University of Glasgow

Roderic Page

As part of my mantra that it\'s not about the data, it\'s all about the
links between the data, I\'ve started exploring matching GenBank
sequences to GBIF occurrences using the specimen_voucher codes recorded
in GenBank sequences. It\'s quickly becoming apparent that this is not
going to be easy. Specimen codes are not unique, are written in all
sorts of ways, there are multiple codes for the same specimen (GenBank
sequences may be associated with museum catalogue entries, or which
field or collector numbers).  
  
So why undertake what is fast looking like a hopeless task? There are
several reasons:  

1.  GBIF occurrences have a unique URL which we could potentially use as
    a unique, resolvable identifier for the corresponding specimen.
2.  Linking GenBank to GBIF would make it possible for GBIF to list
    sequences associated with a specimen, as well as the associated
    publication, which means we could demonstrate the \"impact\" of a
    specimen. In the simplest terms this could be the number of
    sequences and publications that use data from the specimen, more
    sophisticated approaches could use PageRank-like measures, see
    [hdl:10101/npre.2008.1760.1](http://hdl.handle.net/10101/npre.2008.1760.1).
3.  Having a unique identifier that is shared across different databases
    makes it easier to combine data from different sources. For example,
    if a sequence in GenBank lacks geographic coordinates but the
    voucher specimen in GBIF is georeferenced, we can use that
    information to locate the sequence in geographic space (and hence
    build geophylogenies or add spatial indexes to databases such as
    TreeBASE). Conversely, if the GenBank sequence is georeferenced but
    the GBIF record isn\'t we can update the GBIF record and possibly
    expand the range of the corresponding taxon (this was part of the
    motivation behind
    [hdl:10101/npre.2009.3173.1](http://hdl.handle.net/10101/npre.2009.3173.1).

  
As an example, below is the [GBIF 1° density
map](http://data.gbif.org/occurrences/taxon/celldensity/taxon-celldensity-54040866.kml)
for the frog [*Pristimantis
ridens*](http://data.gbif.org/species/2425583/) from GBIF, with the
phylogeny from Wang *et al.***Phylogeography of the Pygmy Rain Frog
(Pristimantis ridens) across the lowland wet forests of isthmian Central
America**<http://dx.doi.org/10.1016/j.ympev.2008.02.021> layered over
it. I created the KML tree from the corresponding tree in TreeBASE using
the [tool I described
earlier](http://iphylo.blogspot.com/2012/02/automating-creation-of-geophylogenies.html).
You can grab the [KML for the tree
here](http://dl.dropbox.com/u/639486/kml/Tr5096.kml).  
  
![Density](http://lh4.ggpht.com/-lWaePnxJpZo/T0NyWoKWQaI/AAAAAAAABJg/R-Q5YOG6--E/density.png?imgmax=800 "density.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="377"}  
  
As we\'d expect, there is a lot of overlap in the two sources of data.
If we investigate further, there are records that are in fact based on
the same specimen. For example, if we download the [GBIF KML file with
individual
placemarks](http://data.gbif.org/occurrences/taxon/placemarks/taxon-placemarks-54040866.kml)
we see that in the northern part of the range their are 15 GBIF
occurrences that map onto the same point as one of the terminal taxa in
the tree.  
  
![Gbif](http://lh6.ggpht.com/-QSfss1Qi6nE/T0NyX9Ib75I/AAAAAAAABJo/a4aZdWcVVBM/gbif.png?imgmax=800 "gbif.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="379"}  
  
One of these 15 GBIF records
(<http://data.gbif.org/occurrences/244335848>) is for specimen USNM
514547, which is the voucher specimen for
[EU443175](http://www.ncbi.nlm.nih.gov/nucleotide/EU443175). This gives
us a link between the record in GBIF and the record in GenBank. It also
gives us a URI we can use for the specimen
<http://data.gbif.org/occurrences/244335848> instead of the unresolvable
and potentially ambiguous USNM 514547.  
  
If we view the geophylogeny from a different vantage point we see
numerous localities that don\'t have occurrences in GBIF.  
  
