University of Glasgow

Roderic Page

One of the potentially powerful features of TreeBASE II is availability
of a RDF version of a study. This means that, in principle, one could
take the RDF for a TreeBASE study, combine it with RDF from other
sources, and generate a richer view of a particular study. For example,
if a TreeBASE study has a DOI, then we could link it to bibliographic
details for the study, and through them to other information, such as
GenBank sequences, specimens, etc. (see my [little linked data
browser](http://iphylo.blogspot.com/2010/05/linked-data-part-2.html) for
an example of some of this linking). If we added a phylogeny viewer,
then we\'d have a great tool for browsing the basic components of a
phylogenetic study.  
  
Unfortunately, we\'re not there yet. I\'ve been trying to make sense of
TreeBASE II RDF, and frankly, it\'s a mess. Here are some of the
problems:  
  
**TreeBASE URIs aren\'t linked data compliant**  
The canonical URI for a study (e.g.,
<http://purl.org/phylo/treebase/phylows/study/TB2:S10423>) doesn\'t
conform to the linked data approach. In fact, the URI crashes the
[linked data validator](http://validator.linkeddata.org/), so I tried
another test.  
  

    curl --include 
       --header "Accept: application/rdf+xml" 
       http://purl.org/phylo/treebase/phylows/study/TB2:S10423

  
To be a valid linked data resource this request should return a 303 HTTP
status code. Instead we get a 302 and some HTML. Linked data clients
won\'t be able to extract information from this URI.  
  
**SKOS matching**  
There are some odd things going on in the RDF. It contains statements of
the form:  

``` brush:xml

   
```

  
(I\'ve tidied this up a little from the original, rather verbose RDF).
This asserts that the TreeBASE OTU **otu1789319** corresponds to the
NCBI taxon with the taxonomy id **76066** (represented by the Uniprot
URI). Except, it doesn\'t really. As far as I understand it, SKOS is
about matching concepts, not documents. The URI
<http://purl.uniprot.org/taxonomy/76066.rdf> is a document URI
(specifically, a RDF document), the URI
<http://purl.uniprot.org/taxonomy/76066> is the taxon. The match should
really be to http://purl.uniprot.org/taxonomy/76066. Then I\'ve come
across statements that match TreeBASE OTUs to
<http://purl.uniprot.org/taxonomy/0.rdf>. This URI doesn\'t exist (we
get a 404). This seems an odd way to say that we don\'t have a match \--
if we don\'t have a match, don\'t include it in the RDF.  
  
**Local URIs for trees don\'t work**  
The RDF is full of local URIs such as
<http://purl.org/phylo/treebase/phylows/#tree1790755>, which don\'t
resolve. In fact they generate a rather spectacular Tomcat exception. I
don\'t understand why we need local URIs. **Everything in TreeBASE
should have a global URI**. Then we can avoid unnecessary statements
such as:  
  
http://purl.org/phylo/treebase/phylows/#tree1790755 owl:sameAs
http://purl.org/phylo/treebase/phylows/tree/TB2:Tr7899  
  
which links a local resource to a global one
<http://purl.org/phylo/treebase/phylows/tree/TB2:Tr7899>. Incidentally,
this URI doesn\'t resolve, despite claims that [this bug has been
fixed](http://sourceforge.net/tracker/?func=detail&aid=3005716&group_id=248804&atid=1126676).  
  
**No links between tree and study**  
But the show stopper for me is that there is **no link between a study
and a tree**! There is no triple in the RDF specifying any relationship
between these two entities. To me this is just about the most important
thing I need. I want to be able to query TreeBASE RDF using a study
identifier (either from TreeBASE itself, or from an external identifier
such as a DOI or a PubMed number). As it stands the TreeBASE II RDF is
almost useless. I can\'t get it via a linked data client, it\'s full of
URIs that don\'t resolve, and it lacks key triples that would glue
things together.  
  
**RDF != XML**  
  
I can\'t help thinking that the RDF output hasn\'t been designed with
end use in mind. I know from my own experience that it\'s not until you
try to do something with the RDF that you realise how poor some design
decisions may have been.  
  
It\'s not enough to pump out RDF and hope for the best. RDF is not XML,
which is just a verbose format for moving data around. RDF brings with
it all sorts of expectations about how clients will resolve it, how they
will interpret URIs, and the kinds of queries that will be performed. We
are achingly close to being able to tie everything together, but not
with RDF TreeBASE II is currently making available.  
  


One of the potentially powerful features of TreeBASE II is availability of a RDF version of a study. This means that, in principle, one could take the RDF for a TreeBASE study, combine it with RDF from other sources, and generate a richer view of a particular study.

Messaggi di Rogue Scholar

TreeBASE II RDF