Towards structured sharing of raw and derived neuroimaging data across existing resources

Data sharing efforts increasingly contribute to the acceleration of scientific discovery. Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted format for the critically important meta-data that is necessary for making use of the combined, available neuroimaging data. In this manuscript, we present work from the Derived Data Working Group, an open-access group sponsored by the Biomedical Informatics Research Network (BIRN) and the International Neuroimaging Coordinating Facility (INCF) focused on practical tools for distributed access to neuroimaging data. The working group develops models and tools facilitating the structured interchange of neuroimaging meta-data and is making progress towards a unified set of tools for such data and meta-data exchange. We report on the key components required for integrated access to raw and derived neuroimaging data as well as associated meta-data and provenance across neuroimaging resources. The components include (1) a structured terminology that provides semantic context to data, (2) a formal data model for neuroimaging with robust tracking of data provenance, (3) a web service-based application programming interface (API) that provides a consistent mechanism to access and query the data model, and (4) a provenance library that can be used for the extraction of provenance data by image analysts and imaging software developers. We believe that the framework and set of tools outlined in this manuscript have great potential for solving many of the issues the neuroimaging community faces when sharing raw and derived neuroimaging data across the various existing database systems for the purpose of accelerating scientific discovery

A Call to Arms: Revisiting Database Design

Good database design is crucial to obtain a sound, consistent database, and - in turn - good database design methodologies are the best way to achieve the right design. These methodologies are taught to most Computer Science undergraduates, as part of any Introduction to Database class. They can be considered part of the "canon", and indeed, the overall approach to database design has been unchanged for years. Moreover, none of the major database research assessments identify database design as a strategic research direction. Should we conclude that database design is a solved problem? Our thesis is that database design remains a critical unsolved problem. Hence, it should be the subject of more research. Our starting point is the observation that traditional database design is not used in practice - and if it were used it would result in designs that are not well adapted to current environments. In short, database design has failed to keep up with the times. In this paper, we put forth arguments to support our viewpoint, analyze the root causes of this situation and suggest some avenues of research.Comment: Removed spurious column break. Nothing else was change

Data Management and Mining in Astrophysical Databases

We analyse the issues involved in the management and mining of astrophysical data. The traditional approach to data management in the astrophysical field is not able to keep up with the increasing size of the data gathered by modern detectors. An essential role in the astrophysical research will be assumed by automatic tools for information extraction from large datasets, i.e. data mining techniques, such as clustering and classification algorithms. This asks for an approach to data management based on data warehousing, emphasizing the efficiency and simplicity of data access; efficiency is obtained using multidimensional access methods and simplicity is achieved by properly handling metadata. Clustering and classification techniques, on large datasets, pose additional requirements: computational and memory scalability with respect to the data size, interpretability and objectivity of clustering or classification results. In this study we address some possible solutions.Comment: 10 pages, Late

Developing a comprehensive framework for multimodal feature extraction

Feature extraction is a critical component of many applied data science workflows. In recent years, rapid advances in artificial intelligence and machine learning have led to an explosion of feature extraction tools and services that allow data scientists to cheaply and effectively annotate their data along a vast array of dimensions---ranging from detecting faces in images to analyzing the sentiment expressed in coherent text. Unfortunately, the proliferation of powerful feature extraction services has been mirrored by a corresponding expansion in the number of distinct interfaces to feature extraction services. In a world where nearly every new service has its own API, documentation, and/or client library, data scientists who need to combine diverse features obtained from multiple sources are often forced to write and maintain ever more elaborate feature extraction pipelines. To address this challenge, we introduce a new open-source framework for comprehensive multimodal feature extraction. Pliers is an open-source Python package that supports standardized annotation of diverse data types (video, images, audio, and text), and is expressly with both ease-of-use and extensibility in mind. Users can apply a wide range of pre-existing feature extraction tools to their data in just a few lines of Python code, and can also easily add their own custom extractors by writing modular classes. A graph-based API enables rapid development of complex feature extraction pipelines that output results in a single, standardized format. We describe the package's architecture, detail its major advantages over previous feature extraction toolboxes, and use a sample application to a large functional MRI dataset to illustrate how pliers can significantly reduce the time and effort required to construct sophisticated feature extraction workflows while increasing code clarity and maintainability

Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

rEMM: Extensible Markov Model for Data Stream Clustering in R

Clustering streams of continuously arriving data has become an important application of data mining in recent years and efficient algorithms have been proposed by several researchers. However, clustering alone neglects the fact that data in a data stream is not only characterized by the proximity of data points which is used by clustering, but also by a temporal component. The extensible Markov model (EMM) adds the temporal component to data stream clustering by superimposing a dynamically adapting Markov chain. In this paper we introduce the implementation of the R extension package rEMM which implements EMM and we discuss some examples and applications.