[Taxacom] Ghost genus? (Stephen Thorpe)

Tony.Rees at csiro.au Tony.Rees at csiro.au
Fri Jun 21 18:06:07 CDT 2013


Dear all,

Jay's suggestion sounds plausible to me.

Of course there are many adventures to be had in the world of phantom genus and/or species names. One favourite(?) was chasing down the supposed genus name "Notliripora" in a well known compilation which shall be nameless (the name will still turn up via Google searches, having propagated from there in a limited manner since). It did not appear to be a misspelling for anything I could trace. The nearest was "Liripora" which got me to imagine the scenario by which this had ended up interpreted as a generic name on a specimen label which is presumably still out there somewhere...

Tony Rees
Manager, Divisional Data Centre,
CSIRO Marine and Atmospheric Research,
GPO Box 1538,
Hobart, Tasmania 7001, Australia
Ph: 0362 325318 (Int: +61 362 325318)
Fax: 0362 325000 (Int: +61 362 325000)
e-mail: Tony.Rees at csiro.au
Manager, OBIS Australia regional node, http://www.obis.org.au/
Biodiversity informatics research activities: http://www.cmar.csiro.au/datacentre/biodiversity.htm
Personal info: http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566
LinkedIn profile: http://www.linkedin.com/pub/tony-rees/18/770/36

> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Jae Cheon Sohn
> Sent: Saturday, 22 June 2013 3:16 AM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Ghost genus? (Stephen Thorpe)
> 
> Hello. I had the same question before. I checked the name in the
> Zoological Records and found no hit.
> My guess is that this name came from an abbreviation 'NAG' meaning "no
> available genus". It was then inappropriately used as a genus name. Let
> me know if someone found this genus name available.
> 
> regrds
> Jay Sohn
> 
> 
> 
> ________________________________________
> From: taxacom-bounces at mailman.nhm.ku.edu [taxacom-
> bounces at mailman.nhm.ku.edu] on behalf of taxacom-
> request at mailman.nhm.ku.edu [taxacom-request at mailman.nhm.ku.edu]
> Sent: Friday, June 21, 2013 1:00 PM
> To: taxacom at mailman.nhm.ku.edu
> Subject: Taxacom Digest, Vol 87, Issue 25
> 
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> Today's Topics:
> 
>    1. Ghost genus? (Stephen Thorpe)
>    2. Re: A new way to view taxonomic publications (Dave Roberts)
>    3. david r smith (stuartf)
>    4. Re: david r smith = still active (Chris Thompson)
>    5. Re: david r smith = still active (Sharkey, Michael J)
>    6. Re: A new way to view taxonomic publications (David.King)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Thu, 20 Jun 2013 22:28:42 -0700 (PDT)
> From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> Subject: [Taxacom] Ghost genus?
> To: "taxacom at mailman.nhm.ku.edu com" <taxacom at mailman.nhm.ku.edu>
> Message-ID:
>         <1371792522.53461.YahooMailNeo at web161901.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
> 
> http://www1.ala.org.au/gallery2/main.php?g2_itemId=29796
> ?
> Does anyone know where the genus name Nag comes from? I cannot find it
> anywhere other than here ...
> 
> ------------------------------
> 
> Message: 2
> Date: Thu, 20 Jun 2013 17:17:50 +0100
> From: Dave Roberts <workpackage6 at gmail.com>
> Subject: Re: [Taxacom] A new way to view taxonomic publications
> To: Roderic Page <r.page at bio.gla.ac.uk>
> Cc: taxacom taxacom <taxacom at mailman.nhm.ku.edu>
> Message-ID: <DB41BE64-5D6E-4460-A355-4071DC6DB9F0 at gmail.com>
> Content-Type: text/plain; charset=windows-1252
> 
> Dear Rod,
> 
> I agree and I was not underestimating the chances of being lucky that
> someone has released some specific paper.  The NHM journals are all in
> BHL, for example..  I am constantly impressed with the rapid growth in
> digital copies [of old materials] that are freely available.  Its often
> worth repeating a search that came up empty before.
> 
> My point was that BHL was forced into a series of ad-hoc agreements
> with individual publishers that, in many cases, did not bring the
> economies of scale.  Quentin's proposal was about that industrial
> scale.  If you have to pick and choose your journals, or worse,
> articles, then the scale just isn't there and we're probably better off
> with small projects focussing on stuff that are priorities for that
> project.
> 
> I indicated support Quentin's idea, but its important to recognise the
> bottlenecks and he resources that will be needed to relieve them.
> 
> Cheers, Dave
> --.
