[Taxacom] Pre-submission peer-review and online import of specimen records from BOLD
Dan Lahr
dlahr at ib.usp.br
Wed Sep 23 08:11:20 CDT 2015
hi Donat,
this is precisely where I wanted to get at. thank you for the link to
"Integrating and visualizing primary data from prospective and legacy
taxonomic literature", which I had not read before.
one of my concerns is exactly with legacy data, but the article
demonstrates that it is possible to increase the visibility and usability
of those data by mark-up (I presume there may be other ways).
I assume the markup process is manual? i.e. one reads through the pdf
marking relevant taxonomic information right? can this be automated?
cheers,
dan
__________________________________
Daniel J. G. Lahr
PhD, Assist. Prof.
Dept of Zoology, Univ. of Sao Paulo, Brazil
Office number: + 55 (11) 3091 0948
http://www.ib.usp.br/zoologia/lahr/
On Wed, Sep 23, 2015 at 5:25 AM, Donat Agosti <agosti at amnh.org> wrote:
> Here two articles on peer review in a wider context
>
> http://www.nature.com/news/a-call-to-deal-with-the-data-deluge-1.18386?TW.mc_id=TWT_NatureNews
>
> http://elifesciences.org/content/4/e10825
>
> the good thing though is, that peer review gets easier through the
> visualization of articles, through which flaws become immediately obvious.
> See eg the many singleton description of new species:
>
> http://dx.doi.org/10.3897/BDJ.3.e5063
>
> In this respect, and if we raise our scientific standards (not to describe
> species based on one single specimen, for example) the future will be
> brighter and exciting, especially if we allow machines to do some of the
> peer review: Eg are all the Code criteria fulfilled to describe a new taxa?
> Are more than X specimen used to describe a new taxon? Are all the
> underlying data online and open accessible?
> Again, using JATS/Taxpub allows to do exactly that - one more reason to
> move publishers into this new world. Pensoft with BDJ and RIO is almost
> there - but the social contract we have to forge.
>
> cheers
>
> Donat
> -----Original Message-----
> From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of JF
> Mate
> Sent: Wednesday, September 23, 2015 6:24 AM
> To: Taxacom <taxacom at mailman.nhm.ku.edu>
> Subject: Re: [Taxacom] Pre-submission peer-review and online import of
> specimen records from BOLD
>
> I think you are talking about a specific case/cases which probably won´t
> matter in the long run (decades). In any case, and regardless of the
> intentionality behind this "misinformation", it already exists in analog
> form so it can´t be made worse by open review. In fact, breaking it wide
> open should help correct these errors. Having said that, I do worry that
> the proportion of experts vs the rest of this "sharing economy" is stacked
> against it somehow. Only way to find out will be to try it out and see what
> happens.
>
> Best
>
> Jason
>
> On 23 September 2015 at 13:22, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> wrote:
> > Jason,
> >
> > I am not talking about that sort of misinformation. It does not matter
> whether the misinformation is intentional or not. The problem arises when
> there is a solid reluctance to admit that a mistake has been made, and an
> equally solid reluctance to fix it. That is what I am talking about. It is
> about individuals and institutions who talk up substandard work, give the
> reader as little actual data as possible, because this could lead to
> mistakes being discovered, and who obstruct others from investigating the
> issue for themselves. It is abou authors who just don't care whether it is
> misinformation or not. Therein lies the problem. There is actually nothing
> terrible with an error if it gets fixed. No blame. Everybody makes
> mistakes, but some are not inclined to admit that they do, and neither are
> they inclined to fix the mistake or let anyone else do it for them.
