University of Glasgow

Roderic Page

Quick notes on an experimental feature I\'ve added to
[BioNames](http://bionames.org). It attempts to identify possible
taxonomic synonyms by extracting pairs of names with the same species
name that appear together on the same page of text. The text could be
full text for an open access article, OCR text from BHL, or the title
and abstract for an article. For example, the following paper creates a
new combination, *Hadwenius tursionis*, for a parasite of the bottlenose
dolphin. This name is a synonym of *Synthesium tursionis*.  
  

> Fernández, M., Balbuena, J. A., & Raga, J. A. (1994, July). [Hadwenius
> tursionis]{style="background-color:yellow"} (Marchi, 1873) n. comb.
> (Digenea, Campulidae) from the bottlenose dolphin Tursiops truncatus
> (Montagu, 1821) in the western Mediterranean. Syst Parasitol. Springer
> Science + Business Media.
> [doi:10.1007/bf00009519](http://dx.doi.org/10.1007/bf00009519)  
>   
> The taxonomic position of [Synthesium
> tursionis]{style="background-color:yellow"} (Marchi, 1873) (Digenea,
> Campulidae) is revised, based on material from 147 worms from four
> bottlenose dolphins Tursiops truncatus stranded off the Comunidad
> Valenciana (Spanish western Mediterranean). The species is transferred
> to Hadwenius, as H. tursionis n. comb., and characterised by a high
> length/width ratio of the body, spinose cirrus and unarmed metraterm.
> Synthesium, a monotypic genus, becomes a synonym of Hadwenius. The
> intraspecific variation of some morphological traits is briefly
> discussed.

  
If we extract taxonomic names from the title and abstract we have the
pair (*Synthesium tursionis*, *Hadwenius tursionis*). If we do this
across all the text currently in BioNames then we discover other pairs
of names that include *Synthesium tursionis*, joining these together we
can create a graph of co-occurrence of names that are synonyms (see
[Synthesium tursionis](http://bionames.org/names/cluster/523974)).  
  
![](data:image/svg+xml;base64,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)  
These graphs are computed automatically, and there is inevitably scope
for error. Taxa that are not synonyms may have the same specific name
(e.g., parasites and hosts may have the same specific name), and some of
the names extracted from the text may be erroneous. At the same time,
anecdotally it is a useful way to discover links between names. Even
better, this approach means that we have the associated evidence for
each pair of names. The interface in BioNames lists the references that
contain the pairs of names, so you can evaluate the evidence for
synonymy. It would be useful to try and evaluate the automatically
detected synonyms by comparisons with existing lists of synonyms (e.g.,
from GBIF).


Quick notes on an experimental feature I've added to BioNames. It attempts to identify possible taxonomic synonyms by extracting pairs of names with the same species name that appear together on the same page of text. The text could be full text for an open access article, OCR text from BHL, or the title and abstract for an article.

Automatically extracting possible taxonomic synonyms from the literature

Playing with some sequence data I found numerous *Plasmodium* sequences
from the following paper: 
 

> Werner, E. B. ., Taylor, W. R., & Holder, A. A. (1998). A Plasmodium
> chabaudi protein contains a repetitive region with a predicted
> spectrin-like structure1Note: Nucleotide sequence data reported in
> this paper are available in the EMBL, GenBank™ and DDJB databases
> under the accession number U43145.1. Molecular and Biochemical
> Parasitology, 94(2), 185--196.
> [doi:10.1016/S0166-6851(98)00067-X](http://dx.doi.org/10.1016/S0166-6851(98)00067-X)

 
These sequences (e.g.,
[U43145](http://www.ncbi.nlm.nih.gov/nuccore/U43145)) give the host as
*Thamnomys rutilans*. You\'d think it would be fairly easy to learn more
about this animal, given that it hosts a relative of the cause of
malaria in humans, and indeed there are a number of biomedical papers
that come up in Google, e.g.: 
 

