University of Glasgow

Roderic Page

![npre20104928-1.thumb.png](http://lh6.ggpht.com/_Gct8lVAxKqQ/TJoRGmYx_8I/AAAAAAAAAw0/vCi3C6uZ33I/npre20104928-1.thumb.png?imgmax=800){border="0"
width="77" height="100" style="float:right;"}Yesterday I uploaded a
manuscript to Nature Precedings that describes the inner workings of
[BioStor](http://biostor.org). The title is \"Finding scientific
articles in a large digital archive: BioStor and the Biodiversity
Heritage Library\", and you can grab it here:
[hdl:10101/npre.2010.4928.1](http://hdl.handle.net/10101/npre.2010.4928.1).  
  
Manuscripts describing databases are usually pretty turgid affairs, and
this isn\'t an exception, despite my attempts to spice it up with the
tale of ~~*Leviathan*~~, oops, *Livyatan* (see
[doi:10.1038/nature09381](http://dx.doi.org/10.1038/nature09381) and
[Wikipedia](http://en.wikipedia.org/wiki/Livyatan_melvillei#Etymology_and_nomenclature)).
Plus, I can\'t escape the thought that BioStor would have been a lot
more fun to write if I\'d used a key-value database like CouchDB. I fear
this is often the way of things. By the time it comes to writing
something up, you realise that if you could start over you\'d do it
rather differently.


Yesterday I uploaded a manuscript to Nature Precedings that describes the inner workings of BioStor.

Finding scientific articles in a large digital archive: BioStor and the Biodiversity Heritage Library

Finally submitted (two days late) a manuscript for the [*BMC
Bioinformatics* Special Issue on Biodiversity
Informatics](http://www.uvm.edu/~insarkar/bmc/) organised by Neil Sarkar
and sponsored by EOL and CBOL. The manuscript, entitled \"bioGUID:
resolving, discovering, and minting identifiers for biodiversity
informatics\" describes my [bioGUID](http://bioguid.info/) project. If
you are interested made pre-print available at Nature Precedings
([hdl:10101/npre.2009.3079.1](http://hdl.handle.net/10101/npre.2009.3079.1)).


Finally submitted (two days late) a manuscript for the

 BMC Bioinformatics

Special Issue on Biodiversity Informatics organised by Neil Sarkar and sponsored by EOL and CBOL. The manuscript, entitled "bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics" describes my bioGUID project. If you are interested made pre-print available at Nature Precedings (hdl:10101/npre.2009.3079.1).

bioGUID manuscript

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhfQfJ_qKaHDWCGypQzExFiLbOVthnC52tNrhgFKsVo-JODIOLgTcX_FAKqzIvRhMF1ogifeWRzHsGCDst0gurnqWfWShyphenhypheneXrz9hsanY6IPWEi35CcIrIuEjOhTpwB0gTdoCLr7/s320/cover.gif){#BLOGGER_PHOTO_ID_5194920985396578738
style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhfQfJ_qKaHDWCGypQzExFiLbOVthnC52tNrhgFKsVo-JODIOLgTcX_FAKqzIvRhMF1ogifeWRzHsGCDst0gurnqWfWShyphenhypheneXrz9hsanY6IPWEi35CcIrIuEjOhTpwB0gTdoCLr7/s1600-h/cover.gif){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
Bit of a rarity these days. My paper on identifiers in biodiversity
informatics, which I mentioned
[earlier](http://iphylo.blogspot.com/2008/04/biodiversity-informatics-challenge-of.html)
when I deposited the preprint at [Nature
Precedings](http://precedings.nature.com/), has been published in
*Briefings in Bioinformatics*
([doi:10.1093/bib/bbn022](http://dx.doi.org/10.1093/bib/bbn022)).  
  
Here\'s the abstract:  

> A major challenge facing biodiversity informatics is integrating data
> stored in widely distributed databases. Initial efforts have relied on
> taxonomic names as the shared identifier linking records in different
> databases. However, taxonomic names have limitations as identifiers,
> being neither stable nor globally unique, and the pace of molecular
> taxonomic and phylogenetic research means that a lot of information in
> public sequence databases is not linked to formal taxonomic names.
> This review explores the use of other identifiers, such as specimen
> codes and GenBank accession numbers, to link otherwise disconnected
> facts in different databases. The structure of these links can also be
> exploited using the PageRank algorithm to rank the results of searches
> on biodiversity databases. The key to rich integration is a commitment
> to deploy and reuse globally unique, shared identifiers \[such as
> Digital Object Identifiers (DOIs) and Life Science Identifiers
> (LSIDs)\], and the implementation of services that link those
> identifiers.


Paper published

[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhENEFieHNtx9KWRuS9risYdlZl9RUTY-ANstikhmr6lkl4s2T9qpH8JPFZk1obFgUDKDchgRxSBSgxzjX8SONSEnfhLnSIHPiLQULHGbNptxyflDst0sDuLDOU3KfgBPUqhKrU/s320/nature.jpg){#BLOGGER_PHOTO_ID_5121668851096326434
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhENEFieHNtx9KWRuS9risYdlZl9RUTY-ANstikhmr6lkl4s2T9qpH8JPFZk1obFgUDKDchgRxSBSgxzjX8SONSEnfhLnSIHPiLQULHGbNptxyflDst0sDuLDOU3KfgBPUqhKrU/s1600-h/nature.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
The kind people at *Nature* have taken pity on my rapidly fading
research career, and have highlighted my note \"Towards a Taxonomically
Intelligent Phylogenetic Database\" in Nature Precedings
([doi:10.1038/npre.2007.1028.1](http://dx.doi.org/10.1038/npre.2007.1028.1))
on the [Nature web site](http://www.nature.com). Frankly this is
probably the only way I\'ll be getting into *Nature*\...


The kind people at

 Nature

have taken pity on my rapidly fading research career, and have highlighted my note "Towards a Taxonomically Intelligent Phylogenetic Database" in Nature Precedings (doi:10.1038/npre.2007.1028.1) on the Nature web site. Frankly this is probably the only way I'll be getting into

 Nature

...

Messaggi di Rogue Scholar

Finding scientific articles in a large digital archive: BioStor and the Biodiversity Heritage Library

bioGUID manuscript

Paper published

Getting into Nature ... sort of