[Taxacom] A new way to view taxonomic publications

Roderic Page r.page at bio.gla.ac.uk
Thu Jun 20 03:03:49 CDT 2013


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.

> 
> 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.

> 
> 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.

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.

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
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> 

---------------------------------------------------------
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




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