> >
> > Stephen
> >
> > --------------------------------------------
> > On Wed, 23/9/15, JF Mate <aphodiinaemate at gmail.com> wrote:
> >
> > Subject: Re: [Taxacom] Pre-submission peer-review and online import
> > of specimen records from BOLD
> > To: "Taxacom" <taxacom at mailman.nhm.ku.edu>
> > Received: Wednesday, 23 September, 2015, 1:19 PM
> >
> > "...to prevent
> > readers from being misled by misinformation published by others,
> > particularly if it contradicts what I might tell them, and yet the
> > misinformation is selling itself as authoritative on the basis of
> > "reputability" of institutions, equally carefully "groomed"
> > reputations of authors, etc. Misinformation is worse than no
> > information."
> >
> > I honestly can´t understand
> > what is bugging you so much Stephen.
> > Intentional or unintentional misinformation? I will assume the
> > latter and simply say, so what? The more "expert" you become the
> > more you realize how little you know and how much knowledge is based
> > on educated guesses. If you let this be your guiding principle you
> > will be paralyzed by fear of "misinforming" and not publish
> > anything. The point, as Robin said, is to tell others what you know
> > so they can use it. If wrong somebody else will then correct it
> > later, maybe inching closer to the "truth"
> >
> > I think Pensoft´s new
> > peer-review is the best thing to have been developed recently in
> > publication. DOIs and hyperlinks are just lights and whistles but
> > this will actually make life a lot easier. Now for a fully digitized
> > biodiversity library that is not pre-1920´s...
> >
> > Jason
> >
> >
> > On 23
> > September 2015 at 10:01, Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> > wrote:
> > > Robin,
> > >
> > > It is a tad unclear what point you are trying to make, and if you
> > are agreeing or disagreeing with me (which, incidentally, is exactly
> > the sort of thing that a reviewer should address for manuscripts,
> > i.e. clarifying the point that the author is trying to make).
> > Whatever your point, I would just like to comment that, for me, the
> > most important thing is not to publish what I know so that others
> > can know it as well (which is not to say that this isn't important),
> > but rather to prevent readers from being misled by misinformation
> > published by others, particularly if it contradicts what I might tell
> > them, and yet the misinformation is selling itself as authoritative
> > on the basis of "reputability" of institutions, equally carefully
> > "groomed" reputations of authors, etc.
> > Misinformation is worse than no information.
> > >
> > > Cheers, Stephen
> > >
> > >
> > --------------------------------------------
> > > On Wed, 23/9/15, Robin Leech <releech at telus.net>
> > wrote:
> > >
> > > Subject:
> > RE: [Taxacom] Pre-submission peer-review and online import of
> > specimen records from BOLD > To:
> > "'Stephen Thorpe'" <stephen_thorpe at yahoo.co.nz>, "'Doug Yanega'"
> > <dyanega at ucr.edu> > Cc: taxacom at mailman.nhm.ku.edu > Received:
> > Wednesday, 23 September, 2015,
> > 11:37 AM
> > >
> > >
> > Stephen,
> > >
> > > Shortly
> > after I had finished
> > > my PhD, and the
> > thesis had been accepted for publication, > > I had finished and
> > had published several > short but contributive papers in a fairly
> > > short period of time in several journals. To > me, getting the
> > information out there was, > and always is to me, far more
> > important than > the particular journal I publish in.
> > >
> > > At
> > that time, I was in Ottawa. At coffee one > morning, an older,
> > estblished taxonomist > said to me, in front of others, > >
> > "Robin, what are you > doing?
> > Setting yourself up as an expert? Everywhere I > look I > see
> > another new paper of > yours."
> > >
> > > I replied,
> > > "Not at all. I am trying to put the information out > there so
> > that others > know what I know, so > that they do not have to ask
> > me for IDs.
> > They can look and
> > > ID
> > > things for themselves."
> > >
> > > There was a moment
> > while he
> > > and several of his buddies
> > guffawed, then I added,
> > >
> > > "But, on the other hand,
> > > if you don't publish much, everyone has to send material > >
> > to you for ID. In that case, you are seen > as the expert."
> > >
> > > I
> > > heard no more caustic comments from him
> > - ever. In fact,
> > > he became rather
> > pleasant
> > > after that.
