) (Peter.Hollas at thomson.com)
> Software Engineer / Systems Administrator
> Thomson Zoological
> Innovation Centre
> York Science Park
> YO10 5DG
> Tel: 01904-435113
> Fax: 01904-435114
> TDWG-GUID mailing list
> TDWG-GUID at mailman.nhm.ku.edu
Professor Roderic D. M. Page
Editor, Systematic Biology
Graham Kerr Building
University of Glasgow
Glasgow G12 8QP
Phone: +44 141 330 4778
Fax: +44 141 330 2792
email: r.page at bio.gla.ac.uk
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Biologists Website: http://systematicbiology.org
Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/
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Rod's rants on phyloinformatics: http://iphylo.blogspot.com
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