[tdwg-tag] SourceForge LSID project websites broken - role for TDWG?

Eamonn O Tuama (GBIF) eotuama at gbif.org
Wed Apr 15 10:58:17 CEST 2009

Hi All,

As one of the largest international organisations directly concerned with
enabling a bioinformatics infrastructure for sustained data sharing, GBIF is
very interested in exploring the possibility of becoming administrator for a
redirection/resolver domain for biodiversity GUIDs regardless of the
technologies that are ultimately deployed - whether LSIDs, DOIs, PURLS,
etc., or, perhaps more realistically, a mixture of several.

Many interesting arguments have been put forward in this sustained thread
and, after internal consultation amongst the GBIF informatics team, we think
that it is worth considering using established GBIF processes as a way to
move to the implementation phase, at the same time helping inform GBIF's
policy/strategy regarding GUIDs in general, and through GBIF, the wider
community of practitioners grappling with challenging issues around
biodiversity informatics. As mentioned previously, we will be making some
resources available to convene a dedicated task group which will provide
recommendations to GBIF on deployment of GUIDs on the GBIF network. The
terms of reference for this group will be released within a week and we
invite you to support the group either directly, by going forward for
nomination - there will be a limited number of places in the core group -,
or by participating in the broader consultation process that the group will

Our plan would be to have the group report back with their recommendations
after about four months. This is considered the minimum timeframe that will
allow meaningful engagement/consultation as feedback from the GBIF community
and others is an essential component of the recommendations drafting

I will inform the list once the call for participation and terms of
reference have been released.

Best regards,


Éamonn Ó Tuama, M.Sc., Ph.D. (eotuama at gbif.org), 
Senior Programme Officer, Inventory, Discovery, Access (IDA), 
Global Biodiversity Information Facility Secretariat, 
Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK 
Phone:  +45 3532 1494; Fax:  +45 3532 1480

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Today's Topics:

   1. FYI: SharedNames (Roger Hyam)
   2. Re: SourceForge LSID project websites broken - role	for
      (Lee Belbin)


Message: 1
Date: Fri, 10 Apr 2009 12:55:50 +0100
From: Roger Hyam <rogerhyam at mac.com>
Subject: [tdwg-tag] FYI: SharedNames
To: Technical Architecture Group mailing list
	<tdwg-tag at lists.tdwg.org>
Message-ID: <690607AB-627E-4B9B-8168-4C412F81FE68 at mac.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

You may be interested in this project to set up PURLs for biomedical  



Message: 2
Date: Sat, 11 Apr 2009 10:00:39 +1000
From: "Lee Belbin" <leebel at netspace.net.au>
Subject: Re: [tdwg-tag] SourceForge LSID project websites broken -
	role	for	TDWG?
To: "'Roderic Page'" <r.page at bio.gla.ac.uk>
Cc: 'Technical Architecture Group mailing list'
	<tdwg-tag at lists.tdwg.org>
Message-ID: <002101c9ba38$8e3c2110$aab46330$@net.au>
Content-Type: text/plain;	charset="us-ascii"

Thanks Rod. Very constructive.


Lee Belbin
TDWG Secretariat

-----Original Message-----
From: Roderic Page [mailto:r.page at bio.gla.ac.uk] 
Sent: Friday, 10 April 2009 1:30 AM
To: Lee Belbin
Cc: 'Technical Architecture Group mailing list'
Subject: Re: [tdwg-tag] SourceForge LSID project websites broken - role for

In a rare attempt at being constructive, here are a few thoughts.

LSIDs and linked data

If adoption of LSIDs proceeds, then we should make efforts to see that  
they play nicely with Linked Data efforts. For example, a HTTP  
resolver would need to support 303 redirects and content negotiation.  
This help avoid us creating our own ghetto, but still exploit whatever  
advantages LSIDs have.

Roger set up something along these lines to handle Biological  
Collections Index (BioCol) LSIDs. There is a nice tool at
  to check whether a URI behaves as Linked Data tools expect. Sadly  
the proxied BioCol LSIDs (e.g.,
  ) don't validate, but this should be easy to fix. The TDWG resolver  
similarly fails.

I've implemented a simple resolver at bioGUID that returns either raw  
RDF or a clumsily formatted HTML version of the XML, but which passes  
the http://validator.linkeddata.org tests. An example URI is
, which validates http://tinyurl.com/cgje5n

So, my first recommendation is to ensure that a TDWG HTTP proxy passes
  . This means we can play with the Semantic Web crowd with LSIDs.

Note that getting HTTP URIs to play with Linked Data is not trivial,  
so whatever technology we adopt we'll need clear guidelines as to how  
to use it. As an aside bioGUID can make DOIs play nice as well (they  
don't by default), and Kinglsey Idehen http://www.openlinksw.com/blog/ 
~kidehen/ of OpenLink Software is supporting LSIDs in the Linked Data  
tools he's developing.


As part of my experiment to wikify taxonomic names, literature, etc.,  
I've been playing with the TDWG vocabularies. I've a few grizzles, but  
in general they've been really useful, and I think these will be key  
(as Donald and Lee have emphasised).


Ironically one of the examples Lee listed when defending the TDWG's  
resolver (urn:lsid:gdb.org:GenomicSegment:GDB132938) seems to have  
disappeared (I think TDWG has a cached copy). This raises the ongoing  
problem of service availability. TDWG's resolver could help here, in  
that could be used to generate reports on service quality and notify  
providers when something's wrong. Whatever GUID technology adopted  
this will be an issue, and the challenge is to build tools and  
mechanisms to manage this.


I've nothing useful to say here, other than to suggest that clearly  
the integration of biodiversity data sales pitch hasn't (yet?)  
succeeded. I think us techies get it, but we've not made that vision  
real or compelling. If we had, I think we'd have institutions falling  
over themselves to ensure the infrastructure exists and persists.  
Naive, I know, but we could ask why we haven't managed to convince  
those with the purse strings that this stuff matters.

One quick and dirty way that might help is if the TDWG LSID resolver  
stored all the metadata in the LSIDs it resolves in a triple store and  
exposes a SPARQL query interface to that metadata. We could then start  
to look for interesting links between data.



Roderic Page
Professor of Taxonomy
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK

Email: r.page at bio.gla.ac.uk
Tel: +44 141 330 4778
Fax: +44 141 330 2792
AIM: rodpage1962 at aim.com
Facebook: http://www.facebook.com/profile.php?id=1112517192
Twitter: http://twitter.com/rdmpage
Blog: http://iphylo.blogspot.com
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html


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