Search results for: Paolo Missier

Items from 1 to 20 out of 38 results

article

Increasing phenotypic annotation improves the diagnostic rate of exome sequencing in a rare neuromuscular disorder

Rachel Thompson, Anastasios Papakonstantinou Ntalis, Sergi Beltran, Ana Töpf, more

Phenotype‐based filtering and prioritization contribute to the interpretation of genetic variants detected in exome sequencing. However, it is currently unclear how extensive this phenotypic annotation should be. In this study, we compare methods for incorporating phenotype into the interpretation process and assess the extent to which phenotypic annotation aids prioritization of the correct variant...

article

TAPER: query-aware, partition-enhancement for large, heterogenous graphs

Hugo Firth, Paolo Missier

Distributed and Parallel Databases > 2017 > 35 > 2 > 85-115

Graph partitioning has long been seen as a viable approach to addressing Graph DBMS scalability. A partitioning, however, may introduce extra query processing latency unless it is sensitive to a specific query workload, and optimised to minimise inter-partition traversals for that workload. Additionally, it should also be possible to incrementally adjust the partitioning in reaction to changes in...

chapter

Facilitating reproducible research by investigating computational metadata

Priyaa Thavasimani, Paolo Missier

2016 IEEE International Conference on Big Data (Big Data) > 3045 - 3051

2016 IEEE International Conference on Big Data (Big Data)

Computational workflows consist of a series of steps in which data is generated, manipulated, analysed and transformed. Researchers use tools and techniques to capture the provenance associated with the data to aid reproducibility. The metadata collected not only helps in reproducing the computation but also aids in comparing the original and reproduced computations. In this paper, we present an approach,...

chapter

Accelerating Disease Gene Identification Through Integrated SNP Data Analysis

Paolo Missier, Suzanne Embury, Conny Hedeler, Mark Greenwood, more

Lecture Notes in Computer Science > Data Integration in the Life Sciences > Modeling of Life Science Data > 215-230

Information about small genetic variations in organisms, known as single nucleotide polymorphism (SNPs), is crucial to identify candidate genes that have a role in disease susceptibility, a long-standing research goal in biology. While a number of established public SNP databases are available, the specification of effective techniques for SNP analysis remains an open issue. We describe a secondary...

chapter

The Service to Businesses Project: Improving Government-to-Business Relationships in Italy

Marco Bertoletti, Paolo Missier, Monica Scannapieco, Pietro Aimetti, more

Lecture Notes in Computer Science > Electronic Government > Workshop: Global Relations and Regional Development > 468-471

The paper describes the main ideas and results of a project improving the government to business relationships in Italy by a cooperative architecture based on a Publish & Subscribe communication paradigm.

chapter

Building Scientific Workflow with Taverna and BPEL: A Comparative Study in caGrid

Wei Tan, Paolo Missier, Ravi Madduri, Ian Foster

Lecture Notes in Computer Science > Service-Oriented Computing – ICSOC 2008 Workshops > Fourth International Workshop on Engineering Service-Oriented Applications (WESOA 2008) > 118-129

With the emergence of “service oriented science,” the need arises to orchestrate various services to facilitate scientific investigation – that is, to create “science workflows.” In this paper we summarize our findings in providing a workflow solution for the caGrid service-based grid infrastructure. We choose BPEL and Taverna as candidate solutions, and compare their usability in the full lifecycle...

chapter

Data Lineage Model for Taverna Workflows with Lightweight Annotation Requirements

Paolo Missier, Khalid Belhajjame, Jun Zhao, Marco Roos, more

Lecture Notes in Computer Science > Provenance and Annotation of Data and Processes > Papers > 17-30

The provenance, or lineage, of a workflow data product can be reconstructed by keeping a complete trace of workflow execution. This lineage information, however, is likely to be both imprecise, because of the black-box nature of the services that compose the workflow, and noisy, because of the many trivial data transformations that obscure the intended purpose of the workflow. In this paper we argue...

