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

Thu Apr 16 16:55:20 CEST 2009

OK, here's what I think GBIF (or somebody, anybody) should do. Set up  
a proxy that handles ANY GUID, and add services such as those http://bit.ly 
  have (e.g., http://bit.ly/info/3R6apo ). Wouldn't this be cool!   
Think about it, we get resolvable apps plus potentially the killer app  
for biodiversity informatics in one.

Rod

On 15 Apr 2009, at 09:58, Eamonn O Tuama (GBIF) wrote:

> 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
> employ.
>
> 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
> process.
>
> I will inform the list once the call for participation and terms of
> reference have been released.
>
> Best regards,
>
> Éamonn
>
> _______________________________________________
> 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
>
>
>
> -----Original Message-----
> From: tdwg-tag-bounces at lists.tdwg.org
> [mailto:tdwg-tag-bounces at lists.tdwg.org] On Behalf Of
> tdwg-tag-request at lists.tdwg.org
> Sent: 11 April 2009 12:00
> To: tdwg-tag at lists.tdwg.org
> Subject: tdwg-tag Digest, Vol 36, Issue 17
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> Today's Topics:
>
>   1. FYI: SharedNames (Roger Hyam)
>   2. Re: SourceForge LSID project websites broken - role	for
> TDWG?
>      (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
> resources
>
> http://sharedname.org/page/Main_Page
>
>
>
>
> ------------------------------
>
> 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
>
> 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
> TDWG?
>
> 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
> http://validator.linkeddata.org/
>  to check whether a URI behaves as Linked Data tools expect. Sadly
> the proxied BioCol LSIDs (e.g.,
> http://biocol.org/urn:lsid:biocol.org:col:15670
>  ) 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
> http://bioguid.info/urn:lsid:indexfungorum.org:names:213649
> , which validates http://tinyurl.com/cgje5n
>
> So, my first recommendation is to ensure that a TDWG HTTP proxy passes
> http://validator.linkeddata.org/
>  . 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.
>
> Ontology
> =======
>
> 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).
>
> Service
> ======
>
> 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.
>
> Funding
> ======
>
> 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.
>
> Regards
>
> Rod
>
>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> DEEB, FBLS
> 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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---------------------------------------------------------
Roderic Page
Professor of Taxonomy
DEEB, FBLS
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