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Mind Your Metadata: Exploiting Semantics for Configuration, Adaptation, and Provenance in Scientific Workflows [chapter]

Yolanda Gil, Pedro Szekely, Sandra Villamizar, Thomas C. Harmon, Varun Ratnakar, Shubham Gupta, Maria Muslea, Fabio Silva, Craig A. Knoblock
2011 Lecture Notes in Computer Science  
We present an approach where semantic metadata is generated as scientific data is being prepared, and then subsequently used to configure models and to customize them to the data.  ...  In addition, all aspects of data processing are documented, and the system is able to generate extensive provenance records for new data products based on the metadata.  ...  Semantic reasoning in Wings is used to provide interactive assistance and automation in many aspects of workflow design and configuration.  ... 
doi:10.1007/978-3-642-25093-4_5 fatcat:naj4gzeap5ccnoaiyjk62jysl4

LabelFlow Framework for Annotating Workflow Provenance

Pinar Alper, Khalid Belhajjame, Vasa Curcin, Carole Goble
2018 Informatics  
In this paper we investigate whether provenance can be exploited to support reporting. Specifically; we outline a case-study based on a real-world workflow and set of reporting queries.  ...  We provide a tool that takes as input a workflow, and produces as output a Labelling Pipeline for that workflow, comprised of Labelling Operators.  ...  Acknowledgments: Authors would like to thank the members of the e-Science Lab at the University of Manchester for their with using Taverna workflow system's APIs.  ... 
doi:10.3390/informatics5010011 fatcat:g2wyaqo7hva55mc4qcem7lbopy

Implementing FAIR Data Infrastructures (Dagstuhl Perspectives Workshop 18472)

Natalia Manola, Peter Mutschke, Guido Scherp, Klaus Tochtermann, Peter Wittenburg, Kathleen Gregory, Wilhelm Hasselbring, Kees den Heijer, Paolo Manghi, Dieter Van Uytvanck
2020 Dagstuhl Manifestos  
The open science movement is gaining strength and momentum worldwide, signalling a fundamental shift in how scientific research is made accessible and reusable.  ...  to implementing and promoting the establishment of FAIR-compliant infrastructures for research data.  ...  The editors especially wish to thank all contributing authors for their input to this manifesto and all participants for their quality check.  ... 
doi:10.4230/dagman.8.1.1 dblp:journals/dagstuhl-manifestos/ManolaMSTWGHHMU20 fatcat:6z4yhlp3xzahfp7whrdn3x2xa4

An approach for pipelining nested collections in scientific workflows

Timothy M. McPhillips, Shawn Bowers
2005 SIGMOD record  
Moreover, he thanks Gianluigi Greco for his recent contribution to the weighted extension, and Alfredo Mazzitelli for his valuable work in designing and implementing the tools for experiments.  ...  When you see these people, please thank them personally for their role in achieving quick reviews of submitted papers.  ...  Metadata for Workflow Reuse and Provenance. Scientific workflows are pivotal knowledge components in e-Science.  ... 
doi:10.1145/1084805.1084809 fatcat:sgtpcat7vzc3veb4dx2jgskpte

A Selection of Research Data Management Tools Throughout the Data Lifecycle

Jan Krause
2016 Figshare  
In this document, several useful research data management tools are listed and described for each step of their research throughout the data lifecyle management.  ...  DataCite Metadata Schema is a standard designed with datasets in mind, and hence more adapted then DublinCore mentioned just above.  ...  workflows and laboratory management myExperiment "is a social website for sharing [...] scientific workflows [...]" and integrates many tools such as Taverna and Bioclipse [49, 50]. 1 Data repositories  ... 
doi:10.6084/m9.figshare.3458723.v1 fatcat:su5cbc4kkrb3hj5nr3kufa6m4e

Computational Challenges in Global Environmental Research Infrastructures [chapter]

Paul Martin, Yin Chen, Alex Hardisty, Keith Jeffery, Zhiming Zhao
2017 Zenodo  
the use of a standard reference model and the use of a formal framework for semantically linking similar concepts in different contexts.  ...  It also requires a pragmatic bridging between the different standards and controlled vocabularies currently in use or preparation by different scientific communities, a process that can be expedited by  ...  In many cases researchers have to configure their own workflows.  ... 
doi:10.5281/zenodo.3361569 fatcat:x7rpqudzrvh5hflrtwd3i7c6xy

Laboratory notebooks in the digital era: the role of ELNs in record keeping for chemistry and other sciences

Colin L. Bird, Cerys Willoughby, Jeremy G. Frey
2013 Chemical Society Reviews  
Egyptian evidence of scientific records dates back almost 50 centuries. In more recent times da Vinci and Faraday provide role models for scrupulous recording of ideas, observations, and conclusions.  ...  We examine the foundations of the emerging opportunities for preserving and curating electronic records focussing on electronic laboratory notebooks (ELNs), with an emphasis on their characteristics and  ...  and acknowledge funding from JISC for the SRF project.  ... 
doi:10.1039/c3cs60122f pmid:23864106 fatcat:53csweonhnghdcnph7o2suw72m

Challenges of Translating HPC Codes to Workflows for Heterogeneous and Dynamic Environments

