University of Glasgow

Roderic Page

Back in 2006 in a short post entitled [\"Building the encyclopedia of
life\"](http://ispecies.blogspot.com/2006/03/building-encyclopedia-of-life.html)
I wrote that GenBank is a potentially rich source of information on
host-parasite relationships. Often sequences of parasites will include
information on the name of the host (the example I used was sequence
[AF131710](http://www.ncbi.nlm.nih.gov/nucleotide/7108724) from the
platyhelminth *Ligophorus mugilinus*, which records the host as the
Flathead mullet [*Mugil
cephalus*](http://en.wikipedia.org/wiki/Flathead_mullet)).  
  
I\'ve always wanted to explore this idea a bit more, and have finally
made a start, in part inspired by the recent [VIZBI
2011](http://vizbi.org/) meeting. I\'ve grabbed a large chunk of
GenBank, mined the sequences for host records, and created some simple
visualisations of what I\'m terming (with tongue firmly in cheek) the
\"symbiome\". Jonathan Eisen [will not be
happy](http://phylogenomics.blogspot.com/search?q=bad+omics+word), but I
need a word that describes the complete set of hosts, mutualists,
symbionts with which an organism is associated, and \"symbiome\" seems
appropriate.  
  
**Human symbiome**  
To illustrate the idea, below is the human \"symbiome\". This diagram
shows all the taxa in GenBank arranged in a circle, with lines
connecting those organisms that have DNA sequences where humans are
recorded as their host.  
  
![Human](http://lh6.ggpht.com/_Gct8lVAxKqQ/TYyqOWcwrpI/AAAAAAAAA3k/VzhEulakY1U/human.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400"}  
  
At a glance, we have a lot of bacteria (the gray bar with ***E. coli***)
and fungi (blue bar with **Yeast**), and a few nematodes and
arthropods.  
  
**Fig tree symbiome**  
Next up are organisms collected from fig trees (genus *Ficus*).  
  
![Ficus](http://lh5.ggpht.com/_Gct8lVAxKqQ/TYyqPRPPYeI/AAAAAAAAA3o/--9egoxhRC8/ficus.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400"}  
Fig trees have [wasp pollinators](http://en.wikipedia.org/wiki/Fig_wasp)
(the dark line landing near the honey bee *Apis*), as well as nematodes
(dark line landing near *Caenorhabditis elegans*). There are also some
associations with fungi and other arthropods.  
  
**Which taxa host insects?**  
Next up is a plot of all associations involving insects and a host.  
  
![Insect](http://lh3.ggpht.com/_Gct8lVAxKqQ/TYyqP20T2QI/AAAAAAAAA3s/FZtKjqnnf9U/insect.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400"}  
The diagram is dominated by insect-flowering plant interactions,
followed by insect-vertebrate associations (most likely bird and mammal
lice).  
  
**Which taxa are hosted by insects?**  
We can reverse the question and ask what organisms are hosted by
insects:  
  
![Insectashost](http://lh6.ggpht.com/_Gct8lVAxKqQ/TYyqQuTPt0I/AAAAAAAAA3w/ptmNCkC8EIk/insectashost.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400"}  
Lots of associations between insects and fungi, as well as bacteria, and
a few other organisms, such as nematodes, and *Plasmodium* (the organism
which causes malaria).  
  
**Frog symbiome**  
Lastly, below is the symbiome of frogs. \"Worms\" feature prominently,
as well as the fungus that causes
[chytridiomycosis](http://en.wikipedia.org/wiki/Chytridiomycosis).  
  
![Frog](http://lh4.ggpht.com/_Gct8lVAxKqQ/TYyqRNF7-2I/AAAAAAAAA30/Me3HoYOL6C8/frog.png?imgmax=800){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="400" height="324"}**How the visualisation was made**  
  
The symbiome visualisations were made as follows. Firstly DNA sequences
were downloaded from EMBL and run through a script that extracted as
much metadata as possible, including the contents of the `host` field
(where present). I then took the NCBI taxonomy and generated an ordered
list of taxa by walking the tree in postorder, which determines where on
the circumference of the circle the taxon lies. Pairs of taxa in an
association are connected by a quadratic Bezier curve. The illustration
was created using SVG.  
  
