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

Sat Aug 8 14:00:31 CDT 2009

HI!

I'll join "first time commenting on TAXACOM" tread started by Mike although
Richard's last comments made me scrap half of the message so that I don't
repeat some of the points word for word. 

This leaves me only with small observation on this topic. I am also more of
a techie, mostly of the time listening an learning from this forum.

> I believe it is vital to distinguish between databases and the
> applications that allow users to interact with them.  Databases are
> simply storage for data.  In almost all cases, users access data via
> the intermediary of an application.  A wiki is just one type of
> application a database might support.

Here is the most important part for me: 

"databases and applications"

Taxonomists (just as everybody else) need tools. Online tools? Perhaps. How
many of you DO your research online? 

Taxonomic research does mean working with e.g. specimens (GBIF? ok.),
citations (crossref? BHL? CiteBank and others? - OK!), GIS (GE? really? just
kidding, that's not GIS), media (Flickr? YouTube? Vimeo? Morphbank? - sure),
and names of course (Wikispecies,TOL, COL, Species 2000,EDIT, ITIS,
Zoobank,Index Fungorum, EOL, GNA/GNI/GNUB, etc.? - of course! ). In practice
you need to work with most of not all of these sources and in this sense you
really DO you research online. Head spinning list and I think I just
casually picked few examples without giving it a thought. Which means, as it
has been said already countless times - we need STANDARDS. And it is that
obvious. And we need those standards to "standardize" across the board (ok,
that's another story). And here comes and afterthought: so who exactly needs
those standards? scientists? Well, there are definitely some that really
NEED them, but the rest need TOOLS. Applications. Wikispecies is a good
application as Mike and others agree. It has its purpose and as any
application it can become "better" (and more complex as a result) or it can
simply polish what it does and concentrate on what it is doing. Other
applications, like what Rod specializes in - would be happiest if standards
settle and everybody would just adopt them. With all this variety of online
sources we DO need aggregators. No point in going in details with this one.

Applications that are close to my heart are tools in a bit simpler meaning -
like machines, something that is really specialized to the job at hand. It
doesn't have to be online. How many of you switched from desktop Word/Sheet
processing tools to online ones (ok, I see some hands of course)? My vision
of ideal taxonomic tool is the one that streamlined for typical tasks
taxonomist going through, including databasing, management, querying,
mapping, publishing, etc. but which can make use of those standards to
connect to existing databases (all those mentioned above, for instance) and
pull the data into local database (ideally also push the data back, or
simply "sync with a cloud"). A "local-cloud" hybrid.

My point in short: I agree that some resources have to concentrate on
standard development, but, please, don't forget the tools that will actually
use those standards.

Cheers,
Evgeniy

evgeniy at earthcape.com
http://www.earthcape.com
http://www.twitter.com/emeyke
http://www.helsinki.fi/science/metapop/

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Mike Sadka
> Sent: 8. elokuuta 2009 17:47
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Wikispecies is not a database: part 3 (after
> thinking about it!)
> 
> Hi Taxacomers.
> 
> 
> 
> I've never posted to Taxacom before - I am a techie and usually just
> observe the learned debate <humour>and sometimes wonder how some of you
> manage to get anything else done!</humour>
> 
> 
> 
> But I can't resist some comments on this thread.
> 
> 
> 
> >Wikispecies ... cannot do some (important?) things that databases can
> do
> 
> 
> 
> I'm surprised that anyone would question the importance of being able
> to query a back end data store.  What is data for if not to answer
> questions?
> 
> 
> 
> 
> 
> > (1) Is Wikispecies a database?
> > I now think so again! I don't see any good reason to adopt Rod Page's
> > overly narrow concept of a database, but instead see more sense in
> > Tony Rees' broader concept (as per his Wikipedia article), into which
> > he was (at least initially) willing to include Wikispecies.
> 
> 
> 
> The term "database" has already been defined by the appropriate
> discipline.
> 
> 
> 
> >From Wikipedia: "... an integrated collection of logically related
> records or files which consolidates records previously stored in
> separate files into a common pool of data records that provides data
> for many applications.  ..."  [my empahsis]
> 
> 
> 
> Rod Page's concept isn't narrow - it is correct.  And I disagree with
> Rod only in that I think it does matter what you call it.
> 
> 
> 
> I believe it is vital to distinguish between databases and the
> applications that allow users to interact with them.  Databases are
> simply storage for data.  In almost all cases, users access data via
> the intermediary of an application.  A wiki is just one type of
> application a database might support.
> 
> 
> 
> Wikispecies is an instance of the MediaWiki application, which uses a
> database to store the data it presents to the user.  In principle that
> database is queryable just like any other - but the MediaWiki
> application interface does not expose that functionality to users.
> 
> 
> 
> So Wiki vs Database is a false and very misleading debate.  (As Richard
> Pyle said, this thread has arguably been about the differences between
> closed- or open-access databases - regardless of what kind of
> application is used to populate them.)  What is needed is a data model
> for taxonomic information that can support all sorts of applications,
> including wikis (as others including Jim Croft have said).
> 
> 
> 
> All this may sound unnecessarily pedantic, but IT is no different from
> systematics in that respect!  If one doesn't use the terminology
> correctly one runs the risk of talking from a dubious orifice...
> 
> 
> 
> In my opinion (for what it's worth) I think many of the sensible things
> that have been suggested in this and related discussions (eg, inter
> alia - better flow of data between grass-roots databases and large
> aggregators) are not achievable until there are robust standards for
> storing and manipulating taxonomic data.
> 
> 
> 
> I would also suggest that this is less my opinion and more a statement
> of technical reality.  All IT applications that can readily exchange
> data need common data standards in order to do so.
> 
> 
> 
> Development of standards is arduous, but once standards and protocols
> are in place, applications can proliferate - just look what the HTTP
> and IP protocols with HTML and other web technology standards have done
> for the web in just a few years.
> 
> 
> 
> I would totally sympathise with anyone who groans at my mention of
> "standards" - but I don't see any getting away from that in the end.
> So rather than numerous competing high-level money-sapping aggregation
> projects, it would be better (if harder to fund) to put resources into
> developing such standards.
> 
> 
> 
> 
> 
> >I just do think you [Rod] are nitpicking just a wee bit on
> Wikispecies' weaknesses, rather than giving due credit to its strengths
> 
> 
> 
> Maybe - but conversely I suspect you maybe do not appreciate how
> significant the weaknesses are.
> 
> 
> 
> The strengths are good I agree, but those weaknesses are critical, and
> mean that wikispecies fails to exploit the full potential of the
> digital medium.  Without the ability to search across pages,
> wikispecies is more like a paper book that a proper digital publication
> (as someone else was driving at).
> 
> 
> 
> But that doesn't mean ditch it - to me it means extend the interface to
> include query (and other) capabilities - or use other tools to do that
> on the same back-end datasource).  That said, effective querying does
> depend on an effective underlying data model - which brings us back to
> standards again - sorry!
> 
> 
> 
> 
> 
> >(6) the 3 most important things about any kind of taxonomic database
> > are data quality, data quality, and (you guessed it) data quality!
> 
> 
> 
> Absolutely!  And not just taxonomic databases - data quality is always
> important, and that is exactly what databases are for and good at.  If
> you want to store a lot of data you need a database.  You can (and
> probably should) build a wiki on top - but a wiki won't store or
> protect your data.
> 
> 
> 
> 
> 
> Cheerio, Mike
> 
> 
> 
> 
> 
> 
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