eXframe: reusable framework for storage, analysis and visualization of genomics experiments

<p>Abstract</p> <p>Background</p> <p>Genome-wide experiments are routinely conducted to measure gene expression, DNA-protein interactions and epigenetic status. Structured metadata for these experiments is imperative for a complete understanding of experimental conditions, to enable consistent data processing and to allow retrieval, comparison, and integration of experimental results. Even though several repositories have been developed for genomics data, only a few provide annotation of samples and assays using controlled vocabularies. Moreover, many of them are tailored for a single type of technology or measurement and do not support the integration of multiple data types.</p> <p>Results</p> <p>We have developed eXframe - a reusable web-based framework for genomics experiments that provides 1) the ability to publish structured data compliant with accepted standards 2) support for multiple data types including microarrays and next generation sequencing 3) query, analysis and visualization integration tools (enabled by consistent processing of the raw data and annotation of samples) and is available as open-source software. We present two case studies where this software is currently being used to build repositories of genomics experiments - one contains data from hematopoietic stem cells and another from Parkinson's disease patients.</p> <p>Conclusion</p> <p>The web-based framework eXframe offers structured annotation of experiments as well as uniform processing and storage of molecular data from microarray and next generation sequencing platforms. The framework allows users to query and integrate information across species, technologies, measurement types and experimental conditions. Our framework is reusable and freely modifiable - other groups or institutions can deploy their own custom web-based repositories based on this software. It is interoperable with the most important data formats in this domain. We hope that other groups will not only use eXframe, but also contribute their own useful modifications.</p

A semantic web framework to integrate cancer omics data with biological knowledge

BACKGROUND: The RDF triple provides a simple linguistic means of describing limitless types of information. Triples can be flexibly combined into a unified data source we call a semantic model. Semantic models open new possibilities for the integration of variegated biological data. We use Semantic Web technology to explicate high throughput clinical data in the context of fundamental biological knowledge. We have extended Corvus, a data warehouse which provides a uniform interface to various forms of Omics data, by providing a SPARQL endpoint. With the querying and reasoning tools made possible by the Semantic Web, we were able to explore quantitative semantic models retrieved from Corvus in the light of systematic biological knowledge. RESULTS: For this paper, we merged semantic models containing genomic, transcriptomic and epigenomic data from melanoma samples with two semantic models of functional data - one containing Gene Ontology (GO) data, the other, regulatory networks constructed from transcription factor binding information. These two semantic models were created in an ad hoc manner but support a common interface for integration with the quantitative semantic models. Such combined semantic models allow us to pose significant translational medicine questions. Here, we study the interplay between a cell's molecular state and its response to anti-cancer therapy by exploring the resistance of cancer cells to Decitabine, a demethylating agent. CONCLUSIONS: We were able to generate a testable hypothesis to explain how Decitabine fights cancer - namely, that it targets apoptosis-related gene promoters predominantly in Decitabine-sensitive cell lines, thus conveying its cytotoxic effect by activating the apoptosis pathway. Our research provides a framework whereby similar hypotheses can be developed easily

Knowledge extraction from unstructured data and classification through distributed ontologies

