[tdwg-content] RDF/OWL - Please answer these questions.

Wed Nov 16 16:54:26 CET 2011

Rod,
What you have suggested (looking at known RDF providers) can and 
certainly should be done.  However, looking at the sources we already 
know about isn't going to help us discover the sources we don't know 
about.  That's what the survey is for.  Also, the list you provided is 
(as is typical for TDWG) heavy on taxonomy and light on the broad range 
of resources we want to be relating (Occurrences, Identifications, 
Locations, genes, DNA sequences, etc.).  Hopefully we can discover more 
examples of how people are modeling those things in RDF.

Steve

Roderic Page wrote:
> Dear Joel,
>
> I guess part of the problem with surveys is that they require people 
> to do work without any immediately obvious benefit to them.
>
> Couldn't many of the questions here be tackled simply by looking at 
> the RDF people are pumping out, given that it's essentially 
> self-describing?
>
> For example, harvest a record from each of the major RDF users (uBio, 
> ION, IPNI, Index Fungorum, ZooBank, CoL, WoRMS, ALA, UniProt, etc.) and:
>
> 1. build list of vocabularies used
> 2. list shared vocabularies
> 3. look for any shared identifiers
>
> One quick way to do this would be to look at the cache for 
> http://lsid.tdwg.org (assuming it has one). If tdwg.org 
> <http://tdwg.org> doesn't have a cache I have one at 
> http://darwin.zoology.gla.ac.uk/~rpage/lsid/tester/cache/ 
> <http://darwin.zoology.gla.ac.uk/%7Erpage/lsid/tester/cache/> (and 
> another one at http://bioguid.info ). This will give a good sense of 
> what is actually being used (rather than what people say is being used).
>
> Then the task is to discover what is unique to a particular project, 
> and what vocabularies are used for the same things (why oh why do we 
> have two different sets of vocabularies for taxonomic names, for 
> example?).
>
> My recent grumbles about RDF mainly concern the lack of shared 
> identifiers, which is harder to assess because you need to look at a 
> multiple records. But my guess is that very few RDF providers reuse 
> other providers' identifiers. People who aggregate may well end up 
> using lots of identifiers to cope with this, but ideally we'd want 
> taxonomic concept databases (e.g., CoL) to use nomenclator identifiers 
> for names (e.g., ION, ZooBank, IPNI, Index Fungorum), and existing 
> identifiers for literature (e.g., DOIs, PubMed). So, the question is, 
> how connected is the biodiversity data web? (not very, is the short 
> answer). It shouldn't be too hard to quantify this, and identify what 
> needs to be done to fix the problem (for example, what links could we 
> add to make the biodiversity data cloud coalesce more rapidly?).
>
> What we're seeing outside biodiversity is the growth of services that 
> say identifier x is the same as identifier y (e.g., http://sameas.org/ 
> and http://identifiers.org/), which reflects the adage that there's no 
> problem in computer science that can't be solved by adding a layer of 
> indirection. t I'd argue that this is symptomatic of a failure of to 
> reuse identifiers -- which one could also argue is a natural 
> consequence of the way the we use the web, but that' s another argument ;)
>
> Regards
>
> Rod
>
> On 16 Nov 2011, at 04:18, joel sachs wrote:
>
>> Hi Everyone,
>>
>> One of the action items out of the kick-off meeting of the new RDF/OWL
>> best practices group was a questionnaire with two purposes: i) to assess
>> people's expectations and wishes for the group; and ii) to serve as 
>> an RDF
>> audit, a partial "state of the semantic web in TDWG".
>>
>> The questionnaire is at http://code.google.com/p/tdwg-rdf/wiki/Survey
>>
>> All are encouraged to participate (especially the 20 or so people who
>> volunteered to do so at the kick-off).
>>
>> Filling out the survey myself, I realized that it can actually take a 
>> lot
>> of time to present and explain an organization's rdf . So please, 
>> don't be
>> shy about answering in parts. Take ten minutes to provide some
>> pointers now, and then return later to provide more detailed 
>> explanations.
>>
>> For the first ten people to complete the survey, I will buy beer at
>> iEvoBio 2012 (or whenever I next see you).
>>
>> Thanks!
>> Joel.
>>
>>
>> _______________________________________________
>> tdwg-content mailing list
>> tdwg-content at lists.tdwg.org <mailto:tdwg-content at lists.tdwg.org>
>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>
>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email: r.page at bio.gla.ac.uk <mailto:r.page at bio.gla.ac.uk>
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rodpage1962 at aim.com <mailto: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
>

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

postal mail address:
VU Station B 351634
Nashville, TN  37235-1634,  U.S.A.

delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235

office: 2128 Stevenson Center
phone: (615) 343-4582,  fax: (615) 343-6707
http://bioimages.vanderbilt.edu

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tdwg.org/pipermail/tdwg-content/attachments/20111116/a4f04ec0/attachment.html 