[Taxacom] Zootaxa papers now in BioStor

Wed Feb 10 14:36:26 CST 2010

Mike:

>it is easier to generate wiki-type content from structured data than the reverse

Perhaps, but it is far easier (and far cheaper) to create wiki-type content period (i.e., not from structured data, but from primary taxonomic literature)

>So if resources are limited, I would spend them creating the most structured dataset I could

If resources are limited (if???), I would spend them creating as much useful information as possible, as quickly as possible

>IT has already proved so useful for systematics - ie - parsimony analysis would not be possible without computers

I think only cladists find it useful!

At any rate, to cross threads just a little bit, EOL is no better off than Wikispecies by these arguments ...

Stephen

________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Mike Sadka [M.Sadka at nhm.ac.uk]
Sent: Thursday, 11 February 2010 3:27 a.m.
To: Roderic Page; TAXACOM
Subject: Re: [Taxacom] Zootaxa papers now in BioStor

Fair comment Rod.

And yes, RDF exports would go a long way towards satisfying me (although
they are probably easier to generate from a highly structured
datasource, I suspect).

But it still seems to me that it is easier to generate wiki-type content
from structured data than the reverse.  So if resources are limited, I
would spend them creating the most structured dataset I could, because I
believe that this represents the most flexible format for data storage
and maximises opportunities for data reuse (although I accept that
models and tools are perhaps not as developed or available as they might
be... and admittedly databases is what I do so I may be biased!).

In all likelihood, a diversity of technical approaches (within reason)
is probably useful.

But my main point was more that some contributors to this list seem
unaware that there is anything more to consider than output and tend to
ignore or even resent technological implications (almost to the point of
luddism sometimes I feel!).

I believe this is a huge mistake, but one commonly made in the
museum/systematics sector - and which is perhaps one of the reasons why
the sector lags behind other sciences in its adoption of IT (cf
molecular biology for example).

In a way this is strange, given that IT has already proved so useful for
systematics - ie - parsimony analysis would not be possible without
computers.

Cheerio, Mike

__________________________

Mike Sadka

Interactive Media

x5462

-----Original Message-----
From: Roderic Page [mailto:r.page at bio.gla.ac.uk]
Sent: 08 February 2010 20:28
To: TAXACOM
Cc: Mike Sadka
Subject: Re: [Taxacom] Zootaxa papers now in BioStor

Dear Mike,

On 8 Feb 2010, at 18:30, Mike Sadka wrote:

> Hi Stephen
>
>
> IMO Wikis are for content, not data.  Arguably, putting data into
> wiki's
> severely limits subsequent use or manipulation, because essentially
> there is no data model - only pages of information which are not
> accessible to machines (although appropriate metadata markup could
> make
> them more so)   and, without search capability, only partially
> accessible to humans.
>

This may be true for most wikis, but not for all.
http://semantic-mediawiki.org/wiki/Semantic_MediaWiki
  has explicit structure and supports queries. It's essentially a
Semantic Web database, and is being used by open data initiatives such
as OpenEI (Open Energy Info), see  http://en.openei.org/wiki/
Main_Page . I've discussed applying this tool to taxonomy on my blog
http://iphylo.blogspot.com/search?q=itaxon

Given that Semantic Mediwiki exports data in RDF, one could argue that
it could meet your requirements for reuse, especially as it requires
data to be annotated with vocabularies, which makes it arguably more
useful than, say, text files or SQL dumps.

Generalising about wikis can be tricky, especially as some
implementations may contain considerable structure under the hood .

