[Taxacom] RSS feeds for new (or newly digitised) names
Roderic Page
r.page at bio.gla.ac.uk
Sun May 10 06:38:40 CDT 2009
Dear Paul,
Just to be clear, mashing, blogging, twitter aren't rocket science
either.
I didn't mean to devalue the role of curators (who are starting to get
the wider recognition they deserve, e.g. http://dx.doi.org/10.1038/455047a
), I'm just keen to get the maximum value out of all that hard work,
and hopefully provide some useful annotations/corrections/links in
return.
Having good mechanisms for annotation would be very useful. Many of us
will know of records (names, localities, sequences, papers, etc.) that
we know have errors, but these are rarely (a) made public, and (b)
fixed. When I was editing Systematic Biology I would read reviews of
manuscripts where a reviewer would demonstrate that a GenBank
sequenced used in the manuscript was clearly misidentified, and the
author would remove the sequence from their data set and redo the
analysis. But this knowledge that the sequence was erroneous didn't
make it's way back to GenBank, so the error would remain uncorrected.
It's this sort of thing that it would be helpful to record somewhere
so we could avoid reusing erroneous data.
Regards
Rod
On 10 May 2009, at 11:35, Paul Kirk wrote:
> It's an unfortunate fact (probably a generalization) that the
> database curators (and compilors) are less valued/resourced (it's
> not rocket science, after all) than the aggregators doing all the
> rocket science stuff (mashing, blogging, twittering ...); but I do
> agree that aggregating highlights contradictions/errors ... but it's
> the mechanisms to annotate those contradictions/errors that need to
> be developed - like one for GenBank sequence data, and perhaps one
> for GBIF occurrence data - so that users of aggregated data can
> chose to go with the annotation ... rather than the uncorrected data
> which should have been corrected by the aforementioned under-
> resourced curator in the source database.
>
> Paul
>
> From: taxacom-bounces at mailman.nhm.ku.edu on behalf of Roderic Page
> Sent: Sun 10/05/2009 10:15
> To: Paul van Rijckevorsel
> Cc: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] RSS feeds for new (or newly digitised) names
>
>
> On 10 May 2009, at 08:04, Paul van Rijckevorsel wrote:
>
> > From: "Roderic Page" <r.page at bio.gla.ac.uk>
> > Sent: Saturday, May 09, 2009 9:35 AM
> >> I don't see this as a case of either/or. However, I'll make a
> couple
> >> of points.
> >
> >> Specialist projects are great, but that doesn't mean that they
> can't
> >> benefit from opening the data to a wider audience. Each project
> I've
> >> encountered has errors (I've found some in IPNI as a result of
> making
> >> the RSS feeds, see http://tinyurl.com/qp2yhp ), and often these
> >> errors
> >> are only found when one tries to integrate the project with the
> wider
> >> world.
> >
> >> I also agree that we need people to do the fiddly bits. One reason
> >> I've been playing with wikis is that in every integration project
> >> I've
> >> played with I keep coming across errors (from all kinds of sources,
> >> not just taxonomic) that need to be fixed. Some of these can be
> found
> >> by machines, but some need people to detect and correct. Note that
> >> these need not be specialists. Anybody can figure out that frogs
> >> don't
> >> live in the middle of the Atlantic Ocean.
> >
> > ***
> > On and off, I have been thinking about this, as well as about the
> > "Species
> > Pages" of Roger Hyam (February 23, 2009 12:44 AM). I do see a
> > dichotomy,
> > between websites with a limited objective (bottom up, driven by
> > information)
> > and sites trying to do 'everything' (top down, driven by a desire
> for
> > information). There is ever more available on the web, more scanned
> > literature, more useful information on species (including pictures),
> > and
> > more and more databases (and databases that harvest other
> > databases). The
> > actual information on species is usually not in the form of a
> > Species Page,
> > and it certainly is no rarity to need five or more sources to gather
> > anything like a complete whole.