chapter

Workflows for Information Integration in the Life Sciences

Paolo Missier, Norman Paton, Peter Li

Lecture Notes in Computer Science > Search Computing > Part 7: Bio-SeCo > 215-225

The increasingly computationally- and data-intensive nature of experimental science motivates recent interest in workflows, as a way to specify complex data processing and integration pipelines in a fairly intuitive way. Such workflows orchestrate the invocation of data retrieval services in a way that resembles, to some extent, Search Computing query plans. While the former are manually specified,...

chapter

A Linked Data Approach to Sharing Workflows and Workflow Results

Marco Roos, Sean Bechhofer, Jun Zhao, Paolo Missier, more

Lecture Notes in Computer Science > Leveraging Applications of Formal Methods, Verification, and Validation > Tools in Scientific Workflow Composition > 340-354

A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the ‘Materials and Methods’ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find...

chapter

Managing Information Quality in e-Science Using Semantic Web Technology

Alun Preece, Binling Jin, Edoardo Pignotti, Paolo Missier, more

Lecture Notes in Computer Science > The Semantic Web: Research and Applications > Semantic Annotation > 472-486

We outline a framework for managing information quality (IQ) in e-Science, using ontologies, semantic annotation of resources, and data bindings. Scientists define the quality characteristics that are of importance in their particular domain by extending an OWL DL IQ ontology, which classifies and organises these domain-specific quality characteristics within an overall quality management framework...

chapter

Taverna, Reloaded

Paolo Missier, Stian Soiland-Reyes, Stuart Owen, Wei Tan, more

Lecture Notes in Computer Science > Scientific and Statistical Database Management > Scientific Workflow and Provenance > 471-481

The Taverna workflow management system is an open source project with a history of widespread adoption within multiple experimental science communities, and a long-term ambition of effectively supporting the evolving need of those communities for complex, data-intensive, service-based experimental pipelines. This short paper describes how the recently overhauled technical architecture of Taverna addresses...

chapter

Exploiting Provenance to Make Sense of Automated Decisions in Scientific Workflows

Paolo Missier, Suzanne Embury, Richard Stapenhurst

Lecture Notes in Computer Science > Provenance and Annotation of Data and Processes > Papers > 174-185

Scientific workflows may include automated decision steps, for instance to accept/reject certain data products during the course of an in silico experiment, based on an assessment of their quality. The trustworthiness of these workflows can be enhanced by providing the users with a trace and explanation of the outcome of these decisions. In this paper we present a provenance model that is designed...

chapter

Janus: From Workflows to Semantic Provenance and Linked Open Data

Paolo Missier, Satya S. Sahoo, Jun Zhao, Carole Goble, more

Lecture Notes in Computer Science > Provenance and Annotation of Data and Processes > Papers > 129-141

Data provenance graphs are form of metadata that can be used to establish a variety of properties of data products that undergo sequences of transformations, typically specified as workflows. Their usefulness for answering user provenance queries is limited, however, unless the graphs are enhanced with domain-specific annotations. In this paper we propose a model and architecture for semantic, domain-aware...

chapter

Metadata Management in S-OGSA

Oscar Corcho, Pinar Alper, Paolo Missier, Sean Bechhofer, more

Lecture Notes in Computer Science > Computational Science – ICCS 2007 > 712-719

Metadata-intensive applications pose strong requirements for metadata management infrastructures, which need to deal with a large amount of distributed and dynamic metadata. Among the most relevant requirements we can cite those related to access control and authorisation, lifecycle management and notification, and distribution transparency. This paper discusses such requirements and proposes a systematic...

chapter

Understanding Collaborative Studies through Interoperable Workflow Provenance

Ilkay Altintas, Manish Kumar Anand, Daniel Crawl, Shawn Bowers, more

Lecture Notes in Computer Science > Provenance and Annotation of Data and Processes > Papers > 42-58

The provenance of a data product contains information about how the product was derived, and is crucial for enabling scientists to easily understand, reproduce, and verify scientific results. Currently, most provenance models are designed to capture the provenance related to a single run, and mostly executed by a single user. However, a scientific discovery is often the result of methodical execution...

