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

Michel Dumontier michel.dumontier at gmail.com
Fri Jan 13 06:47:04 PST 2012


Cool.  Can you help me formulate a SPARQL query to get the most current
version of each ontology?

m.

On Tue, Jan 10, 2012 at 10:47 PM, manuelso <manuelso at stanford.edu> wrote:

> 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
>
>
>


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