> On 20 Jun 2013, at 13:40, Roderic Page <r.page at bio.gla.ac.uk> wrote:
> 
> > Dave,
> >
> > 1. BHL has a LOT of post 1923 content, much of it provided by member
> institutions. The bulk of the major US museum in-house publications are
> in BHL, including papers published this century. Most of the NHM's
> Bulletins are in BHL as well. There is a persistent myth that BHL has
> only "old" stuff (i.e., pre-1923) which is totally wrong.
> >
> > 2. There is a lot of literature being made available in digital
> archives across the planet (e.g., Gallica in France, CiNii in Japan,
> DSpace archives across the world).
> >
> > 3. Many "smaller" taxonomic journals are putting PDFs online.
> >
> > 4. Yes, there are massive gaps, but we're in a lot better shape than
> you might think. I estimate a user of http://bionames.org has about a 1
> in 4 chance of getting at least one digitised original description for
> most taxa (some of which will be copyrighted)
> >
> > 5. We can wring our hands about the gaps, or we can do something
> about it. It is easy to identity the major publishers of taxonomy (see
> http://iphylo.blogspot.co.uk/2013/06/bionames-and-where-taxonomy-is-
> published.html ), why not start talking to them about what benefits
> taxonomic indexing could bring to them?
> >
> > Regards
> >
> > Rod
> >
> >
> > On 20 Jun 2013, at 13:21, Dave Roberts wrote:
> >
> >> +1
> >>
> >> but isn't that what BHL set out to do, but ran headlong into the
> copyright wall?  OK increasing amounts of modern literature are open-
> source, but that still leaves a huge gap in coverage.
> >>
> >> Cheers, Dave
> >> --
> >> On 20 Jun 2013, at 12:40, Roderic Page <r.page at bio.gla.ac.uk> wrote:
> >>
> >>> +1
> >>>
> >>> On 20 Jun 2013, at 12:21, Quentin Groom wrote:
> >>>
> >>>> Dear Rod, Donat and others,
> >>>> This is a little off topic, but it seems to me that we need a
> project on the scale of the Human Genome Project to get accurate
> transcriptions and markup of all the legacy text. At the moment there
> are many small scale trials, but to push the cost down and cover the
> vast corpus of literature we need to scale up. I'm sure that OCR could
> be improved and that automatic markup is possible, indeed we need a big
> project to give incentive to innovations on this topic. Perhaps we need
> to start pushing our funders in this direction.
> >>>> Rod, what you're doing is useful as it, at very least, shows us
> what is and might be possible.
> >>>> Regards
> >>>> Quentin
> >>>>
> >>>> Roderic Page wrote:
> >>>>>
> >>>>> I guess I'm struggling to see what we're arguing about.
> >>>>>
> >>>>> I have no issue with publishing structured documents going
> forward, and all power to ZooKeys (and sister journals) for pioneering
> this. The taxonomic literature viewer I built last night is possible
> because of Pensoft.
> >>>>>
> >>>>> However, the vast majority of animal taxa have not been published
> in this way, and until we have described >10^6 new species in
> structured documents, this will always be the case. So, what do do
> about this legacy? How do we tackle that in a way that is scalable? How
> do we do this across all taxa, not just a few select groups (ants are
> cool, but there's a LOT more to life than ants).
> >>>>>
> >>>>> Furthermore, how do we integrate the taxonomic literature with
> the broader biodiversity literature (e.g., ecology, genomics, etc.).
> How do we make taxonomic literature as findable and as accessible? When
> people publish articles in Nature, why is the taxonomic literature
> cited not linked in the same way as the other papers? Why is most of
> the taxonomic literature effectively invisible in the digital age?
> >>>>>
> >>>>> These are the things that motivate me to build things like
> BioNames, which currently has about 3.9 million names, and 400,000
> articles (of which about a quarter I've linked to some form of digital
> identifier). Is it complete, obviously not. Is it a ridiculous thing to
> attempt, of course it is. Is it useful, I hope so.
> >>>>>
> >>>>> Regards
> >>>>>
> >>>>> Rod
> >>>>>
> >>>>> On 20 Jun 2013, at 10:52, Donat Agosti wrote:
> >>>>>
> >>>>>
> >>>>>> May be Chuck will now ? that's how I recapitulate my exchanges
> along the history of BHL.
> >>>>>>
> >>>>>> I don't say treatment only ? we have most of the names already
> done in ants (see HNS), the literature has been refenced, scanned and
> linked to the citations well before BHL existed (Smithsonian supported
> the scanning as their first grant by the Atherton Seidall foundation,
> parallel to Biologia Centrali Americana and the mosiqto group), so the
> next logic step is to dig into content. And that is treatment in the
> content of names (even Linnaeus didn't just supply binomen, but they
> all are linked to a treatment), and materials citations, which are
> children of the treatment (and even Linnaeus had them).
> >>>>>>
> >>>>>> May be one should turn it around. You work like crazy to
> discover articles in a massive body of legacy, and then dig out names.