![Nogbif](http://lh6.ggpht.com/-RMa6W21ShVo/T0NyZdAJLxI/AAAAAAAABJw/Rfj6ruIGOMk/nogbif.png?imgmax=800 "nogbif.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="378"}  
  
Close inspection reveals that some of the specimens listed in the Wang
*et al.* paper are actually in GBIF, but lack geographic coordinates.
For example the OTU \"*Pristimantis ridens* Nusagandi AJC 0211\" has the
voucher specimen FMNH 257697. This specimen is in GBIF as
<http://data.gbif.org/occurrences/57919777/>, but without coordinates,
so it doesn\'t appear on the GBIF map. However, both the Wang *et al.*
paper and the GenBank record for the sequence from this specimen
[EU443164](http://www.ncbi.nlm.nih.gov/nucleotide/EU443164) give the
latitude and longitude. In this example, GBIF gives us a unique
identifier for the specimen, and GenBank provides data on location that
GBIF lacks.  
  
Part of GBIFs success is due to the relative ease of integrating data by
taxonomic names (despite the problems caused by synonyms, homonyms,
misspellings, etc.) or using spatial coordinates (which immediately
enables integration with environmental data. But if we want to integrate
at deeper levels then specimen records are the glue that connects GBIF
(and its contributing data sources) to sequence databases, phylogenies,
and the taxonomic literature (via lists of material exampled). This will
not be easy, certainly for legacy data that cites ambiguous specimen
codes, but I would argue that the potential rewards are great.  
  


As part of my mantra that it's not about the data, it's all about the links between the data, I've started exploring matching GenBank sequences to GBIF occurrences using the specimen_voucher codes recorded in GenBank sequences. It's quickly becoming apparent that this is not going to be easy.

Linking GBIF and Genbank

This is a follow up to my previous post TDWG Challenge - what is RDF good for? where I'm being, frankly, a pain in the arse, and asking why we bother with RDF? In many ways I'm not particularly anti-RDF, but it bothers me that there's a big disconnect between the reasons we are going down this route and how we are actually using RDF.

Reflections on the TDWG RDF "Challenge"

[![](http://www.cnah.org/images/herps/1374.jpg){style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 320px;"
border="0"}](http://www.cnah.org/images/herps/1374.jpg){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
As part of the slow rebuild of [bioguid.info](http://bioguid.info), and
as part of the
[Challenge](http://iphylo.blogspot.com/2008/08/elsevier-grand-challenge.html),
I\'ve started making an OpenURL resolver for specimens. Partly this is
just a wrapper around DiGIR providers, but it\'s also a response to the
lack of GUIDs for specimens. In the same way that I think OpenURL for
papers only really makes sense in a world without GUIDs for literature
(DOIs pretty much take care of that), given the lack of specimen GUIDs
we are left to resolve specimens based on metadata.  
  
For example, the holotype of *Pseudacris fouquettei* (shown in photo by
Suzanne L. Collins, original
[here](http://www.cnah.org/detail.asp?id=1374)) is TNHC 63583. In a
digital world, I want the paper describing this taxon, and the
specimen(s) assigned to it to be a click away. In this spirit, here is
an OpenURL link for the specimen:
[http://bioguid.info/openurl/?genre=specimen &institutionCode=TNHC
&collectionCode=Herps
&catalogNumber=63583](http://bioguid.info/openurl/?genre=specimen&institutionCode=TNHC&collectionCode=Herps&catalogNumber=63583){target="_blank"}.
Click on this link and you get a page with some very basic information
on the specimen. If you want more, append \"&display=json\" to the URL
to [get a JSON
response](http://bioguid.info/openurl/?genre=specimen&institutionCode=TNHC&collectionCode=Herps&catalogNumber=63583&display=json).  
  
So, armed with this, [TNHC
63583](http://bioguid.info/openurl/?genre=specimen&institutionCode=TNHC&collectionCode=Herps&catalogNumber=63583){target="_blank"}
becomes resolvable, and joining the pieces becomes a little easier.


As part of the slow rebuild of bioguid.info, and as part of the Challenge, I've started making an OpenURL resolver for specimens. Partly this is just a wrapper around DiGIR providers, but it's also a response to the lack of GUIDs for specimens.

Postagens de Rogue Scholar

Linking GBIF and Genbank

Reflections on the TDWG RDF "Challenge"

OpenURL for specimens