chapter

Managing Information Quality in e-Science: A Case Study in Proteomics

Paolo Missier, Alun Preece, Suzanne Embury, Binling Jin, more

Lecture Notes in Computer Science > Perspectives in Conceptual Modeling > Quality Driven Processes > 423-432

We describe a new approach to managing information quality (IQ) in an e-Science context, by allowing scientists to define the quality characteristics that are of importance in their particular domain. These preferences are specified and classified in relation to a formal IQ ontology, intended to support the discovery and reuse of scientists’ quality descriptors and metrics. In this paper, we present...

book

Data Integration in the Life Sciences

Norman W. Paton, Paolo Missier, Cornelia Hedeler

Lecture Notes in Computer Science

Data integration in the life sciences continues to be important but challe- ing. The ongoing development of new experimental methods gives rise to an increasingly wide range of data sets, which in turn must be combined to allow more integrative views of biological systems. Indeed, the growing prominence of systems biology, where mathematical models characterize behaviors observed in experiments of...

article

Provenance and data differencing for workflow reproducibility analysis

Paolo Missier, Simon Woodman, Hugo Hiden, Paul Watson

Concurrency and Computation: Practice and Experience > 28 > 4 > 995 - 1015

One of the foundations of science is that researchers must publish the methodology used to achieve their results so that others can attempt to reproduce them. This has the added benefit of allowing methods to be adopted and adapted for other purposes. In the field of e‐Science, services – often choreographed through workflow, process data to generate results. The reproduction of results is often not...

chapter

eScience

Jun Zhao, Oscar Corcho, Paolo Missier, Khalid Belhajjame, more

Handbook of Semantic Web Technologies > Semantic Web Applications > 701-736

This chapter looks into how the use of semantic technologies can provide support to common needs in eScience projects, including data-intensive science, facilitating experiment knowledge reuse and recycle among scientists, lowering the barriers of knowledge exchange for interdisciplinary research, and bridging the gap between data from different sources and the gap between data sharing and digital...

chapter

Bootstrapping Personalised Human Activity Recognition Models Using Online Active Learning

Tudor Miu, Paolo Missier, Thomas Plotz

2015 IEEE International Conference on Computer and Information Technology; Ubiquitous Computing and Communications; Dependable, Autonomic and Secure Computing; Pervasive Intelligence and Computing > 1138 - 1147

In Human Activity Recognition (HAR) supervised and semi-supervised training are important tools for devising parametric activity models. For the best modelling performance, typically large amounts of annotated sample data are required. Annotating often represents the bottleneck in the overall modelling process as it usually involves retrospective analysis of experimental ground truth, like video footage...

