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[bioontology-support] NCBO Bioportal Bio2RDF service - bug report

Michel Dumontier michel.dumontier at gmail.com
Tue Jan 10 12:15:18 PST 2012


Hi BioPortal,
 We're updating the Bio2RDF scripts package, and I'm now reviewing what has
been done at the NCBO to automatically generate the Bio2RDF downloadable
services, so we can add this data to the Bio2RDF network.

i used the following to do my assessment:
http://rest.bioontology.org/bioportal/ontology/dump_n3/40865


1. URI syntax
The general form of the Bio2RDF URI syntax is
http://bio2rdf.org/namespace:identifier
  where namespace is specified in a lower case, and the identifier case is
as per the issuer.

so URIs of the form <http://bio2rdf.org/ns#identifier> are not valid.

example: <http://bio2rdf.org/obo#term>
should be <http://bio2rdf.org/obo:term>

example <http://bio2rdf.org/ns/obo_resource:name>
should be <http://bio2rdf.org/obo:name>

example: <http://bio2rdf.org/ns/ICF>
should be <http://bio2rdf.org/ns:icf>

2. Descriptions

We suggest the use of rdf:type, rdfs:label and dc:description (where dc is
for dcterms) for all bio2rdf resources, where possible

<http://bio2rdf.org/icf:b> rdf:type <http://bio2rdf.org/obo:term> .
<http://bio2rdf.org/icf:b> rdfs:label "b. BODY FUNCTIONS [icf:b]" .
<http://bio2rdf.org/icf:b> dc:description "Definitions: Body functions are
the physiological functions of body systems (including psychological
functions). ... the rest of the description.... ".

3. triples

looking at the provided example ontology i see

<http://bio2rdf.org/CausalFactorTerm> <http://bio2rdf.org/ns/obo#is_a> <
http://bio2rdf.org/ICF:EtiologyTerm> .

so, since CausalFactorTerm is in the ICF namespace, this triple should read
<http://bio2rdf.org/icf:CausalFactorTerm> <http://bio2rdf.org/obo:is_a> <
http://bio2rdf.org/icf:EtiologyTerm> .

That's it for now, thanks!

m.

-- 
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com
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