> > >
> > > Robin
> > >
> > > -----Original
> > Message-----
> > > From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
> > > On Behalf Of Stephen Thorpe
> > > Sent:
> > >
> > September-22-15 4:03 PM
> > > To: Doug
> > Yanega
> > > Cc: taxacom at mailman.nhm.ku.edu
> > > Subject: Re: [Taxacom] Pre-submission > peer-review and online
> > import of specimen records from > BOLD > > I wouldn't take >
> > too much notice of Doug's sermon about Wikipedia. It > works OK
> > for very simple stuff, but not for anything else.
> > > It isn't only vandals and/or
> > crackpots who get blocked
> > > from
> > editing. There are many "power games" going > on behind the scenes.
> > Everybody wants to do things their > way, and nobody likes anyone
> > coming in and making > contributions on a significantly large scale.
> > Actually very > little taxonomy/biodiversity related stuff gets
> > done now at > all on Wikipedia. Doug's own contributions are really
> > > loittle more than a drop in an ocean of oceans! The reason > why
> > it comes up first in a Google search has nothing > whatsoever to do
> > with the quality of content. It is > unfortunate that the very first
> > thing a young person might > find on a topic could well be a load
> > of Wikipedia > rubbish.
> > >
> > >
> > Stephen
> > >
> > >
> > --------------------------------------------
> > > On Wed, 23/9/15, Doug Yanega <dyanega at ucr.edu> > wrote:
> > >
> > > Subject: Re:
> > > [Taxacom] Pre-submission peer-review and online import of >
> > specimen records from BOLD
> > > To:
> > > Cc: "taxacom at mailman.nhm.ku.edu"
> > > <taxacom at mailman.nhm.ku.edu>
> > > Received: Wednesday, 23
> > September, 2015, 9:38
> > > AM
> > >
> > > On
> > 9/22/15 12:50 PM,
> > > Neal
> > > Evenhuis wrote:
> > > >
> > >
> > No Doug, the problem is
> > > not the print
> > > journals. They do what businesses do
> > > >
> > >
> > -- they make money.
> > > >
> > >
> > > > The problem(s) are
> > > academic systems
> > > that evaluate their professors on the
> > > >
> > >
> > basis of the journals they publish in (the > > higher impact the
> > better). That
> > > > has
> > > resulted in the "Big
> > Power
> > > Publishers" to have
> > > academics by
> > > the
> > > > short-and-curlies
> > >
> > > (actually more like
> > racketeering) and can thus charge
> > > > oodles of money to
> > subscribe and
> > > authors
> > > are forced to shy away
> > from
> > > > online
> > > only/low impact
> > > journals in order to get high
> > ranking,
> > >
> > >
> > rewards,
> > > > evals,
> > etc.
> > >
> > > >
> > > > Once the evaluation
> > > system for taxonomists
> > changes, taxonomists
> > > can feel
> > > > free to publish
> > elsewhere
> > > than high impact
> > > print journals because
> > > they are
> > > > no
> > > longer
> > >
> > being held hostage by the current academic evaluation
> > > system.
> > > I'm not trying to
> > > be overly
> > > contentious, as I do see
> > your
> > > point, but:
> > > can anyone offer any
> > > statistics to back this
> > > up? Specifically,
> > > if you
> > > ignore fossil taxa
> > >
> > > entirely, just for
> > the moment, what percentage of all
> > > cumulative taxonomic works,
> > worldwide,
> > > appear
> > > in legitimately "high
> > > impact"
> > > journals? My
> > > impression is that it is a very small > > percentage;
> > > in fact, for many of the
> > > taxonomists I know (mostly
> > working on
> > > arthropods), if
> > they stopped publishing in
> > > their present journals of
> > >
> > > choice and
> > > switched to, say, Zootaxa
> > or
> > > ZooKeys, their impact factor
> > >
> > > would
> > probably go UP rather than down. I
> > > honestly don't think
> > I've ever
> > > heard of a
> > taxonomist (who did not work on
> > > fossils) whose job was
> > >
> > > imperiled by the
> > low
> > > impact factor of
> > their
> > > publications, as opposed to
> > > how much grant
> > > money they brought in, or some
> > > other less
> > > arbitrary
> > > criteria. As such,
> > > while I have little doubt it
> > exists, I have to
> > > wonder
> > > just how serious a force this
> > is
> > > behind our
> > > present predicament.