> >
> > A lot of databases appear to have no function other than to
> clutter up
> > Google searches by having their empty pages show up higher than
> > pages that
> > do offer content. Whether adding (yet another) a wiki would be
> > useful is
> > debatable (wasn't EoL a wiki? It does not appear to be moving
> > forward all
> > that fast).
>
> EOL isn't a wiki, which I think in part explains why it's moving so
> slowly (don't get me started...).
>
> I think there is a need for aggregators, tools to bring things
> together (e.g., Roger's species pages, my iSpecies, EOL, etc.). I also
> think we need tools to make sense of that aggregation, and to refine/
> filter/edit it.
>
>
> > I am quite dubious about the "Anybody can figure out that frogs
> > don't live in the middle of the Atlantic Ocean." as negatives
> > generally are
> > not particular useful. Noticing an error or potential error is not
> > necessarily useful; it is fixing them (properly) that matters; that
> > usually
> > takes a great deal more work (and skill and knowledge).
>
>
> Not sure what you mean by negatives are not particularly useful. The
> fact that, for example, the GBIF distribution map for the amphibian
> family Caeciliidae (http://data.gbif.org/species/13148933 ) includes
> insects found well outside the amphibian's distribution (due to
> homonymy) is likely to adversely affect sensible inferences about
> these amphibians.
>
> I agree that fixing errors matters, but I'd argue that we need to be
> able to find them (which is best achieved by aggregating stuff
> together to discover contradictions), and provide simple means to fix
> them (i.e., not sending an email to some unnamed database curator who
> may or may not bother to deal with the issue).
>
> I'd argue that many errors don't require specific expertise. A lot of
> taxonomic research is essentially bibliographic and lexicographic (who
> published this name when, how did they spell it, etc.). There's a lot
> of things that anybody with generic research skills (finding sources,
> reconciling conflicting accounts) could do (let's not kid ourselves,
> this ain't rocket science). Of course, there will always be areas
> where expertise is vital, and some errors or inconsistencies will
> require skill to resolve.
>
>
> Again, I don't see this as either/or.
>
> Regards
>
> Rod
>
>
>
>
> >
> >
> > Paul
> >
> >
> >
> > _______________________________________________
> >
> > Taxacom Mailing List
> > Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >
> > The Taxacom archive going back to 1992 may be searched with either
> > of these methods:
> >
> > (1) http://taxacom.markmail.org
> >
> > Or (2) a Google search specified as: site:mailman.nhm.ku.edu/
> > pipermail/taxacom your search terms here
> >
>
> ---------------------------------------------------------
> 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
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>
>
>
>
>
>
>
> _______________________________________________
>
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>
> The Taxacom archive going back to 1992 may be searched with either
> of these methods:
>
> (1) http://taxacom.markmail.org
>
> Or (2) a Google search specified as: site:mailman.nhm.ku.edu/
> pipermail/taxacom your search terms here
>
> P Think Green - don't print this email unless you really need to
>
> ************************************************************************
> The information contained in this e-mail and any files transmitted
> with it is confidential and is for the exclusive use of the intended
> recipient. If you are not the intended recipient please note that
> any distribution, copying or use of this communication or the
> information in it is prohibited.
>
> Whilst CAB International trading as CABI takes steps to prevent the
> transmission of viruses via e-mail, we cannot guarantee that any e-
> mail or attachment is free from computer viruses and you are
> strongly advised to undertake your own anti-virus precautions.
>
> If you have received this communication in error, please notify us
> by e-mail at cabi at cabi.org or by telephone on +44 (0)1491 829199 and
> then delete the e-mail and any copies of it.
>
> CABI is an International Organization recognised by the UK
> Government under Statutory Instrument 1982 No. 1071.
>
> **************************************************************************
>
---------------------------------------------------------
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
Twitter: http://twitter.com/rdmpage
Blog: http://iphylo.blogspot.com
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
More information about the Taxacom
mailing list