Structural Informatics Group (SIG) logo
Home | Projects | Demos | Downloads | Publications | Local Info | About Us | New site

Sample queries from JBI submission

"A Query Manager and Integrator for the Query Web"

 

This page is intended as suplemental material for the JBI submission "A Query Manager and Integrator for the Query Web".

.

Query #LanguageDescription

.

37vSPARQLThis query processes complex description logic patterns in the OWL version of the NCI Thesaurus (NCIt) and reduces them into simpler, more direct, triple patterns for human consumption and understanding.

.

50vSPARQLThis query extracts the neuro-anatomical subset (or "view") of the Foundational Model of Anatomy, as the stand-alone NeuroFMA ontology.

.

93XQueryThis demonstrates distributed data integration via query for the purpose of quality control checks. In this query records are joined from two sources XNAT, which contains image quality information and RedCap which contains exam date. For "unusable" images the query reports the number of days left to acquire usable results (i.e. within a 7 day window).

.

95SPARQLA template query which takes as its only template parameter the rdfs:label of a seed class in the Foundational Model of Anatomy (FMA). It returns the labels of all classes that can be reached from the seed by recursively following the alternation of 2 kinds of part properties from the seed; regional_part and constitutional_part.

.

97SPARQLQuery the NeuroFMA, from a given White matter (WM) structure (e.g. Right SLF), return a graph of all the gray matter (GM) structures that the WM structure either projects_to or projects_from. For each GM structure, return the FMA name, FMAIDs, AAL labels, and AAL IDs.

.

102XQueryFind the AAL IDs of Gray Matter regions connected by the right SLF, then use the AAL IDs to call the AIS webservice that takes the IDs and an fMRI file as arguements, then returns the mean activation for all included brain regions of a NIfTI image

.

108SPARQLSimplified view of Biopax level 3 format TCA cycle, as downloaded from Reactome on 1/15/11: "Pyruvate metabolism and Citric Acid (TCA) cycle" http://www.reactome.org/cgi-bin/biopaxexporter?DB=gk_current_pathway_diagram&level=3&ID=71406, and cached as Reactome_71406.owl.

.

109SPARQLTemplate query for a protein controller for a step in the TCA cycle, as a query over the simplified view of the Reactome Biopax TCA cycle, as saved in query 108.

.

130vSPARQLThis query demonstrates the generation of the seed entity set for a module extraction of the OCRe admin model.

.

132XQueryThis query converts OCRe RDF value set definitions to XSD format. The template parameters are <#0> - the URL of the value set in RDF and <#1> - the desired name of the xsd value set element generated.

.

135SPARQLThis template query creates a value set whose members are the instances of a specified class within a specified ontology. The template substitution parameters (<#0> ,<#1>, and <#2>) are the URI of the value set, the URL fo the ontology, and the rdfs:label of the root class.

.

157XQueryThis query demonstrates using distributed queries as an alternative mechanism for integrating the (green) data from the caBIG prostate SPORE project. Specifically it finds prostatectomies performed on men whose age at surgery was 70 or more. A source registry is used so that the set of sources can change without the need to change the query.

.

163XQueryThis query demonstrates the utility of leveraging ontologies to perform smarter queries over data. In this case data are pulled from several distributed sources based on a source registry. Records (clinical trial metadata) from those sources are tagged with specific study design types (i.e. Parallel group study design). The query asks for all of those records in that fall in a broader study design type classification (in this Case interventional study design). Which specific study design types belong to the more general category is not discoverable within the data source alone. But the association between the general and specific design types, if there is one, is represented in the OCRe ontology.

.

164SPARQLThis template query creates an RDF value set containing all of the subclasses of the specified class in a pre-inferred and merged version of the OCRe ontology. The template parameter specifies the seed class via rdfs:label.

.

165XQueryGroup a dataset into two distinct groups, healthy patients vs. schizophrenic and set separate visualization hints (i.e. marker color, shape, size) for each (to be used by data visualization tool).

.

177IMLThis IML query extracts Cerebral_hemisphere parts from fma_3_2. Replaces subClassOf, regional_part and constitutional_part with part. Then for all these parts extracts common brain atlas synonyms.

.

178vSPARQLStarting from the Dorsolateral_prefrontal_cortex, follow the transitive closure of part links in a simplified Cerebral_hemisphere view (as generated from query 177). For each such part include associated synonyms from various brain atlases. Results of 177 are materialized for efficiency.

.

179vSPARQLSame as query 178 above, but instead of starting from the fixed resource Dorsolateral_prefrontal_cortex, a template replacement parameter is used to allow the seed node to be specified at query execution time.

.

181URLSaved URL query call to template query 179 above with the argument (seed node) fma:Temporal_lobe.

.

188XQueryFrom BIRN data extract only those sites that are located within a given brain region as specified by the input template argument. This argument is in turn passed as a parameter to template query 179, which finds parts of the brain from a view of the FMA. Query chain:188->179->177 (materialized)

.

189URLSaved URL query call to template query 188 above with template substitution value fma:Dorsolateral_prefrontal_cortex

.

192XQueryLike query 165, but adds count information to groups (healthy, Sz, total).

.

193vSPARQLStarting from Gastric Mucosa-Associated Lymphoid Tissue Lymphoma in NCIt, create a simplified view similar to query 37 but in RDF. This query uses vSPARQL Skolem functions to dynamically generate new RDF resources.

.

195vSPARQLFrom the FMA, generate a graph, to be used by physiology modelers, representing portions of blood contained in the heart. The results include heart parts and the blood portions they contain, where “contains” is a modified definition than that used by the FMA. In the FMA, only spaces are allowed in the domain of the contains property; in this use case, if a space contains blood, the structures that it is a part of should also be said to contain blood.

.

196vSPARQLThis query combine information from two independent ontologies (FMA and Ontology of Physics for Biology (OPB )) to create new information for a biosimulation model editing application. Properties of fluids defined in the FMA should be combined with the kinetic properties of fluids defined in the OPB. For example, concepts like arterial blood and capillary blood in the FMA can be combined with flow, pressure, viscosity in the OPB, resulting in new concepts like arterial blood flow, capillary blood viscosity, etc. The result contains the newly created resources and their properties which can be used to annotate computational models of physiology.

.

197URLURL reference to template query with use case specific arguments included, for generating RDF version of Telecommunication scheme. The source ontology (arg <#1>) is the result of module extraction query 92 over OCRe.

.

198URLSaved URL for XSD transformation of OCRe Telecommunication scheme value set (reference to query 132). Passes in arguments: <#0> url of query that produces RDF value set, <#1> name of XSD element representing value set. Because it has query 197 as a source, this query indirectly accesses a module extracted from OCRe on the fly, rather than OCre itself.

.

202XQueryAre samples available for patients who still need any qPCR completed?

.

203ModuleConfigDemonstration of a syntactic locality module "query" whose signature is produced by another query (130) over a pre-merged and inferred OCRe source ontology.

.

205URLURL query sets parameter for template query 109 to be a reaction step in the TCA cycle, finds the protein controller (enzyme) for that step.