Hi! On 11-03-08 4:35 PM, "Peter Ansell" <[email protected]> wrote: >Did a SPARQL interface (and the configuration to map Biomarts to RDF >and URIs) make it into the 0.8 release candidates? The release of RC5 is about to happen very very soon and by then we will not have a finished SPARQL-interface ready.
However, there is rudimentary SPARQL-support build into RC5. You will be able to run all queries over attributes with the SPARQL-queries that are generated by the SPARQL-button. Depending on how your filters are named, you can also restrict the result-set the same way as you can by using filters in the web-interface. There is a temporary playground at http://dcc-dev.res.oicr.on.ca:9005 where you can experiment with SPARQL a bit. For example, I set "Limit to results:" to "...with Disease ID" and picked the attributes "Pathway ID", "Pathway Name", "Disease ID" and "Disease Name". The SPARQL-button generates the following query: BASE <datasets:kegg> PREFIX biomart: <http://www.biomart.org/ontology#> SELECT ?a0 ?a1 ?a2 ?a3 WHERE { ?f0 biomart:pathway__pathway_dis__disease_bool_104_has_value "only" . ?a0 a biomart:pathway__entry_101 . ?a1 a biomart:pathway__name_101 . ?a2 a biomart:pathway__pathway_dis__disease_104 . ?a3 a biomart:pathway__pathway_dis__disease_1_104 } This query can be executed via a RESTful-interface (use http://meyerweb.com/eric/tools/dencoder/ to encode the plain-text to an HTTP suitable format): http://dcc-dev.res.oicr.on.ca:9005/rest/sparql/RDF/pathway_config_1/get?que ry=BASE%20<datasets[and so on] How does SPARQL-know what to query? Well, that is defined by the "rdf"-property of attributes in MartConfigurator. The "rdf"-property of "Pathway Name" in the KEGG Mart is set to: ^^http://www.biomart.org/ontology#pathway__name_101| http://www.biomart.org/ontology#pathway__name_101_has_value;pathway__name_1 01| http://www.biomart.org/ontology#pathway__name_101_of;pathway__table_key_101 This property means: - the attribute has the RDF-type "http://www.biomart.org/ontology#pathway__name_101"; (the ^^-entry) - the attribute is subject of the predicate "http://www.biomart.org/ontology#pathway__name_101_has_value"; with attribute "pathway__name_101" that acts as object (that is actually the attribute itself) - the attribute is subject of the predicate "http://www.biomart.org/ontology#pathway__name_101_of"; with the attribute "pathway__table_key_101" that stands in for the object (the main attribute of the mart; the primary key used to create the mart) Now, I am sure this is all confusing, especially since the "rdf"-property was generated automatically. If you create a mart yourself, you will be able to play around with the property a bit. In the example above, you see that only the RDF-type definition is used to get hold of the attributes in the query, but you are also able to use something like: SELECT ?name WHERE { ?name biomart:pathway__name_101_of ?key } LIMIT 5 Returning meta-data of a mart (i.e. information about what you can actually query by SPARQL) is not implemented yet and proper SPARQL-support will be included in RC6, which will be released in April. Joachim _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