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PROVENANCE (6)
SEMANTIC WEB (4)
COMPUTATIONAL MODELING (3)
REPRODUCIBILITY (3)
SCIENTIFIC WORKFLOWS (3)
SEMANTICS (3)
BIOINFORMATICS (2)
BIOLOGICAL SYSTEM MODELING (2)
CLOUD COMPUTING (2)
DATA QUALITY (2)
LINKED DATA (2)
ONTOLOGIES (2)
PUBLISHING (2)
SCIENTIFIC WORKFLOW (2)
TAVERNA (2)
WORKFLOWS (2)
ACCESS CONTROL LANGUAGE (1)
ARCHITECTURE (1)
BIG DATA (1)
BPEL (1)
BROKERING SERVICE (1)
BUNDLE OF DATA (1)
CAGRID (1)
CLUSTERING (1)
COMPUTER TELEPHONY INTEGRATION (1)
CONCEPT WEB (1)
CONGENITAL MYASTHENIC SYNDROMES (1)
CONTEXT (1)
DATA DRIVEN WORKFLOWS (1)
DATA INTEGRATION (1)
DATA MODELS (1)
DATA VISUALIZATION (1)
DATA-INTENSIVE SCIENCE (1)
DATABASES (1)
DEEP PHENOTYPING (1)
DIAGNOSIS (1)
DIGITAL PRESERVATION (1)
DISTRIBUTED HASH TABLES (1)
E-GOVERNMENT (1)
E-SCIENCE (1)
ELECTRONIC SERVICE DELIVERY (1)
EXOME SEQUENCING (1)
EXOMISER (1)
EXPLICIT METADATA (1)
E‐SCIENCE (1)
FORMAL SEMANTICS (1)
FUNCTIONAL PROGRAMMING (1)
FUNCTIONAL UNITS (1)
FUNCTIONAL-STYLE SERVICE ANNOTATIONS (1)
GENOMICS (1)
GRAPH DATABASES (1)
GRAPH REPARTITIONING (1)
GRID (1)
HARDWARE (1)
HUMAN PHENOTYPE ONTOLOGY (1)
INFORMATION ECONOMICS (1)
INFORMATION EXTRACTION (1)
INFORMATION MARKET (1)
INTEGER LINEAR PROGRAMMING (1)
INTER-OPERABILITY (1)
JAVA CALL CONTROL (1)
KNOWLEDGE REPRESENTATION LANGUAGES (1)
KNOWLEDGE TRANSFER (1)
LIBRARIES (1)
LIFE SCIENCES (1)
LOSSLESS MAPPINGS (1)
METADATA (1)
MOBILE COMMUNICATION (1)
MONITORING (1)
NATURAL SCIENCES COMPUTING (1)
NEXT GENERATION NETWORKS (1)
NOWORKFLOW (1)
NUMERICAL MODELS (1)
OPEN PROGRAMMABLE NETWORKS (1)
OWL SEMANTIC WEB LANGUAGE (1)
PEER TO PEER COMPUTING (1)
PIPELINES (1)
PROCESS MINING (1)
PROCESS MODELLING (1)
PROGRAM PROCESSORS (1)
PROTEINS (1)
QUALITY (1)
QUALITY COST OPTIMIZATION (1)
REPRESENTATION (1)
RESEARCH OBJECT (1)
REUSE (1)
SEMANTIC GRID (1)
SEMANTIC OVERLAY NETWORKS (1)
SEMANTIC PUBLISHING (1)
SEMANTIC WEB SERVICES (1)
SERVICE ANNOTATIONS (1)
SERVICE DISCOVERY (1)
SERVICE INTERFACES (1)
SERVICE ORIENTED ARCHITECTURE (1)
SHARING (1)
STOCHASTIC MODELLING (1)
TAVERNA 2 (1)
TRACE SEMANTICS (1)
TRAINING (1)
TRUST (1)
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INFONA - science communication portal

Search results for: Paolo Missier

Increasing phenotypic annotation improves the diagnostic rate of exome sequencing in a rare neuromuscular disorder

TAPER: query-aware, partition-enhancement for large, heterogenous graphs

Facilitating reproducible research by investigating computational metadata

Accelerating Disease Gene Identification Through Integrated SNP Data Analysis

The Service to Businesses Project: Improving Government-to-Business Relationships in Italy

Building Scientific Workflow with Taverna and BPEL: A Comparative Study in caGrid

Data Lineage Model for Taverna Workflows with Lightweight Annotation Requirements

Workflows for Information Integration in the Life Sciences

A Linked Data Approach to Sharing Workflows and Workflow Results

Managing Information Quality in e-Science Using Semantic Web Technology

Taverna, Reloaded

Exploiting Provenance to Make Sense of Automated Decisions in Scientific Workflows

Janus: From Workflows to Semantic Provenance and Linked Open Data

Metadata Management in S-OGSA

Understanding Collaborative Studies through Interoperable Workflow Provenance

Managing Information Quality in e-Science: A Case Study in Proteomics

Data Integration in the Life Sciences

Provenance and data differencing for workflow reproducibility analysis

eScience

Bootstrapping Personalised Human Activity Recognition Models Using Online Active Learning

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