  
**Next steps**  
There are several ways this visualisation could be improved. It\'s based
only only a subset of data (I haven\'t run all of the sequence databases
though the parser yet), and the matching of host taxa is based on exact
string matching. All manner of weird and wonderful things get entered in
the `host` field, so we\'ll need some more sophisticated parsing (see
\"LINNAEUS: A species name identification system for biomedical
literature\"
[doi:10.1186/1471-2105-11-85](http://dx.doi.org/10.1186/1471-2105-11-85%22)
for a more general discussion of this issue).  
  
The visualisation is fairly crude at this stage. Circle plots like this
are fairly simple to create, and pop up in all sorts of situations
(e.g., RNA secondary structure methods, which [I did some work on years
ago](http://taxonomy.zoology.gla.ac.uk/rod/circles/)). Of course,
[Circos](http://mkweb.bcgsc.ca/circos/) would be an obvious tool to use
to create the visualisations, but the overhead of installing it and
learning how to use it meant I took a shortcut and wrote some SVG from
scratch.  
  
Although I\'ve focussed on GenBank as a source of data, this
visualisation could also be applied to other data. I briefly touched on
this in [Tag trees: displaying the taxonomy of names in
BHL](http://iphylo.blogspot.com/2009/11/tag-trees-displaying-taxonomy-of-names.html)
where a [page in the Biodiversity Heritage
Library](http://www.biodiversitylibrary.org/page/2298491) contains the
names of a flea and it\'s mammalian hosts. I think these circle plots
would be a great way to highlight possible ecological associations
mentioned in a text.  


Back in 2006 in a short post entitled "Building the encyclopedia of life" I wrote that GenBank is a potentially rich source of information on host-parasite relationships.

Visualising the symbiome: hosts, parasites, and the Tree of Life

Following on from [adding
specimens](http://iphylo.blogspot.com/2008/10/openurl-for-specimens.html)
to my [OpenURL resolver](http://bioguid.info/openurl/), I\'ve added
support for GenBank records. Either an OpenURL request such as
<http://bioguid.info/openurl?id=genbank:DQ502033>, or the short URL
<http://bioguid.info/genbank/DQ502033> will resolve the GenBank record
for accession number DQ502033.  
  
The HTML isn\'t much to look at, the real goodness is the JSON (obtained
by appending \"&display=json\" to the OpenURL request, or \".json\" to
the short form, e.g. <http://bioguid.info/genbank/DQ502033.json>).  
  
The resolver gets the sequence form NCBI, does a little post processing,
then displays the result. Postprocesisng includes parsing the latitude
and longitude coordinates (something of a mess in GenBank, see my
earlier [metacrap](http://iphylo.blogspot.com/2008/01/metacrap.html)
rant), extracting specimen codes, adding bibliographic GUIDs (such as
DOIs, Handles, or URLs), finding uBio namebankID\'s for hosts, etc. Note
that some records have a key called \"taxonomic_group\". This is to
provide clues for resolving museum specimens \-- often the DiGIR
provider needs to know what kind of taxon you are searching for.  
  
The aim is to have a simple service that returns somewhat cleaned up
GenBank records that I (and others) can play with.


Following on from adding specimens to my OpenURL resolver, I've added support for GenBank records. Either an OpenURL request such as http://bioguid.info/openurl?id=genbank:DQ502033, or the short URL http://bioguid.info/genbank/DQ502033 will resolve the GenBank record for accession number DQ502033.

OpenURL for Genbank records

OMG. Playing with extracting identifiers from text, I have a regular
expression for GenBank accession numbers that looks something like
this:  
(A\[A-Z\])\[0-9\]{6} \| (U\[0-9\]){5} \| (D\[A-Z\])\[0-9\]{6} \|
(E\[A-Z\])\[0-9\]{6} \| (NC\_)\[0-9\]{6}).  
OK, it won\'t get everything, but what is more worrying are the things
it will pickup that **aren\'t** GenBank accession numbers.  
  
