[Taxacom] Wikispecies is not a database: part 3 (after thinkingabout it!)

[Roderic Page]

Dear Tony,

Gosh, if providing supporting evidence was a prerequisite for posting  
to TAXACOM it'd be a pretty quiet place indeed! In the absence of  
evidence, let me try misdirection and arm waving to encourage you to  
avert your eyes from what must be an unpleasant sight (here in Glasgow  
we get chilly pretty much 24/7).

1. I doubt any major biodiversity informatics project is using a key- 
value database, but that probably reflects a degree of conservatism.  
For examples of experiments using key-value databases in  
bioinformatics, see http://tinyurl.com/okq7m5 and http://tinyurl.com/ce92qs 
  .

My sense is that big social network sites, such as FaceBook, Digg,  
Last.fm are all using some form of key-value databases (see http://www.metabrew.com/article/anti-rdbms-a-list-of-distributed-key-value-stores/ 
  ). And if we think of linked data (AKA semantic web), then triple  
stores are key-value databases.

2. Many people use relational databases, but I'd suggest they use them  
primarily for persistent storage rather than for things such as  
referential integrity. For example, Catalogue of Life uses MySQL but  
has no foreign keys, nor does it use the MySQL database engine that  
supports referential integrity.

3.  Referential integrity won't ensure all the kinds of integrity we  
care about, such as whether a classification is a tree. I discovered  
this the hard way when I first started playing with the ITIS database  
(which does have foreign keys).

Regards

Rod


On 15 Aug 2009, at 22:12, <Tony.Rees at csiro.au> <Tony.Rees at csiro.au>  
wrote:

> Dear Rod,
>
> I note we have not exactly been overwhelmed with evidence supporting  
> your claim. Methinks the emperor may be feeling a little chilly in  
> the evenings.
>
> See http://www.ffrf.org/awards/emperor/ or elsewhere...
>
> Regards - Tony
>
> ________________________________________
>
> -----Original Message-----
> From: Tony.Rees at csiro.au [mailto:Tony.Rees at csiro.au]
> Sent: 14 August 2009 06:40
> To: r.page at bio.gla.ac.uk
> Cc: Mike Sadka; taxacom at mailman.nhm.ku.edu
> Subject: RE: [Taxacom] Wikispecies is not a database: part 3 (after
> thinkingabout it!)
>
> Rod Page wrote...
>
> <snip>
>
> 1. The notion of a database espoused by Tony and Mike (i.e.,
> relational databases with tables with columns and rows) is but one
> view of databases, and a view some might say is old fashioned (key-
> value databases are the new hotness, there is a generation of
> programmers emerging for whom relational databases seem as relevant as
> FORTRAN).
>
> </snip>
>
> Maybe ... but tell me this: is there a single major database-driven
> biodiversity informatics provider that is NOT using a "conventional"
> relational database? My suspicion is that you are talking [b]leading
> edge here (if not vapourware) in the present context...
>
> Just my 2 cents...
>
> Tony
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>
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>
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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
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Blog: http://iphylo.blogspot.com
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html