Regards

Rod

> Personally I feel data should be put into a format which maximises its
> potential for re-use - especially science data, as nobody can foresee
> how scientists might want to use or query data in the future.
>
> Cheerio, Mike
>
>
>
>
>
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Stephen
> Thorpe
> Sent: 06 February 2010 23:54
> To: David Wagner
> Cc: taxacom
> Subject: Re: [Taxacom] Zootaxa papers now in BioStor
>
> Hi David,
>
> You ask a very good question, though one we have "touched on" already
> several times on Taxacom. First off, I am in COMPLETE AGREEMENT with
> you
> about:
>
>> I am confounded by all these global programs which seem to me to be
> overlapping, hugely duplicative efforts. I can't help but think
> there is
> a lot of resources being wasted here
>
> The answer is that IMHO, Wikispecies is by far the best option, though
> at present it is still hideously undervalued by the scientific
> community, alas!
>
> I have to be a tad careful about what I say on Taxacom about "the
> competition", like EoL, for example. It wouldn't be the first time
> that
> the director of some such outfit has responded to me in an overly
> defensive manner, magnifying and twisting my actual words!
>
> Suffice it to say this: the advantages of Wikispecies are as follows:
>
> (1) it is already up and running;
>
> (2) it is free;
>
> (3) it covers all species of everything, with global scope, including
> fossils;
>
> (4) it can be updated far more quickly than the alternative sites;
>
> (5) errors can be fixed immediately when spotted, by anyone who
> notices
> them;
>
> (6) it doesn't restrict who can contribute;
>
> (7) information added to Wikispecies is subject to true open-ended
> global peer review ...
>
> The alternative sites are expensive, restrict who can contribute,
> difficult to keep up-to-date, and errors are locked in, and it is
> typically very difficult to get them corrected ...
>
> As for the expectation that you should add information to Wikispecies
> for free, well you get out of it what you put in. If you need good
> biodiversity information on a regular basis, then you should be
> prepared
> to make a contribution. The alternative is for millions of dollars
> to be
> spent on perpetuating the huge beauracracies associated with the
> closed
> sites, potentially or actually at the expense of funding for primary
> taxonomic research ...
>
> A basic, but reasonably good example of my Wikispecies contributions
> is
> http://species.wikimedia.org/wiki/Doxozilora_punctata, with features:
> (1) an image of a specimen that I have taken and uploaded and
> identified
> (possibly the only photo on the web, or even in existence, of that
> genus);
> (2) DOI linking to references;
> (3) utilisation of Internet Archive (if you click on the Internet
> Archive link to the Broun reference, the original description should
> pop
> up like magic!)
>
> Stephen
>
> ________________________________________
> From: David Wagner [davidwagner at mac.com]
> Sent: Sunday, 7 February 2010 12:22 p.m.
> To: Stephen Thorpe
> Cc: taxacom
> Subject: Re: [Taxacom] Zootaxa papers now in BioStor
>
> Stephen,
>
> Why are you putting energy into Wikispecies instead of EOL
> (encyclopedia of life) or GBIF (global biodiversity information
> facility) or any of a number of other ambitious, database web sites?
>
> I am confounded by all these global programs which seem to me to be
> overlapping, hugely duplicative efforts. I can't help but think there
> is a lot of resources being wasted here that could be better directed
> towards immediate, concrete conservation needs.
>
> There many sites of a more restricted, regional focus, too. I've
> refused to contribute to most of them, despite numerous invitations,
> because I am wearied by the thought of pounding sand down the wrong
> rat hole.
>
> And, I'm surprised at the expectation of many that I should offer for
> free, without royalties or tight copyright retention, unfunded
> independent work that I should be compensated for.
>
> Your insights?
>
> Is this appropriate for another thread? I'm new to taxacom and maybe
> have missed these kinds of discussions.
>
> David
>
> David H. Wagner, Ph.D.
> Northwest Botanical Institute
> P.O. Box 30064
> Eugene, OR 97403-1064
>
> davidwagner at mac.com
> 541-344-3327
>
> http://web.mac.com/davidwagner/Site/FernZenMosses.html
>
> On Feb 6, 2010, at 2:43 PM, Stephen Thorpe wrote:
>
>> on Wikispecies I am placing Zootaxa papers
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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
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