19,730 research outputs found
Multiplierz: An Extensible API Based Desktop Environment for Proteomics Data Analysis
BACKGROUND. Efficient analysis of results from mass spectrometry-based proteomics experiments requires access to disparate data types, including native mass spectrometry files, output from algorithms that assign peptide sequence to MS/MS spectra, and annotation for proteins and pathways from various database sources. Moreover, proteomics technologies and experimental methods are not yet standardized; hence a high degree of flexibility is necessary for efficient support of high- and low-throughput data analytic tasks. Development of a desktop environment that is sufficiently robust for deployment in data analytic pipelines, and simultaneously supports customization for programmers and non-programmers alike, has proven to be a significant challenge. RESULTS. We describe multiplierz, a flexible and open-source desktop environment for comprehensive proteomics data analysis. We use this framework to expose a prototype version of our recently proposed common API (mzAPI) designed for direct access to proprietary mass spectrometry files. In addition to routine data analytic tasks, multiplierz supports generation of information rich, portable spreadsheet-based reports. Moreover, multiplierz is designed around a "zero infrastructure" philosophy, meaning that it can be deployed by end users with little or no system administration support. Finally, access to multiplierz functionality is provided via high-level Python scripts, resulting in a fully extensible data analytic environment for rapid development of custom algorithms and deployment of high-throughput data pipelines. CONCLUSION. Collectively, mzAPI and multiplierz facilitate a wide range of data analysis tasks, spanning technology development to biological annotation, for mass spectrometry-based proteomics research.Dana-Farber Cancer Institute; National Human Genome Research Institute (P50HG004233); National Science Foundation Integrative Graduate Education and Research Traineeship grant (DGE-0654108
A Query Integrator and Manager for the Query Web
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 in whatever language is appropriate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontology view generation using a combination of graph-based and logical approaches, value set generation for clinical data management, image annotation using terminology obtained from an ontology web service, ontology-driven brain imaging data integration, small-scale clinical data integration, and wider-scale clinical data integration. Such use cases illustrate the current range of applications of QI and lead us to speculate about the potential evolution from smaller groups of interconnected queries into a larger query network that layers over the document and semantic web. The resulting Query Web could greatly aid researchers and others who now have to manually navigate through multiple information sources in order to answer specific questions
Learning Tuple Probabilities
Learning the parameters of complex probabilistic-relational models from
labeled training data is a standard technique in machine learning, which has
been intensively studied in the subfield of Statistical Relational Learning
(SRL), but---so far---this is still an under-investigated topic in the context
of Probabilistic Databases (PDBs). In this paper, we focus on learning the
probability values of base tuples in a PDB from labeled lineage formulas. The
resulting learning problem can be viewed as the inverse problem to confidence
computations in PDBs: given a set of labeled query answers, learn the
probability values of the base tuples, such that the marginal probabilities of
the query answers again yield in the assigned probability labels. We analyze
the learning problem from a theoretical perspective, cast it into an
optimization problem, and provide an algorithm based on stochastic gradient
descent. Finally, we conclude by an experimental evaluation on three real-world
and one synthetic dataset, thus comparing our approach to various techniques
from SRL, reasoning in information extraction, and optimization
RDF Querying
Reactive Web systems, Web services, and Web-based publish/
subscribe systems communicate events as XML messages, and in
many cases require composite event detection: it is not sufficient to react
to single event messages, but events have to be considered in relation to
other events that are received over time.
Emphasizing language design and formal semantics, we describe the
rule-based query language XChangeEQ for detecting composite events.
XChangeEQ is designed to completely cover and integrate the four complementary
querying dimensions: event data, event composition, temporal
relationships, and event accumulation. Semantics are provided as
model and fixpoint theories; while this is an established approach for rule
languages, it has not been applied for event queries before
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