by Chimezie Ogbuji
I recently had a need to manage a set of queries against an OWL2 EL biomedical ontology: the Foundational Model of Anatomy. I have an open source SPARQL service implementation that I had some thoughts about extending with support for managing queries. It’s called Triclops and is part of a collection of RDF libraries and tools I have been accumulating. The name is a reference to an initial attempt to build an RDF querying and navigation interface as part of the 4Suite repository back in the day (circa 2002).
This later evolved to a very rudimentary web interface that sat in front of the Oracle 11g and MySQL/SPARQL patient dataset that Cyc’s SKSI interacted with. This was part of an interface tailored to the task of identifying patient cohorts, known as the Semantic Research Assistant (SRA). A user could dispatch handwritten SPARQL queries, browse clickable results, or return them as CSV files. This capability was only used by informaticians familiar with the structure of the RDF dataset and most investigators used the SRA.
It also implemented a RESTful protocol for ticket-based querying that was used for stopping long-running SPARQL/MySQL queries. This is not currently documented. Around the time this was committed as an Apache-licensed, Google code library, layercake-python added core support for APIs that treated remote SPARQL services as local Graph objects as well as general support for connecting SPARQL services. This was based on Ivan Herman’s excellent SPARQL Endpoint interface to Python.
Triclops (as described in the wiki) can now be configured as a “Proxy SPARQL Endpoint”. It can be deployed as a light-weight query dispatch, management, and mediation kiosk for remote and local RDF datasets. The former capability (dispatching) was already in place, the latter (mediation) can be performed using FuXi’s recent capabilities in this regard.
Specifically, FuXi includes an rdflib Store that uses its sideways-information passing (sip) strategies the in-memory SPARQL algebra implementation for use as a general-purpose framework for semweb SPARQL (OWL2-RL/RIF/N3) entailment regimes. Queries are mediated over the SPARQL protocol using global schemas captured as various kinds of semweb ontology artifacts (expressed in a simple Horn form) that describe and distinguish their predicates by those instantiated in a database (or factbase) and those derived via the semantic properties of these artifacts.
So the primary capability that remained was query management and so this recent itch was scratched over the holidays. I discovered that CodeMirror , a JavaScript library that can be used to create a relatively powerful editor interface for code, had excellent support for SPARQL. I integrated it into Triclops as an interface for managing SPARQL queries and their results. I have a running version of this at http://metacognition.info/sparql/queryMgr. Note, the service is liable to break at any point as Webfaction kills of processes that use up alot of CPU and I have yet to figure out how to configure it to restart the service when it dies in such a fashion.
The dataset this interface manages queries for is a semantic web of content comprising 3 of the primary, ancient Chinese, classical texts (the Analects, Doctrine of the Mean, and the Tao Te Ching). I record the information in RDF because it is an intuitive knowledge representation to use in capturing provenance, exposition, and other editorial meta data. Below is a screen shot of the main page listing a handful of queries, their name, last date of modification, date of last run, and number of solutions in the recent result.
Above the list is a syntax-highlighted text area for dispatching adhoc SPARQL queries. This is where CodeMirror is integrated. If I click on the name of the query titled “Query for Analects and the Doctrine of the Mean english chapter text (Confucius)”, I go to a similar screen with another text area whose content corresponds to the text of the query (see the screen shot below).
From here queries can be updated (by submitting updated CodeMirror content) or cloned (using the name field for the new copy). Alternatively, the results of previous queries can be rendered. This sends back a result document with an XSLT processing instruction that causes the browser to trigger a request for a stylesheet and render an XHTML document from content in the result document on the client side.
Finally, a query can be re-executed against a dataset, saving the results and causing the information in the first screen to show different values for the last execution run (date and number of solutions). Results can also be saved or viewed as CSV using a different stylesheet against the result document.
The last capability added is a rudimentary template system where any variable in the query or text string of the form ‘$ …. $’ is replaced with a provided string or a URI. So, I can change the pick list value on the second row of the form controls to $searchExpression$ and type “water”. This produces a SPARQL query (visible with syntax highlighting via CodeMirror) that can be used as a template to dispatch queries against the dataset.
In addition, solutions for a particular variable can be used for links, providing a small framework for configurable, navigation workflows. If I enter “[Ww]ater” in the field next to $searchExpression$, select classic from the pick list at the top of the Result navigation template area, pick “Assertions in a (named) RDF graph” from the next pick list, and enter the graphIRI variable in the subsequent text input.
Triggering this form submission will produce the result screen pictured below. As specified in the form, clicking any of the the dbpedia links for the Doctrine of the Mean will initiate the invokation of the query titled “Assertions in a (named) RDF graph”, and shown below (with the graphIRI variable pre-populated with the corresponding URI):
SELECT DISTINCT ?s ?p ?o where {
GRAPH ?graphIRI {
?s ?p ?o
}
}
The result of such an action is shown in the screen shot. Alternatively, a different subsequent query can be used: “Statements about a resource”. The relationship between the schema of a dataset and the factbase can be navigated in a similar way. Picking the query titled “Classes in dataset” and making the following modifications. Select “Instances of a class and graph that the statements are asserted in” from the middle pick list of the Result navigation template section. Enter ?class in the text field to the right of this. Selecting ‘Execute..’ and executing this query results in a clickable result set comprised of classes of resources and clicking any such link shows the instances of that class.
This latter form of navigation seems well suited for exploring datasets for which either there is no schema information in the service or it is not well known by the investigator writing the queries.
In developing this interface, at least 2 architectural principles were re-used from my SemanticDB development days: the use of XSLT on the client side to build rich, offloaded (X)HTML applications and the use of the filesystem for managing XML documents rather than a relational database. The latter (use of a filesystem) is particularly more relevant where querying across the documents is not a major requirement or even a requirement at all. The former is via setting the processing instruction of a result document to refer to a dynamically generated XSLT document on the server.
The XSLT creates a tabular, row-distinguishing, tabular interface where the links to certain columns trigger queries via a web API that takes various input, including: the variable in the current query whose solutions are ‘streamed’, a (subsequent) query specified by some function of the MD5 hash of its title, a variable in that query that is pre-populated with the corresponding solution, etc:
../query=...&action=update&innerAction=execute,templateValue=...,&valueType=uri&variable=..
Eventually, the API should probably be made more RESTful and target the query, possibly leveraging some caching mechanism in the process. Perhaps it can even work in concert with the SPARQL 1.1 Graph Store HTTP Protocol.