> Essentially we in the ant world  have that and want more, and we have
> learned a lesson: This approach is extremely inefficient.  So, the
> questions I am really interested in is: how can we avoid make you work
> that much? And the only way is to promote the publishing of structured
> (eg semantically enhanced linked publications), that also include the
> elements the Linnaeus foresaw in his minimalist Systema: names AND
> treatments with some structure (description, ecology/behavior,
> distribution/ citations). And that's why there is taxpub and needs
> being promoted by good implementations like those of Pensoft.
> >>>>>>
> >>>>>>
> >>>>>> Donat
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> From: Roderic Page [mailto:r.page at bio.gla.ac.uk]
> >>>>>> Sent: Thursday, June 20, 2013 2:03 PM
> >>>>>> To: Donat Agosti
> >>>>>> Cc: taxacom at mailman.nhm.ku.edu; 'Lyubomir Penev'
> >>>>>> Subject: Re: [Taxacom] A new way to view taxonomic publications
> >>>>>>
> >>>>>> Hi Donat,
> >>>>>>
> >>>>>> Quick comment on "BHL deliberately allows access to single
> pages, because their scientists wanted to be able to link directly to
> the page of the treatment, protologue"
> >>>>>>
> >>>>>> BHL allows access to pages because that's the physical unit they
> scan, and the obvious thing to expose on their web page. They also
> didn't have an easy way of locating articles (which has been one of the
> biggest complaints about BHL). I seriously doubt it was a decision to
> enable people to link to protologues. It's the standard way you expose
> scanned literature.
> >>>>>>
> >>>>>> I get that linking to the actual treatment/nomenclatural event
> is desirable, all I'm arguing is that article-level linking is more
> tractable, and enables a bunch of things that are bigger than simply
> providing access to taxonomic names. The prize is much bigger than
> that.
> >>>>>>
> >>>>>> Regards
> >>>>>>
> >>>>>> Rod
> >>>>>>
> >>>>>> On 20 Jun 2013, at 10:15, Donat Agosti wrote:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> From: Roderic Page [mailto:r.page at bio.gla.ac.uk]
> >>>>>> Sent: Thursday, June 20, 2013 12:34 PM
> >>>>>> To: Donat Agosti
> >>>>>> Cc: taxacom at mailman.nhm.ku.edu com; Lyubomir Penev
> >>>>>> Subject: Re: [Taxacom] A new way to view taxonomic publications
> >>>>>>
> >>>>>> Hi Donat,
> >>>>>>
> >>>>>>
> >>>>>> In the demo you skip one of the nice elements, the treatment
> element. And in my view this is a loss of quality, which you can easily
> see, when you start looking up one of the new descriptions, eg .
> Paedophryne dekot. If you look it up on the right hand in Biostor, you
> finally end up up at the article level and the treatment itself, which
> is the relevant information that I need, not the publication. Similar
> the pdf that you show in biostor has lost all the links that are in the
> original pdf.
> >>>>>>
> >>>>>> It would be straightforward to list treatments in the "Contents"
> section. The articles discovered in the reference are typically in PDF
> or image form, but obviously the next step is to display them in the
> same way, where possible.
> >>>>>> DA: this is the huge problem: How to get them out of the pdf
> (text born, or images) ? this right now does not scale to your 10^6.
> And it might be also questionable whether this underlies the big data
> paradigm, since there are not plenty of treatment covering the same but
> rather singletons, and thus errors in the conversion play a different
> role?
> >>>>>>
> >>>>>>
> >>>>>> I know, you are not interested in the treatment but names and
> publications. I as a taxonomist in the world you describe, a
> publication being a database, which happens when you convert it into
> XML, and even more so an XML that is domain specific, don't want to be
> stuck in the world or articles, just because we grew up with it. The
> goal is customized information, and that means treatment (in the
> context of a scientific publication). And with Zookeys at hand you have
> all to make this happen.
> >>>>>>
> >>>>>> Finally, most of the functionality is already in the Zookeys
> article itself when you look at it in the html version instead of the
> pdf your link to
> (http://www.pensoft.net/journals/zookeys/article/1963/at-the-lower-
> size-limit-for-tetrapods-two-new-species-of-the-miniaturized-frog-
> genus-paedophryne-anura-microhylidae-) , and even more so in their
> species profiles
> http://ptp.pensoft.eu/external_details.php?type=1&query=Paedophryne .
> The interesting step then is to get this done for other journals and
> see, how it looks like. There, the production of clean OCR or text
> extraction from PDF, the semantic mark-up is not done, that is served
> on a silver platter
> >>>>>> by Pensoft, with a pretty overhead in the production of the
> article.
