University of Glasgow

Roderic Page

Last month, feeling particularly grumpy, I fired off an [email to the
TDWG-TAG](http://lists.tdwg.org/pipermail/tdwg-tag/2011-September/002381.html)
mailing list with the subject **Lobbing grenades: a challenge**. Here\'s
the email:  

> It\'s morning and the coffee hasn\'t quite kicked in yet, but reading
> through recent TDWG TAG posts, and mindful of the upcoming meeting in
> New Orleans (which sadly I won\'t be attending) I\'m seeing a mismatch
> between the amount of effort being expended on discussions of
> vocabularies, ontologies, etc. and the concrete results we can point
> to.  
>   
> Hence, a challenge:  
>   
> \"What new things have we learnt about biodiversity by converting
> biodiversity data into RDF?\"  
>   
> I\'m not saying we can\'t learn new things, I\'m simply asking what
> have we learnt so far?  
>   
> Since around 2006 we have had literally millions of triples in the
> wild (uBio, ION, Index Fungorum, IPNI, Catalogue of Life, more
> recently Biodiversity Collections Index, Atlas of Living Australia,
> World Register of Marine Species, etc.), most of these using the same
> vocabulary. What new inferences have we made?  
>   
> Let\'s make the challenge more concrete. Load all these data sources
> into a triple store (subchallenge - is this actually possible?).
> Perhaps add other RDF sources (DBpedia, Bio2RDF, CrossRef). What novel
> inferences can we make?  
>   
> I may, of course, simply be in \"grumpy old arse\" mode, but we have
> millions of triples in the wild and nothing to show for it. I hope
> I\'m not alone in wondering why\...

  
In the context of the TDWG meeting (happening as we speak and which I\'m
following via Twitter, hashtag
[\#tdwg](http://twitter.com/#!/search/tdwg)) Joel Sachs asked me whether
I had any specific data in mind that could form the basis of a
discussion. So, here goes. I\'ve assembled some small RDF data sets that
it might be fun to play with. Each data set is for frogs, and I\'ve
divided them into two sets.  
  
**Primary data**  
These data sets are essentially unmodified RDF fetched from data
providers:  

- [uniprot.rdf](http://dl.dropbox.com/u/639486/tdwg-rdf/uniprot.rdf)
  Uniprot RDF for frogs in GenBank
- [ion.rdf](http://dl.dropbox.com/u/639486/tdwg-rdf/ion.rdf) Index of
  Organism Names (ION) RDF for taxonomic names for frogs (filtered to
  just those names that are also in GenBank, the RDF comes from ION
  LSIDs)
- [crossref.rdf](http://dl.dropbox.com/u/639486/tdwg-rdf/crossref.rdf)
  CrossRef RDF for DOIs for publications that published new frog names
  (obtaining using [CrossRef\'s support for Linked Data for
  DOIs](http://www.crossref.org/CrossTech/2011/04/content_negotiation_for_crossr.html))
- [dbpedia.rdf](http://dl.dropbox.com/u/639486/tdwg-rdf/dbpedia.rdf)
  Dbpedia RDF for frogs in GenBank (Update 2011-10-20: the dbpedia.rdf
  file is a bit big, so here is
  [subset.rdf](http://dl.dropbox.com/u/639486/tdwg-rdf/subset.rdf) which
  has just the conservation status and thumbnail image)

  
  
These sources give us information on genomics (at least, they tell us
which taxa have been sequenced), where and when the original taxonomic
description was published, and by whom, as well as some information on
conservation status and what the frog looks like (via Dbpedia). Ideally
we just load these files into a triple store and then ask a bunch of
questions, such as what is the conservation status of frogs sequenced in
Genbank?, is there correlation between the conservation status of a frog
and the date it was discovered?, who has described the most frog
species?, etc.  
  
My contention is that actually we can\'t do any of this because the data
is siloed due to the lack of shared identifiers and vocabularies (I
suspect that there is not a single identifier any of these files share).
The only way we can currently link these data sets together is by shared
string literals (e.g., taxonomic names), in which case why bother with
RDF? So my first challenge is to see whether any of the questions I\'ve
just listed can actually be tackled using this data.  
  