The World Wide Web has changed the way humans use and share any kind of information. The Web removed several access barriers to the information published and has became an enormous space where users can easily navigate through heterogeneous resources (such as linked documents) and can easily edit, modify, or produce them. Documents implicitly enclose information and relationships among them which become only accessible to human beings. Indeed, the Web of documents evolved towards a space of data silos, linked each other only through untyped references (such as hypertext references) where only humans were able to understand. A growing desire to programmatically access to pieces of data implicitly enclosed in documents has characterized the last efforts of the Web research community. Direct access means structured data, thus enabling computing machinery to easily exploit the linking of different data sources. It has became crucial for the Web community to provide a technology stack for easing data integration at large scale, first structuring the data using standard ontologies and afterwards linking them to external data. Ontologies became the best practices to define axioms and relationships among classes and the Resource Description Framework (RDF) became the basic data model chosen to represent the ontology instances (i.e. an instance is a value of an axiom, class or attribute). Data becomes the new oil, in particular, extracting information from semi-structured textual documents on the Web is key to realize the Linked Data vision. In the literature these problems have been addressed with several proposals and standards, that mainly focus on technologies to access the data and on formats to represent the semantics of the data and their relationships. With the increasing of the volume of interconnected and serialized RDF data, RDF repositories may suffer from data overloading and may become a single point of failure for the overall Linked Data vision. One of the goals of this dissertation is to propose a thorough approach to manage the large scale RDF repositories, and to distribute them in a redundant and reliable peer-to-peer RDF architecture. The architecture consists of a logic to distribute and mine the knowledge and of a set of physical peer nodes organized in a ring topology based on a Distributed Hash Table (DHT). Each node shares the same logic and provides an entry point that enables clients to query the knowledge base using atomic, disjunctive and conjunctive SPARQL queries. The consistency of the results is increased using data redundancy algorithm that replicates each RDF triple in multiple nodes so that, in the case of peer failure, other peers can retrieve the data needed to resolve the queries. Additionally, a distributed load balancing algorithm is used to maintain a uniform distribution of the data among the participating peers by dynamically changing the key space assigned to each node in the DHT. Recently, the process of data structuring has gained more and more attention when applied to the large volume of text information spread on the Web, such as legacy data, news papers, scientific papers or (micro-)blog posts. This process mainly consists in three steps: \emph{i)} the extraction from the text of atomic pieces of information, called named entities; \emph{ii)} the classification of these pieces of information through ontologies; \emph{iii)} the disambigation of them through Uniform Resource Identifiers (URIs) identifying real world objects. As a step towards interconnecting the web to real world objects via named entities, different techniques have been proposed. The second objective of this work is to propose a comparison of these approaches in order to highlight strengths and weaknesses in different scenarios such as scientific and news papers, or user generated contents. We created the Named Entity Recognition and Disambiguation (NERD) web framework, publicly accessible on the Web (through REST API and web User Interface), which unifies several named entity extraction technologies. Moreover, we proposed the NERD ontology, a reference ontology for comparing the results of these technologies. Recently, the NERD ontology has been included in the NIF (Natural language processing Interchange Format) specification, part of the Creating Knowledge out of Interlinked Data (LOD2) project. Summarizing, this dissertation defines a framework for the extraction of knowledge from unstructured data and its classification via distributed ontologies. A detailed study of the Semantic Web and knowledge extraction fields is proposed to define the issues taken under investigation in this work. Then, it proposes an architecture to tackle the single point of failure issue introduced by the RDF repositories spread within the Web. Although the use of ontologies enables a Web where data is structured and comprehensible by computing machinery, human users may take advantage of it especially for the annotation task. Hence, this work describes an annotation tool for web editing, audio and video annotation in a web front end User Interface powered on the top of a distributed ontology. Furthermore, this dissertation details a thorough comparison of the state of the art of named entity technologies. The NERD framework is presented as technology to encompass existing solutions in the named entity extraction field and the NERD ontology is presented as reference ontology in the field. Finally, this work highlights three use cases with the purpose to reduce the amount of data silos spread within the Web: a Linked Data approach to augment the automatic classification task in a Systematic Literature Review, an application to lift educational data stored in Sharable Content Object Reference Model (SCORM) data silos to the Web of data and a scientific conference venue enhancer plug on the top of several data live collectors. Significant research efforts have been devoted to combine the efficiency of a reliable data structure and the importance of data extraction techniques. This dissertation opens different research doors which mainly join two different research communities: the Semantic Web and the Natural Language Processing community. The Web provides a considerable amount of data where NLP techniques may shed the light within it. The use of the URI as a unique identifier may provide one milestone for the materialization of entities lifted from a raw text to real world object

Cyberinfrastructure for the digital brain:spatial standards for integrating rodent brain atlases

Biomedical research entails capture and analysis of massive data volumes and new discoveries arise from data-integration and mining. This is only possible if data can be mapped onto a common framework such as the genome for genomic data. In neuroscience, the framework is intrinsically spatial and based on a number of paper atlases. This cannot meet today’s data-intensive analysis and integration challenges. A scalable and extensible software infrastructure that is standards based but open for novel data and resources, is required for integrating information such as signal distributions, gene-expression, neuronal connectivity, electrophysiology, anatomy, and developmental processes. Therefore, the International Neuroinformatics Coordinating Facility (INCF) initiated the development of a spatial framework for neuroscience data integration with an associated Digital Atlasing Infrastructure (DAI). A prototype implementation of this infrastructure for the rodent brain is reported here. The infrastructure is based on a collection of reference spaces to which data is mapped at the required resolution, such as the Waxholm Space (WHS), a 3D reconstruction of the brain generated using high-resolution, multi-channel microMRI. The core standards of the digital atlasing service-oriented infrastructure include Waxholm Markup Language (WaxML): XML schema expressing a uniform information model for key elements such as coordinate systems, transformations, points of interest (POI)s, labels, and annotations; and Atlas Web Services: interfaces for querying and updating atlas data. The services return WaxML-encoded documents with information about capabilities, spatial reference systems and structures, and execute coordinate transformations and POI-based requests. Key elements of INCF-DAI cyberinfrastructure have been prototyped for both mouse and rat brain atlas sources, including the Allen Mouse Brain Atlas, UCSD Cell-Centered Database, and Edinburgh Mouse Atlas Project

