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

Sun Aug 9 01:57:40 CDT 2009

> In the end of the day, there is certain level of selfishness and  
> closeness in > taxonomy world which in my view very hard to combat
Well, my torpedos are armed and aimed! :)
A taxonomist friend calls this "survival of the most obnoxious"!
I think you have a good grasp of the problems, but I'm not so sure  
about the "let the enemy win and hope they will then be kind to us"  
solution, but that's just me! Don't get me wrong, MOST taxonomists in  
the world are great, but as always it is the few which tarnish the  
reputation of the many. I could tell you some horror stories, believe  
me ...

Stephen

Quoting Evgeniy Meyke <evgeniy.meyke at helsinki.fi>:

> Stephen,
>
>> I don't see the
>> lack of "standards" as a problem.
>
> I agree, we have enough (in absolute number). They just need more work from
> my point of view. A lot of work. And kudos to TDWG and community around it
> for doing it.
>
>> Rather, the problem is that we are
>> too busy building new infrastructures
>
> Oh we definitely need new infrastructures.
>
>  instead of just sitting down at a computer
>> online and typing in taxonomic information, making sure that the
>> people doing so (or at least those overseeing them) are experienced
>> and knowledgeable enough to actually UNDERSTAND what it is that they
>> are typing in.
>
> I dont see it quite working this way. But that's me.
>
>
>> so we don't
>> need working taxonomists to help build our databases,
>
> We need working taxonomists to build THEIR own databases (I am sorry, but
> that's what most of them care the most) and given proper tools, they will
> help build "our"/"your" databases with pleasure. In the end of the day,
> there is certain level of selfishness and closeness in taxonomy world which
> in my view very hard to combat - we just need a good workaround.
>
> Evgeniy
>
>>
>> Stephen
>>
>> Cheers,
>>
>> Stephen
>>
>>
>>
>> Quoting Evgeniy Meyke <evgeniy.meyke at helsinki.fi>:
>>
>> > 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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>> >>
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