> >>>>>>
> >>>>>> Two points, one minor, one not so. The minor point is that, yes
> Pensoft displays marked-up HTML, but it is surrounded by lots of
> publish-specific stuff. This is one reason why PDFs are still so
> popular, publishers can't resist surrounding HTML with junk (logos,
> links, etc.).
> >>>>>>
> >>>>>> The second point is that Pensoft has a platform for their
> journals. Great, but I want platform  that is publisher-agnostic. I
> don't care who publishes the stuff, I want a consistent way to explore
> it. I chose ZooKeys because yes, it is essentially pre-processed, so I
> can focus on just the rendering. But I want PLoS, BMC, SciElo journals
> looking like this, I want Zootaxa to look like this, etc.
> >>>>>> DA: I agree, we want to have an independent site, but we also
> need to have a business model behind (University pays, EU-pays,
> somebody pays). The consistent way is clearly the goal.
> >>>>>>
> >>>>>>
> >>>>>> Then this needs to be compared to other similar sites, like
> Species-ID http://species-id.net/wiki/Paedophryne_dekot , that allows
> the crowd to edit and add content or Plazi, the treatment repository
> http://tinyurl.com/nku2rdd , which allows to get back to the treatment
> and not end up in the article.
> >>>>>>
> >>>>>> So, the challenge has to be that Bionames does not loose
> granularity, and operates at the level we cite (not article but a page
> within an article, essentially linking to the treatment), and to show
> mechanisms to read in pdfs that have no XML, not text in fact,  and
> make this fly, something you have demonstrated to find articles within
> the BHL body. This time just one level down.
> >>>>>>
> >>>>>> I realise you want treatments, and I'm not saying I don't, but I
> have to choose the level of granularity that scales across 10^6 names
> and 10^5 publications. I need an infrastructure that enables me to make
> links between names and publications, and that means working at the
> level of articles. This is also where citation networks operate, and
> where links to other kinds of data operate (e.g., links between
> sequences, phylogenies, and publications). The reality is the
> publication is the fundamental unit we keep track of.
> >>>>>>
> >>>>>> DA: I would argue, that this is an artifact. BHL deliberately
> allows access to single pages, because their scientists wanted to be
> able to link directly to the page of the treatment, protologue. All the
> references in HNS are linked to the particular page, not the article.
> Yes  we have to cite, and we measure citations, but this is just a
> historical legacy, similar that BHL works on journals (and not
> articles, that what you are digging out with a lot of pain) is because
> of constraints outside the taxonomists control (the libraries have them
> in the stacks this way). All the microcitations point to pages, not
> articles.
> >>>>>>
> >>>>>> Now, there are interesting developments in making publications
> more granular. PLoS has had DOIs for figures for some time, and BMC
> figures are retrospectively having DOIs assigned by figshare (e.g.,
> http://dx.doi.org/10.6084/m9.figshare.34256 ).
> >>>>>>
> >>>>>> I would argue that if you are serious about treatments being
> citable and discoverable, you'd give them DOIs, so that, for example,
> the treatments within a ZooKeys article would have their own DOIs. It's
> time we started playing the bigger game. It's not about treatments per
> see, it's about linking citable entities.
> >>>>>> DA: We are serious, just not as fast as you. We also decided for
> the time being to make use of stable http URI for identifiers instead
> of DOIs, not least because the goal is getting this content into the
> semantic web. This follows the venue CETAF is going by using this
> system for their specimen data (see also the discussion on stable
> identifiershttps://plus.google.com/u/1/117201190352607228695/posts/RXEw
> pGWu18o)
> >>>>>>
> >>>>>>
> >>>>>> Cheers
> >>>>>> Donat
> >>>>>>
> >>>>>> Regards
> >>>>>>
> >>>>>> Rod
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> Cheers
> >>>>>>
> >>>>>> Donat
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Roderic Page
> >>>>>> Sent: Thursday, June 20, 2013 12:50 AM
> >>>>>> To: taxacom at mailman.nhm.ku.edu com
> >>>>>> Subject: [Taxacom] A new way to view taxonomic publications
> >>>>>>
> >>>>>> I've developed a somewhat experimental viewer for articles in
> the journal ZooKeys which might be of interest. There is a blog post
> here http://iphylo.blogspot.co.uk/2013/06/a-new-way-to-view-taxonomic-
> publications.html
> >>>>>>
> >>>>>> You can try a live example here:
> http://bionames.org/labs/zookeys-viewer/?doi=10.3897/zookeys.154.1963
> >>>>>>
> >>>>>> This viewer is one of the motivations behind http://bionames.org
> I'm aiming for a platform where we can embed the taxonomic literature
> and have names and publications seamlessly linked together, enabling us
> to navigate through the primary taxonomic literature in a single place.