**Glue**  
In a slightly more constructive mode, to see if we can make progress
I\'m providing some additional RDF files, based on projects I\'m working
on to link data together. These files may help provide some of the
missing \"glue\" to connect these data sets.  
  

- [linkout.rdf](http://dl.dropbox.com/u/639486/tdwg-rdf/linkout.rdf) The
  list of links between NCBI and Dbpedia (based on mapping in [iPhylo
  LinkOut](http://iphylo.org/linkout))
- [ion_doi.rdf](http://dl.dropbox.com/u/639486/tdwg-rdf/ion_doi.rdf) A
  subset of publications listed in ION have DOIs, this file links the
  corresponding ION LSIDs to those DOIs (this file is from an ongoing
  project mapping names to primary literature)

  
  
The first file links the ION and CrossRef RDF, so we could start to ask
questions about dates of discovery, who described what species, etc..
The second file links NCBI taxon ids (in this case in the form of
UniProt URIs) to Wikipedia (in the form of Dbpedia URIs). Dbpedia has
information on conservation status, and some frogs will also have
pictures, so we can start to join genomics to conservation, as well as
make some visualisations.  
  
**Update**  
I\'ve now added another RDF file for 1000 georeferenced GenBank
sequences for frogs. The file is
[genbank.rdf](http://dl.dropbox.com/u/639486/tdwg-rdf/genbank.rdf). This
file is generated from a local, processed version of EMBL, and uses a
mixture of Dublin Core and TDWG vocabularies. Here\'s an example of a
single record:  

``` {style="font-size:10px;border:1px solid rgb(192,192,192);background-color:rgb(240,240,240);"}

xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" 
xmlns:owl="http://www.w3.org/2002/07/owl#" 
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" 
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" 
xmlns:tcommon="http://rs.tdwg.org/ontology/voc/Common#" 
xmlns:toccurrence="http://rs.tdwg.org/ontology/voc/TaxonOccurrence#" 
xmlns:uniprot="http://purl.uniprot.org/core/">
  
    2008-07-06
    2010-12-23
    EU566842
    Xenopus borealis voucher MHNG:Herp:2644.64 
cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial.
    
    
      
      Xenopus borealis
      0.66
      0.66
      37.5
      37.5
      0.66 N 37.5 E
      Kenya
      MHNG:Herp:2644.64
    
  
```

  
I\'ve added this simply so one could do some geographical queries.  
  
**Missing links**  
There are still lots of missing links here (for example, there\'s no
explicit link between NCBI and ION, so we\'d need to create this using
taxonomic names), and we could add further links to the literature via
sequences for taxa. Then there\'s the lack of geographic data. We could
get some of this via georeferenced sequences in GenBank, but there\'s no
RDF for this ([Bio2RDF](http://bio2rdf.org/) does have RDF for sequences
but it ignores the bulk of the organismal metadata such as voucher
specimens and latitude and longitude).  
  
In many ways it\'s this lack of links that was point of my original
email. The reality is that \"linked data\" isn\'t linked to anything
like the extent that makes it useful. Simply pumping out RDF won\'t get
us very far until we tackle this problem (see also my earlier post
[Linked data that isn\'t: the failings of
RDF](http://iphylo.blogspot.com/2011/09/linked-data-that-isn-failings-of-rdf.html)).  
  
So, if you think RDF is the way to go, please tell me what you can learn
from these data files.  
  
  


Last month, feeling particularly grumpy, I fired off an email to the TDWG-TAG mailing list with the subject
<strong>
 Lobbing grenades: a challenge
</strong>
. Here's the email:  In the context of the TDWG meeting (happening as we speak and which I'm following via Twitter, hashtag #tdwg) Joel Sachs asked me whether I had any specific data in mind that could form the basis of a discussion. So, here goes.

Messaggi di Rogue Scholar

TDWG Challenge - what is RDF good for?