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

manuelso manuelso at stanford.edu
Tue Jan 10 19:47:42 PST 2012


Hi Michel.

Alternatively to the dump_n3 service you can use 

http://alphasparql.bioontology.org/

You could run a query like ...

PREFIX owl:  <http://www.w3.org/2002/07/owl#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT DISTINCT ?termURI ?prefLabel ?subClassOf ?description
 FROM <http://bioportal.bioontology.org/ontologies/1411>
 FROM <http://bioportal.bioontology.org/ontologies/globals> 
WHERE {
      ?termURI a owl:Class;
      skos:prefLabel ?prefLabel .
      OPTIONAL {
        ?termURI rdfs:comment ?description .
      }
      OPTIONAL {
        ?termURI rdfs:subClassOf ?subClassOf .
      }
}

We have implemented subPropertyOf reasoning and you do not need to worry about different "label" predicates. They are all mapped into skos:prefLabel. Same happens for comments with rdfs:comment. To use this capability you need to include the graph "globals"  into the query.

The other graph part of the query, http://bioportal.bioontology.org/ontologies/1411, is the graph where the ontology is stored. In this case the id 1411 is the virtual id of the ontology version that you were using as test (40865)

It would not be very complicated to transform the result of this query into the RDF /ntriples format that you need. Eventually you could also try to run a CONSTRUCT query that would do that job.

If you decide to go for this solution I am happy to help with any support you might need.

More documentation about our triple store alpha release:

http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal
http://alphasparql.bioontology.org/examples
https://github.com/ncbo/sparql-code-examples

Best,

Manuel


On Jan 10, 2012, at 12:15 PM, Michel Dumontier wrote:

> 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
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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