> >>>>>>
> >>>>>> Regards
> >>>>>>
> >>>>>> Rod
> >>>>>>
> >>>>>> ---------------------------------------------------------
> >>>>>> Roderic Page
> >>>>>> Professor of Taxonomy
> >>>>>> Institute of Biodiversity, Animal Health and Comparative
> Medicine College of Medical, Veterinary and Life Sciences 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
> >>>>>> Skype: rdmpage
> >>>>>> Facebook: http://www.facebook.com/rdmpage
> >>>>>> Twitter: http://twitter.com/rdmpage
> >>>>>> Blog: http://iphylo.blogspot.com
> >>>>>> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> >>>>>> Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
> >>>>>> Citations:
> http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> >>>>>> ORCID id: http://orcid.org/0000-0002-7101-9767
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Taxacom Mailing List
> >>>>>> Taxacom at mailman.nhm.ku.edu
> >>>>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >>>>>>
> >>>>>> The Taxacom Archive back to 1992 may be searched with either of
> these methods:
> >>>>>>
> >>>>>> (1) by visiting http://taxacom.markmail.org
> >>>>>>
> >>>>>> (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> >>>>>>
> >>>>>> Celebrating 26 years of Taxacom in 2013.
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> ---------------------------------------------------------
> >>>>>> Roderic Page
> >>>>>> Professor of Taxonomy
> >>>>>> Institute of Biodiversity, Animal Health and Comparative
> Medicine
> >>>>>> College of Medical, Veterinary and Life Sciences
> >>>>>> 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
> >>>>>> Skype: rdmpage
> >>>>>> Facebook: http://www.facebook.com/rdmpage
> >>>>>> Twitter: http://twitter.com/rdmpage
> >>>>>> Blog: http://iphylo.blogspot.com
> >>>>>> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> >>>>>> Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
> >>>>>> Citations:
> http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> >>>>>> ORCID id: http://orcid.org/0000-0002-7101-9767
> >>>>>>
> >>>>>>
> >>>>>> ---------------------------------------------------------
> >>>>>> Roderic Page
> >>>>>> Professor of Taxonomy
> >>>>>> Institute of Biodiversity, Animal Health and Comparative
> Medicine
> >>>>>> College of Medical, Veterinary and Life Sciences
> >>>>>> 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
> >>>>>> Skype: rdmpage
> >>>>>> Facebook: http://www.facebook.com/rdmpage
> >>>>>> Twitter: http://twitter.com/rdmpage
> >>>>>> Blog: http://iphylo.blogspot.com
> >>>>>> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> >>>>>> Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
> >>>>>> Citations:
> http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> >>>>>> ORCID id: http://orcid.org/0000-0002-7101-9767
> >>>>>>
> >>>>>>
> >>>>>
> >>>>> ---------------------------------------------------------
> >>>>> Roderic Page
> >>>>> Professor of Taxonomy
> >>>>> Institute of Biodiversity, Animal Health and Comparative Medicine
> >>>>> College of Medical, Veterinary and Life Sciences
> >>>>> 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
> >>>>> Skype: rdmpage
> >>>>> Facebook: http://www.facebook.com/rdmpage
> >>>>> Twitter: http://twitter.com/rdmpage
> >>>>> Blog: http://iphylo.blogspot.com
> >>>>> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> >>>>> Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
> >>>>> Citations:
> http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> >>>>> ORCID id: http://orcid.org/0000-0002-7101-9767
> >>>>>
> >>>>> _______________________________________________
> >>>>> Taxacom Mailing List
> >>>>> Taxacom at mailman.nhm.ku.edu
> >>>>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >>>>>
> >>>>> The Taxacom Archive back to 1992 may be searched with either of
> these methods:
> >>>>>
> >>>>> (1) by visiting http://taxacom.markmail.org
> >>>>>
> >>>>> (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> >>>>>
> >>>>> Celebrating 26 years of Taxacom in 2013.
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>> --
> >>>> Dr. Quentin Groom
> >>>> (Botany and Information Technology)
> >>>>
> >>>> National Botanic Garden of Belgium
> >>>> Domein van Bouchout
> >>>> B-1860 Meise
> >>>> Belgium
> >>>>
> >>>> ORCID: 0000-0002-0596-5376
> >>>>
> >>>> Landline; +32 (0) 226 009 20 ext. 364
> >>>> FAX:      +32 (0) 226 009 45
> >>>>
> >>>> E-mail:     quentin.groom at br.fgov.be
> >>>> Skype name: qgroom
> >>>> Website:    www.botanicgarden.be
> >>>
> >>> ---------------------------------------------------------
> >>> Roderic Page
> >>> Professor of Taxonomy
> >>> Institute of Biodiversity, Animal Health and Comparative Medicine
> >>> College of Medical, Veterinary and Life Sciences
> >>> 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
> >>> Skype: rdmpage
> >>> Facebook: http://www.facebook.com/rdmpage
> >>> Twitter: http://twitter.com/rdmpage
> >>> Blog: http://iphylo.blogspot.com
> >>> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> >>> Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
> >>> Citations:
> http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> >>> ORCID id: http://orcid.org/0000-0002-7101-9767
> >>>
> >>> _______________________________________________
> >>> Taxacom Mailing List
> >>> Taxacom at mailman.nhm.ku.edu
> >>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> >>>
> >>> The Taxacom Archive back to 1992 may be searched with either of
> these methods:
> >>>
> >>> (1) by visiting http://taxacom.markmail.org
> >>>
> >>> (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> >>>
> >>> Celebrating 26 years of Taxacom in 2013.