Fayssal Benkhaldoun, Christophe Cerin, Imad Kissami, Walid Saad
2017 2017 International Conference on High Performance Computing & Simulation (HPCS)  
In this paper we would like to share our experience for transforming a parallel code for a Computational Fluid Dynamics (CFD) problem into a parallel version for the RedisDG workflow engine.  ...  This paper states that new models for High Performance Computing are possible, under the condition we revisit our mind in the direction of the potential of new paradigms such as cloud, edge computing.  ...  In this thesis 'workflow' and 'scientific workflow' are considered equivalent for sake of simplicity.  ... 
doi:10.1109/hpcs.2017.130 dblp:conf/ieeehpcs/BenkhaldounCKS17 fatcat:cxr7q7s46jg4zbf4etyky6llue

Dare Architecture and Technology D2.2

Atkinson Malcolm, Klampanos Iraklis, Andries Valentina, Constantin Aurora, Filgueira Rosa, Genünd André, Gottschämmer Ellen, Karkaletsis Vangelis, Koukourikos Antonis, Levray Amélie, Linder Mike, Magnoni Federica (+6 others)
2020 Zenodo  
in order to create data- and computationally-intensive applications for their domains.  ...  The initial progress with these is presented and evaluated. They lead to a strategy for sustainability.  ...  Some of the replies indicate limitations in the training, e.g., regarding difficulty in finding files and logs when the data catalogue ( §4.2.4) and provenance tools ( §4.3) provide these facilities.  ... 
doi:10.5281/zenodo.4733801 fatcat:nqgcpnkog5gmzgiefuqspiupqe

Seven Bottlenecks to Workflow Reuse and Repurposing [chapter]

Antoon Goderis, Ulrike Sattler, Phillip Lord, Carole Goble
2005 Lecture Notes in Computer Science  
Such a "workflow by example" approach complements the popular view in the Semantic Web Services literature that on-line processes are constructed automatically from scratch, and could help bootstrap the  ...  They repurpose an existing workflow or workflow fragment by finding one that is close enough to be the basis of a new workflow for a different purpose, and making small changes to it.  ...  In this paper we investigated what it would mean for scientific problem-solving knowledge, captured in workflows, to be found and adapted, i.e. repurposed.  ... 
doi:10.1007/11574620_25 fatcat:5zhajofva5d6th63ov5m6jolia

EMPHASIS-PREP Deliverable 4.4: Analysis of imaging approaches

Hendrik de Villiers, Rick van Zedde, Ruud Barth, Tony Pridmore
2019 Zenodo  
This hampers the use and reuse of data, as users of a dataset have to write/adapt their own code to account for the particular structure of a new dataset.  ...  In addition, we consider the question of how to best preserve PHIS' ability to capture provenance metadata while connecting the system to subsequent machine learning workflows (with a special emphasis  ...  with FAIR principles in mind.  ... 
doi:10.5281/zenodo.3767002 fatcat:ys4qmmmjebaxpnnq6i2e6x46rm

EOSC-hub D6.5 Final report on the maintenance and integration of common services

John Alan Kennedy, Abdulrahman Azab, Miguel Caballer, Michele Carpene, Enol Fernández, Germán Moltó, Olivier Rouchon, Heinrich Widmann
2021 Zenodo  
The work described within this document; focusing on service provisioning, maintenance and integration; contributes to the EOSC-hub Key Exploitable Results 4,5 and 8.  ...  This document contains a combined report on the maintenance and integration of common services of the EOSC Hub Service Catalogue for the final project year.  ...  and provenance.  ... 
doi:10.5281/zenodo.5033237 fatcat:vp4nyzsxfvd4ngyiquutephv7y

DARE Architecture and Technology internal report

Malcolm Atkinson, Rosa Filgueira, André Gemünd, Vangelis Karkaletsis, Iraklis Klampanos, Antonis Koukourikos, Amélie Levray, Michael Lindner, Federica Magnoni, Christian Pagé, Andreas Rietbrock, Alessandro Spinuso (+3 others)
2020 Zenodo  
New requirements for users to directly create and control complex computational and data challenges are pushing DARE to extend its integration, automation and optimisation.  ...  The initial plans for these are presented. They lead to a strategy for sustainability.  ...  The authors thank the research software engineers and systems teams that have delivered and tested a succession of releases of the platform, and the research developers and application-domain scientists  ... 
doi:10.5281/zenodo.3697897 fatcat:negi7ssmfbdatcm65wkgymkicy

D5.6 Report on application guidelines

Rigo Wenning
2020 Zenodo  
Because data protection and data processing potentially can cover every aspect of live, boundaries for the comprehensive approach have to be found.  ...  It has three industry partners and as many use cases. Two use cases concern location based services and one concerns a compliance mechanism in a highly regulated environment.  ...  Data is then processed according to the rules expressed in the metadata using the SPECIAL policy language and other metadata vocabularies, e.g. provenance [9] .  ... 
doi:10.5281/zenodo.4586113 fatcat:pdr4pdwoyfaudfqivvdz2ddjje

DMPs for Photon and Neutron RIs

Heike Görzig, Brian Matthews, Abigail McBirnie, Nicolas Soler
2021 Zenodo  
For this purpose, first general existing roles, workflows, and IT systems in projects in the literature and then their relevance to Photon and Neutron (PaN) Research Infrastructures (RIs) are examined.  ...  Using the DMP template developed by PaNOSC, roles, phases in the workflows and IT systems are then mapped to these DMP questions.  ...  and the systems, roles, and workflows needed to support a metadata framework for research data management (RDM) in PaN RIs.  ... 
doi:10.5281/zenodo.5636095 fatcat:lb7vuwn5lvbfjfe6j7awnxb6uu
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