University of Glasgow

Roderic Page

Over on Google Plus (yeah, me neither) [Donat Agosti is giving me a hard
time](https://plus.google.com/115599971535973973155/posts/bMzh7eXsfsJ)
regarding the quality of some data that I am using. I\'ve responded to
Donat directly, but here I just want to quickly outline two different
approaches to cleaning and reconciling bibliographic metadata.  
  
The problem addressed by Donat is the issue of multiple strings for the
same journal (e.g., the plethora of different abbreviations and
permutations people use to refer to the same journal). In trying to make
sense of this mess there are a couple of strategies we can use. One is
to cluster the strings into sets that we think refer to the same thing,
e.g.:  
  
![R1](http://lh5.ggpht.com/-ZoB4Al0Xgkw/UXT9V7wFJYI/AAAAAAAACqo/OxO_dyTR-VE/r1.png?imgmax=800 "r1.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="230"}  
We could then synthesise the preferred journal name from this set. We
could make some sort of consensus string, for example. There are also
some quite nice Bayesian methods for combining contradictory metadata.  
  
Another approach, which I use, is to map the strings to a third party
identifier, in this case an ISSN:  
  
![R2](http://lh5.ggpht.com/-JdOsPwpM-SQ/UXT9XAjIQTI/AAAAAAAACqw/kxMTUxlgIIc/r2.png?imgmax=800 "r2.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="210"}  
Once I\'ve done this I can use the identifier to refer to the journal,
hence ultimately I don\'t particularly care what string is best for the
journal (indeed, I can defer to a third party for this decision).  
  
The point is obsessing with clean, \"correct\" bibliographic metadata is
something of a fool\'s errand. Obviously, it\'s nice to have clean
metadata if you can get it, but in many cases there is no exact answer
to what is the correct metadata. Some journals have multiple names
(e.g., in different languages), some run different volume numbering
schemes in parallel, and date of publication can be rather problematic
(see my Mendeley group on [publication
dates](http://www.mendeley.com/groups/697721/publication-dates/)). If we
can map a publication to a globally unique identifier, such as a DOI,
then we can sidestep this issue and focus on what I think really
matters - linking data together.


Over on Google Plus (yeah, me neither) Donat Agosti is giving me a hard time regarding the quality of some data that I am using.

BioNames update - reconciliation strategies

![Refine](http://lh4.ggpht.com/-HsS8f5sKWWc/Ty_fgRiXiII/AAAAAAAABHg/In4r9NXMkoc/refine.png?imgmax=800){border="0"
width="128" height="128" style="float:right;"}In an [earlier
post](http://iphylo.blogspot.com/2012/02/using-google-refine-and-taxonomic.html)
I discussed using [Open Refine](http://openrefine.org/) (formerly
[Google Refine](https://code.google.com/p/google-refine/)) to clean and
reconcile taxon names. I\'ve added an additional service that can be
used to reconcile author names that uses the [Virtual International
Authority File (VIAF)](http://viaf.org/) API. Using this service we can
match authors to VIAF identifiers (you may have noticed these appearing
on people\'s pages in Wikipedia, e.g. [Mary J.
Rathbun](http://en.wikipedia.org/wiki/Mary_Rathbun)\'s Wikipedia page
lists her VIAF as [61796012](http://viaf.org/viaf/61796012)).  
  
To use the service follow the instructions in the [earlier
post](http://iphylo.blogspot.com/2012/02/using-google-refine-and-taxonomic.html)
but add the service:  
  
http://iphylo.org/\~rpage/phyloinformatics/services/reconciliation_viaf.php  
  
This service is fairly crude, in particular, I make no attempt to score
the matches that VIAR returns because this would require parsing and
normalising author names. This could be added if needed. If you want
some exmaple names to try, here are some taxonomists:  
  

    George A Boulenger
    G A Boulenger
    Wilhelm Michaelsen
    W Michaelsen
    Colin Campbell Sanborn
    Suzanne Hand
    Philip Hershkovitz
    Yehudah Leopold Werner
    W B Spencer
    Norman Platnick


In an earlier post I discussed using Open Refine (formerly Google Refine) to clean and reconcile taxon names. I've added an additional service that can be used to reconcile author names that uses the Virtual International Authority File (VIAF) API.

Messages de Rogue Scholar

BioNames update - reconciliation strategies

Reconciling author names using Open Refine and VIAF