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

Sun Aug 9 00:45:40 CDT 2009

> Other applications, like what Rod specializes in - would be happiest  
> if >standards settle and everybody would just adopt them

Therein lies the problem! Everybody won't just adopt them - we are  
even constantly having to defend ourselves against factions who want  
rid of traditional biological nomenclature altogether! I don't see the  
lack of "standards" as a problem. Rather, the problem is that we are  
too busy building new infrastructures and planning conferences to  
agree on new standards, 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.

It ought to be remembered that we are talking about secondary sources  
of information about the primary taxonomic literature, so we don't  
need working taxonomists to help build our databases, we need people  
who understand taxonomy, nomenclature, and have the skill to properly  
interpret primary taxonomic literature. Such people are rare, many of  
them are working taxonomists, but conversely some working taxonomists  
are not such people, and at the end of the day data quality relies  
heavily on the input of such people. There may be a move to  
"standardise" taxonomy to the point where a primary taxonomic  
publication could be "understood" by a machine, but even if it is  
possible, don't forget the truly VAST amount of taxonomic literature  
from the past and present which could never be interpreted properly by  
anyone without the above skills. The "art of science" ...

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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