> >>
> >> --
> >> Dr D.McL. Roberts,        Tel: +44 (0)20 7942 5086
> >> ViBRANT Project Manager,
> >> Dept. Life Sciences,
> >> The Natural History Museum,
> >> Cromwell Road,
> >> London        SW7 5BD
> >> Great Britain             Email: dmr at nomencurator dot org
> >> Web page:  http://vbrant.eu
> >> Web page:  http://scratchpads.eu
> >> Web page:  http://www.editwebrevisions.info/
> >> --
> >> "You can't just ask customers what they want and then try and give
> it to them.  By the time you get it built, they'll want something new."
> [Steve Jobs, quoted in The Guardian, Technology Section, 25 June 09].
> >> --
> >>
> >>
> >>
> >>
> >>
> >
> > ---------------------------------------------------------
> > Roderic Page
> > Professor of Taxonomy
> > Institute of Biodiversity, Animal Health and Comparative Medicine
> > College of Medical, Veterinary and Life Sciences
> > 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
> > Skype: rdmpage
> > Facebook: http://www.facebook.com/rdmpage
> > Twitter: http://twitter.com/rdmpage
> > Blog: http://iphylo.blogspot.com
> > Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> > Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
> > Citations:
> http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> > ORCID id: http://orcid.org/0000-0002-7101-9767
> >
> 
> --
> Dr D.McL. Roberts,        Tel: +44 (0)20 7942 5086
> ViBRANT Project Manager,
> Dept. Life Sciences,
> The Natural History Museum,
> Cromwell Road,
> London        SW7 5BD
> Great Britain             Email: dmr at nomencurator dot org
> Web page:  http://vbrant.eu
> Web page:  http://scratchpads.eu
> Web page:  http://www.editwebrevisions.info/
> --
> "You can't just ask customers what they want and then try and give it
> to them.  By the time you get it built, they'll want something new."
> [Steve Jobs, quoted in The Guardian, Technology Section, 25 June 09].
> --
> 
> 
> 
> 
> 
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Fri, 21 Jun 2013 11:17:53 +0000
> From: stuartf <stuartf at knights.ucf.edu>
> Subject: [Taxacom] david r smith
> To: "entomo-l at listserv.uoguelph.ca" <entomo-l at listserv.uoguelph.ca>,
>         "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>,
>         "ecn-l at listserv.unl.edu" <ecn-l at listserv.unl.edu>
> Message-ID:
> 
> <E5808E8413228F4384BD4FCE18D3CB1730C47BDB at SN2PRD0710MB372.namprd07.prod
> .outlook.com>
> 
> Content-Type: text/plain; charset="iso-8859-1"
> 
> good morning folks - sorry about the cross post
> 
> my how time flies
> 
> they tell me that david r smith - symphyta - smithsonian has retired
> and i have managed to loose his e-address
> 
> if anyone can supply - please do
> 
> otherwise
> 
> i am interested in contacting folks within the usa who are working with
> tenthredinidae
> 
> thanks in advance
> 
> reply off list server to cut down on the chatter
> 
> cheers!
> 
> rof
> 
> 
> Stuart M Fullerton ROF, Research Associate Arthropod
> 
> Collection (UCFC), Dept. of Biology, University of Central Florida, PO
> 
> Box 162368, Orlando, Florida, 32816-2368, USA. stuartf at knights.ucf.edu
> 
> <mailto:stuartf at pegasus.cc.ucf.edu>(407) 823-6540 (no voice mail),
> http://bugcloset.cos.ucf.edu/
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Fri, 21 Jun 2013 10:10:28 -0400
> From: "Chris Thompson" <xelaalex at cox.net>
> Subject: Re: [Taxacom] david r smith = still active
> To: "stuartf" <stuartf at knights.ucf.edu>,
>         <entomo-l at listserv.uoguelph.ca>,
> <taxacom at mailman.nhm.ku.edu>,
>         <ecn-l at listserv.unl.edu>
> Message-ID: <2AAA1D175F284660BD66660AFF651CCE at ChrisPC>
> Content-Type: text/plain; format=flowed; charset="iso-8859-1";
>         reply-type=original
> 
> David R Smith,
> 
> the long term USDA - Smithsonian specialist on sawflies is live and
> well.
