Brinkley, James F.; Detwiler, Landon T.
We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written...
Detwiler, Landon T; Gatterbauer, Wolfgang; Louie, Brenton; Suciu, Dan; Tarczy-Hornoch, Peter
Mediator-based data integration systems resolve exploratory queries by joining data elements across sources. In the presence of uncertainties, such multiple expansions can quickly lead to spurious connections and incorrect results. The BioRank project investigates formalisms for modeling uncertainty during scientific data integration and for ranking uncertain query results. Our motivating application is protein function prediction. In this paper we show that: (i) explicit modeling of uncertainties as probabilities increases our ability to predict less-known or previously unknown functions (though it does not improve predicting the well-known). This suggests that probabilistic uncertainty models offer utility for scientific knowledge discovery; (ii) small...
This thesis describes the use of independent component analysis (ICA) as
a measure of voxel similarity, which allows the user to find and view
statistically independent maps of correlated voxel activity.
The tool developed in this work uses a specialized clustering technique,
designed to find and characterize clusters of activated voxels, to
compare the independent component spatial maps across patients. This
same method is also used to compare SPM results across patients.
Louie, Brenton; Detwiler, Landon T; Dalvi, Nilesh; Shaker, Ron; Tarczy-Hornoch, Peter; Suciu, Dan
There is a significant need for data integration
capabilities in the scientific domain, which has
manifested itself as products in the commercial world
as well as academia. However, in our experiences in
dealing with biological data it has become apparent to
us that existing data integration products do not
handle uncertainties in the data very well. This leads
to systems that often produce an explosion of less
relevant answers which subsequently leads to a loss of
more relevant answers by overloading the user. How
to incorporate functionality into data integration
systems to properly handle uncertainties and make
results more useful has become an important research
In this paper we describe an enhanced generalpurpose
Warren, Wayne; Agoncillo, Augusto V; Franklin, Joshua D; Brinkley, James F
In this report, we describe a process of applying intelligent scene generation to a newly acquired complete set of 3D models representing the whole human body.
Rosse, Cornelius; Kumar, Anand; Mejino, Jose L V; Cook, Daniel L; Detwiler, Landon T; Smith, Barry
The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies in anatomy, physiology and pathology.
Cho, Hansang; Corina, David P; Brinkley, James F; Ojemann, George A; Shapiro, Linda G
The analysis of single unit recording data requires a spike sorting method to separate blended neuronal spikes into separate neuron classes. A new template matching method for spike sorting based on shape distributions and a weighted Euclidean metric is proposed. The data is first roughly clustered using a Euclidean distance metric. Then the Levenberg-Marquardt method is used to estimate the variances of the neuron classes using curve fitting on the clustered data. Finally, the weighted Euclidean distance method is applied to minimize errors caused by different variances. This method provides optimized template matching results when the neuron variances are considerably...
Gennari, John H; Silberfein, Adam; Wiley, Jesse
Modern genomic research has access to a plethora of knowledge sources. Often, it is imperative that researchers combine and integrate knowledge from multiple perspectives. Although some technology exists for connecting data and knowledge bases, these methods are only just begin-ning to be successfully applied to research in modern cell biology. In this paper, we argue that one way to integrate multiple knowledge sources is through anatomyboth generic cellular anatomy, as well as anatomic knowledge about the tissues and organs that may be studied via microarray gene expression experiments. We present two examples where we have combined a large ontology of...
Re, Chris; Brinkley, James F; Hinshaw, Kevin P; Suciu, Dan
XQuery is increasingly being used for ad-hoc integration of heterogeneous data sources that are logically mapped to XML. For example, scientists need to query multiple scientific databases, which are distributed over a large geographic area, and it is possible to use XQuery for that. However, the language currently supports only the data shipping query evaluation model (through the document() function): it fetches all data sources to a single server, then runs the query there. This is a major limitation for many applications, especially when some data sources are very large, or when a data source is only a virtual XML...
Mejino, Jose L V; Rosse, Cornelius
The need for a sharable resource that can provide deep anatomical knowledge and support inference for biomedical applications has recently been the driving force in the creation of biomedical ontologies. Previous attempts at the symbolic representation of anatomical relationships necessary for such ontologies have been largely limited to general partonomy and class subsumption. We propose an ontology of anatomical relationships beyond class assignments and generic part-whole relations and illustrate the inheritance of structural attributes in the Digital Anatomist Foundational Model of Anatomy. Our purpose is to generate a symbolic model that accommodates all structural relationships and physical properties required to...