> Landau, I., & Chabaud, A. (1994). Advances in Parasitology (Vol. 33,
> pp. 49--90). Elsevier BV.
> [doi:10.1016/S0065-308X(08)60411-X](http://dx.doi.org/10.1016/S0065-308X(08)60411-X)

> Killick-Kendrick, R. (1968). Malaria parasites of Thamnomys rutilans
> (Rodentia, Muridae) in Nigeria. Bull World Health Organ. 1968; 38(5):
> 822--824.
> [PMC2554675](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2554675/)

 
Google also tells me that *Thamnomys rutilans* is an African rodent
(e.g., [6.1.6. Rodent
malaria](http://en.impact-malaria.com/iml/cx/en/layout.jsp?cnt=38E46353-CACE-4CEE-8C28-72140EE77502),
but NCBI has no sequences for \"Thamnomys rutilans\", and
[GBIF](http://data.gbif.org/search/Thamnomys%20rutilans) has no data on
its distribution. If I search [Mammal Species of the
World](http://www.bucknell.edu/msw3/) I get (literally) \"nothing found
\...\". 
 
So, this is an African rodent, host to *Plasmodium*, and we know nothing
about it? A bit of Googling, a trip to
[Wikipedia](http://en.wikipedia.org/wiki/Shining_Thicket_Rat) and
[Google
Books](http://books.google.co.uk/books?id=YnYED-YG0ZYC&lpg=PA1326&ots=1BXv1bIZ47&dq=Grammomys%20poensis&pg=PA1326#v=onepage&q=Grammomys%20poensis&f=false)
reveals that *Thamnomys rutilans* is a synonym of *Grammomys rutilans*,
but it is now called *Grammomys poensis* because the original name (*Mus
rutilans* Peters 1876) is a junior ~~synonym~~ homonym of *Mus rutilans*
Olfers, 1818 (simples). You can see the original description of *Mus
rutilans* Peters 1876 in BioStor <http://biostor.org/reference/105261>
(this took some tracking down, but that\'s another story): 
 
![4ca1a4521753bde9a091661c7694f8ae](http://lh3.ggpht.com/-G3RMdzrWf0Q/UhX_ef0YkyI/AAAAAAAAC_k/bDK9uYsIiB8/4ca1a4521753bde9a091661c7694f8ae.jpg?imgmax=800 "4ca1a4521753bde9a091661c7694f8ae.jpg"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="372" height="600"} 
 
The original description of *Mus rutilans* Olfers, 1818 is given by [The
description of a new species of South American hocicudo, or long-nose
mouse, genus Oxymycterus (Sigmodontinae, Muroidea), with a critical
review of the generic content](http://biostor.org/reference/95684) as: 
 

> Olfers, I. 1818. Bemerkungen zu Illiger\'s Ueberblick der Saugethiere
> nach ihrer Betheilung über die Welttheile rüchsichtlich der
> Südamerikanischen Arten (Species). In Eschwege, W. L., ed., Journal
> von Brasilien, Weimar, 15(2): 192-237.

 
This reference doesn\'t seem to be online. 
 
The upshot of all this information about the host of *Plasmodium
chabaudi* is hidden behind taxonomic name changes, and databases that
one might expect to help simply don\'t. If names are the glue that link
biodiversity data together then we need to get a lot better at making
basic information about name changes accessible, otherwise we are
creating islands of disconnected data.

Playing with some sequence data I found numerous

 Plasmodium

sequences from the following paper: These sequences (e.g., U43145) give the host as

 Thamnomys rutilans

. You'd think it would be fairly easy to learn more about this animal, given that it hosts a relative of the cause of malaria in humans, and indeed there are a number of biomedical papers that come up in Google, e.g.: Google also tells me that

 Thamnomys

Messaggi di Rogue Scholar

Automatically extracting possible taxonomic synonyms from the literature

Sometimes the mess taxonomy creates drives me nuts