> 
> His USDA ARS Systematic Entomology Lab e-mail address should still be
> active
> 
> try david.smith at ars.usda.gov
> 
> Cheers
> 
> Chris Thompson
> from home
> 
> -----Original Message-----
> From: stuartf
> Sent: Friday, June 21, 2013 7:17 AM
> To: entomo-l at listserv.uoguelph.ca ; taxacom at mailman.nhm.ku.edu ;
> ecn-l at listserv.unl.edu
> Subject: [Taxacom] david r smith
> 
> good morning folks - sorry about the cross post
> 
> my how time flies
> 
> they tell me that david r smith - symphyta - smithsonian has retired
> and i
> have managed to loose his e-address
> 
> if anyone can supply - please do
> 
> otherwise
> 
> i am interested in contacting folks within the usa who are working with
> tenthredinidae
> 
> thanks in advance
> 
> reply off list server to cut down on the chatter
> 
> cheers!
> 
> rof
> 
> 
> Stuart M Fullerton ROF, Research Associate Arthropod
> 
> Collection (UCFC), Dept. of Biology, University of Central Florida, PO
> 
> Box 162368, Orlando, Florida, 32816-2368, USA. stuartf at knights.ucf.edu
> 
> <mailto:stuartf at pegasus.cc.ucf.edu>(407) 823-6540 (no voice mail),
> http://bugcloset.cos.ucf.edu/
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom Archive back to 1992 may be searched with either of these
> methods:
> 
> (1) by visiting http://taxacom.markmail.org
> 
> (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom
> your search terms here
> 
> Celebrating 26 years of Taxacom in 2013.
> 
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Fri, 21 Jun 2013 15:05:00 +0000
> From: "Sharkey, Michael J" <msharkey at uky.edu>
> Subject: Re: [Taxacom] david r smith = still active
> To: Chris Thompson <xelaalex at cox.net>, stuartf
>         <stuartf at knights.ucf.edu>,      "entomo-l at listserv.uoguelph.ca"
>         <entomo-l at listserv.uoguelph.ca>,
> "taxacom at mailman.nhm.ku.edu"
>         <taxacom at mailman.nhm.ku.edu>,   "ecn-l at listserv.unl.edu"
>         <ecn-l at listserv.unl.edu>
> Cc: Dave Smith <sawfly2 at aol.com>
> Message-ID:
>         <ADE0C9CF8722084581E6E577699C41DE35803487 at ex10mb02.ad.uky.edu>
> Content-Type: text/plain; charset="us-ascii"
> 
> I correspond with Dr. Smith fairly routinely using the address: Dave
> Smith <sawfly2 at aol.com>
> 
> Dr. Michael Sharkey
> Department of Entomology
> University of Kentucky
> S-225 Ag. Sci. N.
> Lexington, KY 40546-0091
> msharkey at uky.edu
> www.sharkeylab.org
> 
> 
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Chris Thompson
> Sent: Friday, June 21, 2013 10:10 AM
> To: stuartf; entomo-l at listserv.uoguelph.ca; taxacom at mailman.nhm.ku.edu;
> ecn-l at listserv.unl.edu
> Subject: Re: [Taxacom] david r smith = still active
> 
> David R Smith,
> 
> the long term USDA - Smithsonian specialist on sawflies is live and
> well.
> 
> His USDA ARS Systematic Entomology Lab e-mail address should still be
> active
> 
> try david.smith at ars.usda.gov
> 
> Cheers
> 
> Chris Thompson
> from home
> 
> -----Original Message-----
> From: stuartf
> Sent: Friday, June 21, 2013 7:17 AM
> To: entomo-l at listserv.uoguelph.ca ; taxacom at mailman.nhm.ku.edu ; ecn-
> l at listserv.unl.edu
> Subject: [Taxacom] david r smith
> 
> good morning folks - sorry about the cross post
> 
> my how time flies
> 
> they tell me that david r smith - symphyta - smithsonian has retired
> and i have managed to loose his e-address
> 
> if anyone can supply - please do
> 
> otherwise
> 
> i am interested in contacting folks within the usa who are working with
> tenthredinidae
> 
> thanks in advance
> 
> reply off list server to cut down on the chatter
> 
> cheers!
> 
> rof
> 
> 
> Stuart M Fullerton ROF, Research Associate Arthropod
> 
> Collection (UCFC), Dept. of Biology, University of Central Florida, PO
> 
> Box 162368, Orlando, Florida, 32816-2368, USA. stuartf at knights.ucf.edu
> 
> <mailto:stuartf at pegasus.cc.ucf.edu>(407) 823-6540 (no voice mail),
> http://bugcloset.cos.ucf.edu/
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom Archive back to 1992 may be searched with either of these
> methods:
> 
> (1) by visiting http://taxacom.markmail.org
> 
> (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom
> your search terms here
> 
> Celebrating 26 years of Taxacom in 2013.
