The document describes a system for distributed querying of RDF data located across multiple SPARQL endpoints using URI resolution. It normalizes queries and results to a standard format by matching URI patterns to query templates, applying normalization rules, and executing queries on relevant endpoints. This allows for integrated access to numerous biomedical knowledge bases and extension of the system through additional query types and data sources.

1. URI based distributed querying Peter Ansell

4. Normalisation Rules : Rules that define the transformations from a standard normalised URI system to a system matching a particular endpoint, and the reverse if necessary

5. Providers : The entities which provide the information. They can be SPARQL endpoints or even simple URL's. If they are proxied they should return RDF information, but redirects are also available for other providers.

9. /namespace:identifier matches at least http://qut.bio2rdf.org/query:construct and http://qut.bio2rdf.org/query:taglabels

14. If a query type is namespace specific, filter its list of providers based on whether they match any or all of the namespaces according to the query title namespace matching configuration. This time the inclusion is based on the namespace test with the list of namespaces configured for the provider

16. The construct query is namespace specific so only construct providers which handle the given namespace will be included, where the taglabels query is not namespace specific so the any taglabels providers will be included in the final provider list

18. Default providers are intended to make it simpler to configure intermediate servers without having to know about all of the known namespaces

20. If a provider needs a redirect, as opposed to proxying communication, replace any template variables on the endpoint URL and send an HTTP 302 redirect response as the result

22. The normalisation rules are matched against the template variables and replaced as necessary in order to make them specific to the relevant endpoint

24. ${endpointSpecificUri} to allow for the SPARQL endpoint to contain a different URI to the one which is desired

25. ${input_1}, ${input_2}, etc., which correspond to the matching groups from the query type. ${input_1} is typically the namespace, although this is configurable.

27. ${endpointUrl} – this can also have template variables inside it, which are replaced before the redirect check phase

28. ${defaultHostAddress} – the standard base URL for this configuration, ie, http://bio2rdf.org/

29. ${realHostName} – the actual host being used, ie. http://mymirror.local/bio2rdf/

31. ${inputUrlEncoded_normalisedStandardUri} – a version of the standard URI as given by the query type with the ${input_NN} sections internally percent encoded

32. ${xmlEncoded_inputUrlEncoded_normalisedStandardUri} – for use in RDF/XML templates

33. ${inputUrlEncoded_privatelowercase_endpointSpecificUri} – for use with endpoints which contain percent encoded URI's that have the private ${input_NN} variables completely in lowercase without regard to the case given in the ${queryString}

34. ${queryString} – The original input string which matched against the query type regular expression

36. The other variables will be different depending on whether the construct provider for namespace1 is being contacted, or

38. If it is declared as “nocommunication”, ignore it for now. It will be used with the static RDF/XML insertion stage

39. If it is declared as “httpgeturl” then perform HTTP resolution on the provider endpoint URL after replacing the relevant template variables

41. The SPARQL query is matched to the endpoint at this stage by the use of a query type that contains the basic structure of the query, and normalisation rules to make sure the URI's in the SPARQL match the endpoint and Graph combination

43. More than one provider may be attached to the same endpoint and graph combination, so a given URI may resolve using more than one query on the same endpoint and graph depending on the query needs

46. http://qut.bio2rdf.org/admin/configuration/rdfxml

48. The only requirement is that the query type relevant to the tags etc., matches the regular expression for the the URI it is extending. For example http://qut.bio2rdf.org/query:taglabels and http://qut.bio2rdf.org/query:construct both have regular expressions that match the basic http://bio2rdf.org/namespace:identifier URI

50. HTML formatted results for easy browsing, possibly using Pubby as the rendering engine

51. Paged SPARQL calls using OFFSET and LIMIT

52. Alternative configurations for Dbpedia, SharedNames etc. that don't require http://bio2rdf.org/ as the base URI and have different basic queries

53. Import configuration from RDF similar to the current configuration output

55. Bring together the current distributed efforts to provide a complete HTML redirection registry so that a large percentage of Bio2RDF namespaces can be redirected with http://bio2rdf.org/html/namespace:identifier

56. Form ontologies describing the query type, provider, rdf normalisation rule, namespace paradigm