SICS MarketSpace: an agent-based market infrastructure

We present a simple and uniform communication framework for an agent-based market infrastructure, the goal of which is to enable automation of markets with self-interested participants distributed over the Internet

Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model

Food webs, networks of feeding relationships among organisms, provide fundamental insights into mechanisms that determine ecosystem stability and persistence. Despite long-standing interest in the compartmental structure of food webs, past network analyses of food webs have been constrained by a standard definition of compartments, or modules, that requires many links within compartments and few links between them. Empirical analyses have been further limited by low-resolution data for primary producers. In this paper, we present a Bayesian computational method for identifying group structure in food webs using a flexible definition of a group that can describe both functional roles and standard compartments. The Serengeti ecosystem provides an opportunity to examine structure in a newly compiled food web that includes species-level resolution among plants, allowing us to address whether groups in the food web correspond to tightly-connected compartments or functional groups, and whether network structure reflects spatial or trophic organization, or a combination of the two. We have compiled the major mammalian and plant components of the Serengeti food web from published literature, and we infer its group structure using our method. We find that network structure corresponds to spatially distinct plant groups coupled at higher trophic levels by groups of herbivores, which are in turn coupled by carnivore groups. Thus the group structure of the Serengeti web represents a mixture of trophic guild structure and spatial patterns, in contrast to the standard compartments typically identified in ecological networks. From data consisting only of nodes and links, the group structure that emerges supports recent ideas on spatial coupling and energy channels in ecosystems that have been proposed as important for persistence.Comment: 28 pages, 6 figures (+ 3 supporting), 2 tables (+ 4 supporting

A Semantic Collaboration Method Based on Uniform Knowledge Graph

The Semantic Internet of Things is the extension of the Internet of Things and the Semantic Web, which aims to build an interoperable collaborative system to solve the heterogeneous problems in the Internet of Things. However, the Semantic Internet of Things has the characteristics of both the Internet of Things and the Semantic Web environment, and the corresponding semantic data presents many new data features. In this study, we analyze the characteristics of semantic data and propose the concept of a uniform knowledge graph, allowing us to be applied to the environment of the Semantic Internet of Things better. Here, we design a semantic collaboration method based on a uniform knowledge graph. It can take the uniform knowledge graph as the form of knowledge organization and representation, and provide a useful data basis for semantic collaboration by constructing semantic links to complete semantic relation between different data sets, to achieve the semantic collaboration in the Semantic Internet of Things. Our experiments show that the proposed method can analyze and understand the semantics of user requirements better and provide more satisfactory outcomes

Semantic Integration of Cervical Cancer Data Repositories to Facilitate Multicenter Association Studies: The ASSIST Approach

The current work addresses the unifi cation of Electronic Health Records related to cervical cancer into a single medical knowledge source, in the context of the EU-funded ASSIST research project. The project aims to facilitate the research for cervical precancer and cancer through a system that virtually unifi es multiple patient record repositories, physically located in different medical centers/hospitals, thus, increasing fl exibility by allowing the formation of study groups “on demand” and by recycling patient records in new studies. To this end, ASSIST uses semantic technologies to translate all medical entities (such as patient examination results, history, habits, genetic profi le) and represent them in a common form, encoded in the ASSIST Cervical Cancer Ontology. The current paper presents the knowledge elicitation approach followed, towards the defi nition and representation of the disease’s medical concepts and rules that constitute the basis for the ASSIST Cervical Cancer Ontology. The proposed approach constitutes a paradigm for semantic integration of heterogeneous clinical data that may be applicable to other biomedical application domains