> 
> 
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom Archive back to 1992 may be searched with either of these
> methods:
> 
> (1) by visiting http://taxacom.markmail.org
> 
> (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> Celebrating 26 years of Taxacom in 2013.
> 
> 
> 
> ------------------------------
> 
> Message: 6
> Date: Fri, 21 Jun 2013 16:49:57 +0100
> From: David.King <David.King at open.ac.uk>
> Subject: Re: [Taxacom] A new way to view taxonomic publications
> To: "taxacom at mailman.nhm.ku.edu" <taxacom at mailman.nhm.ku.edu>
> Message-ID:
> 
> <60667691F130CD418BD0D4FC512EF91217B79553AF at SALCEYCMS1.open.ac.uk>
> Content-Type: text/plain; charset="us-ascii"
> 
> Hi Donat
> 
> I'm with Rod,  BHL OCR can be excellent. In ViBRANT we tried to
> replicate Qin Wei's work with BHL to re-assess how 'bad' the OCR is but
> just couldn't get the same poor quality results.
> 
> In general OCR is very good with body text where there are enough cues
> for the software to work on. Errors still creep in particularly with
> special characters, for example, English OCR software really doesn't
> like Latin ligatures and tends to mangle the end of taxon names even
> though the other characters in the name are accurately identified.
> Another common problem arises from using male and female symbols in
> text, made worse because the symbols are normally found in the middle
> of a very terse description, often full of abbreviations, so devoid of
> cues for non-specialist software to follow.
> 
> Indeed, we gave up on some of our experimental ViBRANT work using
> parts-of-speech tagging to identify anomalies in OCR text because the
> OCR was not bad enough.
> 
> Sadly OCR does struggle in two very useful sections of a document: the
> table of contents and the index. Part of the problem lies with a page
> full of 'funny' words not in the software's dictionary ;-) Then there
> are other problems usually to do with layout such as non-aligned
> columns and leading lines which break the OCR accuracy.
> 
> Cheers
> Dauvit
> 
> ---------------------------------------------------------
> 
> > Date: Thu, 20 Jun 2013 14:21:48 +0100
> > From: Roderic Page <r.page at bio.gla.ac.uk>
> > Subject: Re: [Taxacom] A new way to view taxonomic publications
> > To: Donat Agosti <agosti at amnh.org>
> > Cc: taxacom taxacom <taxacom at mailman.nhm.ku.edu>
> > Message-ID: <3D62E585-50CF-451A-BD62-5CCAE0D779B6 at bio.gla.ac.uk>
> > Content-Type: text/plain;     charset=windows-1252
> >
> > Donat,
> >
> > Again, this is repeating myths. The OCR in BHL ranges from excellent
> in places to crappy in places. If it was uniformly bad we couldn't have
> indexed it for names, nor would http://biostor.org be possible. The
> quality is variable, but we can quantify this. We don't control the
> original OCR, but we can always redo bits if we need to.
> >
> > Indexing OCR documents is a well known problem, and there is a wealth
> of literature of various techniques that can be used  (see
> http://www.mendeley.com/groups/752871/ocr-optical-character-
> recognition/ for an introduction to the literature ). Why do we simply
> say OMG the BHL OCR is bad? Why not be scientific , quantify its
> quality, and exploit the existing technology to improve things?
> >
> > I am constantly flummoxed by our community's assumption that it knows
> what is possible, and what the limit of the state of the art is outside
> its domain. We have barely scratched the surface of what is possible.
> >
> > Regards
> >
> > Rod
> 
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences 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
> Skype: rdmpage
> Facebook: http://www.facebook.com/rdmpage
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
> Citations:
> http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> ORCID id: http://orcid.org/0000-0002-7101-9767
> 
> 
> 
> --
> The Open University is incorporated by Royal Charter (RC 000391), an
> exempt charity in England & Wales and a charity registered in Scotland
> (SC 038302).
> 
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The entire Taxacom Archive back to 1992 may be searched with either of
> these methods:
> Visit: http://taxacom.markmail.org
> Or use a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom  your-search-terms-here
> 
> Celebrating 26 years of Taxacom in 2013.
> 
> End of Taxacom Digest, Vol 87, Issue 25
> ***************************************
> 
> _______________________________________________
> Taxacom Mailing List
> Taxacom at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
> 
> The Taxacom Archive back to 1992 may be searched with either of these
> methods:
> 
> (1) by visiting http://taxacom.markmail.org
> 
> (2) a Google search specified as:
> site:mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
> 
> Celebrating 26 years of Taxacom in 2013.




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