> > >
> > > Peter
> > > Rauch
> > >
> > wrote:
> > > > How does
> > the
> > >
> > >
> > "peer", as in "peer review", play in
> > > this
> > > >
> > >
> > still-vaguely-described "open
> > >
> > > access" process ?
> > > >
> > > > What mechanism(s) would
> > be needed /
> > > useful
> > > to deal with the presumably
> > huge
> > > > number
> > > of
> > >
> > "reviews" of also-presumably
> > >
> > > still-not-published
> > draft documents ?
> > >
> > > >
> > > > It's easy enough
> > > to say that poor quality
> > reviews can simply be
> > > ignored,
> > > or
> > > > can be
> > > put to rest handily by other,
> > > more
> > >
> > competent reviewers. But, that
> > > >
> > > itself implies that there
> > will be such more
> > > competent
> > > reviewers who will
> > > > indeed have the time
> > > and
> > >
> > patience to read, think about, and comment on
> > > > those incompetent
> > reviews.
> > > >
> > > > I understand --I
> > > think!?!-- the notion of
> > removing physical
> > > paper from the
> > > > final production
> > > process, and I understand
> > > --I think-- the
> > > notion of "open
> > > >
> > >
> > > access" to information.
> > > >
> > > > What I am asking about
> > is what will be
> > > the
> > > mechanisms to address the
> > > > then-open
> > > floodgates to
> > > gratuitous(?) commentary on draft works such
> > > that a
> > > > "fair"
> > > (and
> > > authoritative / professional)
> > handling
> > > of all that input
> > > is
> > > >
> > >
> > possible ?
> > >
> > > Open resources
> > > like Wikipedia deal with this
> > > easily, and
> > > admirably, and
> > > routinely. Any
> > > Wikipedia article has one
> > visible
> > > manifestation, open to
> > > editing, while
> > > commentary goes on a linked
> > > "talk
> > > page". The editing
> > > history
> > > is timestamped, and visible,
> > and subject to
> > > reversion to
> > > previous versions if
> > > necessary - as is the talk
> > > page. There are
> > > many
> > > rules in place
> > >
> > > regarding proper
> > editing procedures and especially
> > > etiquette, and editors who
> > cannot abide by
> > > those
> > rules (e.g., vandalism)
> > > have their
> > > edits reverted, or
> > > if they are persistent and
> > disruptive,
> > >
> > > they can be banned
> > (short-term or
> > > long-term),
> > as has happened to many
> > > trolls
> > > and crackpots who have
> > > tried to set up shop on Wikipedia.
> > > That
> > > kind of behavior is spotted
> > and weeded
> > > out very
> > quickly, because there
> > > are
> > lots of
> > > eyes watching.
> > > The floodgates on Wikipedia are already open >
> > > - to the entire world, in
> > > fact - and yet it
> > > functions quite well,
> > > because it is
> > > self-policing,
> > > based on explicit policies.
> > Transparency
> > >
> > > and
> > inclusivity go a long way, and synergize
> > > well. Articles on WP
> > >
> > > increase in
> > quality,
> > > ratchet-like,
> > over
> > > time, and setbacks are always
> > > only
> > >
> > temporary. If you had a single public > > review forum that
> > included
> > > all of the
> > > world's taxonomists, then
> > it would
> > > function wonderfully
> > > well,
> > > because nothing would slip
> > through
> > > the proverbial
> > cracks, and if we
> > > followed
> > > the example of
> > > Wikipedia for editing policies, your worst > > fears
> > > about gratuitous commentary
> > would
> > > not
> > > be realized.