For example, I ran Robert Mesibov\'s 2005 paper \"The millipede genus
Lissodesmus Chamberlin, 1920 (Diplopoda: Polydesmida:  
Dalodesmidae) from Tasmania and Victoria, with descriptions of a new
genus and 24 new species\" \[[PDF
here](http://museumvictoria.com.au/pages/3905/62_Mesibov.pdf)\] through
a script, and out came loads of GenBank accession numbers \... which is
a worry as there aren\'t any sequences in this paper.  
  
Turns out, Mesibov uses [UTM grid
references](http://en.wikipedia.org/wiki/Universal_Transverse_Mercator_coordinate_system)
to describe localities, and these look like just GenBank accessions.
There is a nice web site
[here](http://www.utas.edu.au/spatial/locations/spagrid.html) which
describes how UTM grid references are determined in Tasmania (from which
the image below is taken).  
[![](http://www.utas.edu.au/spatial/locations/images/tasgrid.gif){style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px;"
border="0"}](http://www.utas.edu.au/spatial/locations/images/tasgrid.gif){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
Not all the \"accession numbers\" in Mesibov(2005) exist in GenBank, but
some do, for example grid reference DQ402119 (41°26\'31\'\'S
146°17\'02\'\'E) is also a sequence
[DQ402119](http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=DQ402119)
and, you guessed it, it\'s not from a millipede. So, I need to be a
little bit careful in extracting identifiers from text.


Reasons text mining will fail. I. UTM Grid References and GenBank accession numbers

Time for some fun. In between some tedious text mining I\'ve been
meaning to explore some visualisations of NCBI. Here\'s the first,
inspired by Jörn Clausen\'s wonderful [Live Earthquake
Mashup](http://www.oe-files.de/gmaps/eqmashup.html) (thanks to [Donat
Agosti](http://biodivcontext.blogspot.com/) for telling me about this).
What I\'ve done is take all the frog sequences in Genbank that are
georeferenced, add the date those Genbank records were created, generate
a KML file, and use Nick Rabinowitz\'s
[timemap](http://code.google.com/p/timemap/) to plot the KML. The
[result is here](http://darwin.zoology.gla.ac.uk/~rpage/timemap/):  
  
[![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxU8yys9mRimzF-Wka90K1k7nh_9to5a4neH26buDgJvbpwBwGhT8o2KNYHnV4BcyeU3EPSb2IWh2HKF37aAoQt69InslZovSf5XpbFe_PGypXF0gXLkBBKKmG3GVQMXy9TBOl/s320/timemap.png){#BLOGGER_PHOTO_ID_5236625340125709106
style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;"
border="0"}](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjxU8yys9mRimzF-Wka90K1k7nh_9to5a4neH26buDgJvbpwBwGhT8o2KNYHnV4BcyeU3EPSb2IWh2HKF37aAoQt69InslZovSf5XpbFe_PGypXF0gXLkBBKKmG3GVQMXy9TBOl/s1600-h/timemap.png){onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}"}  
  
By dragging the time line you can see collections of sequences and where
the frog samples came from. Clicking on a marker on the Google Map takes
displays a link to the Genbank record. It\'s all pretty crude, but fun
to play with. What I\'m toying with is trying to do something like this
for new taxa, i.e., a timemap showing where an when new species are
described. Sort of a live biodiversity map like the earthquake mashup,
albeit not quite so rapidly moving.


Time for some fun. In between some tedious text mining I've been meaning to explore some visualisations of NCBI. Here's the first, inspired by Jörn Clausen's wonderful Live Earthquake Mashup (thanks to Donat Agosti for telling me about this). What I've done is take all the frog sequences in Genbank that are georeferenced, add the date those Genbank records were created, generate a KML file, and use Nick Rabinowitz's timemap to plot the KML.

Postagens de Rogue Scholar

Visualising the symbiome: hosts, parasites, and the Tree of Life

OpenURL for Genbank records

Reasons text mining will fail. I. UTM Grid References and GenBank accession numbers

NCBI visualisations I - Genbank Timemap