> > >
> > > I
> > suggest this
> > > challenge
> > for
> > > those of you who are skeptical:
> > take a
> > >
> > > moment
> > right now to enter the name of a
> > >
> > > higher-level taxon you know very
> > > well
> > > (family or higher) into
> > Google. The odds are
> > > very good
> > that
> > > a
> > >
> > > Wikipedia entry
> > will be the top hit, or
> > > at
> > >
> > least one of the top 5. Open
> > > the
> > > Wikipedia article, and see
> > how much of it is
> > > legitimately
> > > inaccurate
> > >
> > > (not incomplete -
> > that is
> > > unavoidable -
> > or
> > > slightly out-of-date, I mean
> > > actual
> > >
> > factual errors as in "this is not
> > > true
> > >
> > now and never has been
> > > true"). It
> > > should be pretty rare to find
> > such errors, and
> > > it would be
> > >
> > > even
> > rarer if
> > > more taxonomists spent
> > more
> > > time on
> > > Wikipedia.
> > > Self-policing is an
> > > approach that can and does
> > work, and works
> > > better
> > > and better with increasing
> > > community buy-in. I
> > > maintain that the same
> > >
> > > would
> > apply to
> > > online
> > > review of scientific works.
> > >
> > > Sincerely,
> > >
> > >
> > > --
> > >
> > > Doug Yanega
> > > Dept. of Entomology
> > > Entomology
> > > Research Museum
> > > Univ. of California,
> > > Riverside, CA 92521-0314
> > > skype:
> > >
> > dyanega
> > > phone: (951)
> > >
> > > 827-4315
> > (disclaimer: opinions are mine, not UCR's)
> > > http://cache.ucr.edu/~heraty/yanega.html
> > > "There are some
> > enterprises
> > > in which a
> > careful disorderliness
> > >
> > > is the true
> > >
> > method" - Herman Melville,
> > > Moby Dick,
> > > Chap. 82
> > >
> > >
> > >
> > _______________________________________________
> > > Taxacom Mailing List
> > > Taxacom at mailman.nhm.ku.edu
> > > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> > > The Taxacom Archive back to
> > 1992 may be
> > > searched at:
> > http://taxacom.markmail.org
> > >
> > > Celebrating 28 years of
> > > Taxacom in 2015.
> > >
> > >
> > _______________________________________________
> > > Taxacom Mailing List
> > > Taxacom at mailman.nhm.ku.edu
> > > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> > > The Taxacom Archive back to 1992 may be > searched at:
> > http://taxacom.markmail.org > > Celebrating 28 years of >
> > Taxacom in 2015.
> > >
> > >
> > _______________________________________________
> > > Taxacom Mailing List
> > >
> > Taxacom at mailman.nhm.ku.edu
> > > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> > > The Taxacom Archive back to 1992 may be searched at:
> > http://taxacom.markmail.org > > Celebrating 28 years of Taxacom in
> > 2015.
> > _______________________________________________
> > Taxacom Mailing List
> > Taxacom at mailman.nhm.ku.edu
> > http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> > The Taxacom Archive back to 1992 may be searched at:
> > http://taxacom.markmail.org
> >
> > Celebrating 28 years of
> > Taxacom in 2015.
> >
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> The Taxacom Archive back to 1992 may be searched at:
> http://taxacom.markmail.org
>
> Celebrating 28 years of Taxacom in 2015.
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/cgi-bin/mailman/listinfo/taxacom
> The Taxacom Archive back to 1992 may be searched at:
> http://taxacom.markmail.org
>
> Celebrating 28 years of Taxacom in 2015.
>
More information about the Taxacom
mailing list