Carole Goble, Richard Stevens, Duncan Hull et al. · Briefings in Bioinformatics · 2008
In bioinformatics, we are familiar with the idea of curated data as a prerequisite for data integration. We neglect, often to our cost, the curation and cataloguing of the processes that we use to integrate and analyse our data. Programmatic access to services, for data and processes, means that compositions of services can be made that represent the in silico experiments or processes that bioinformaticians perform. Data integration through workflows depends on being able to know what services exist and where to find those services. The large number of services and the operations they perform, their arbitrary naming and lack of documentation, however, mean that they can be difficult to use. The workflows themselves are composite processes that could be pooled and reused but only if they too can be found and understood. Thus appropriate curation, including semantic mark-up, would enable processes to be found, maintained and consequently used more easily. This broader view on semantic annotation is vital for full data integration that is necessary for the modern scientific analyses in biology. This article will brief the community on the current state of the art and the current challenges for process curation, both within and without the Life Sciences.
Cited by 66Open access
Ségolène Tarte · OpenEdition (OpenEdition) · 2011
Cited by 0Open access
Bobby Glushko, Erika Basile, Janis Oram et al. · OSF Preprints (OSF Preprints) · 2020
Cited by 0
Thu-Mai Christian, Sophia Lafferty-Hess · OSF Preprints (OSF Preprints) · 2017
Materials for the 2017 Data Matters "Data Curation: Managing Data throughout the Research Lifecycle" course.
Cited by 0
Chen, Yitong · Figshare · 2023
This PowerPoint is the final project material of MLIM7350 at the University of Hong Kong. It covers the contents related to data curation, including data sharing, data reuse, open data, etc. This material aims to help researchers understand the importance of research data curation, and provide guidance on how to achieve it. The content in this material is on a basic level.
Cited by 0Open access
Gilles Marcou, Alexandre Varnek · 2017
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Altamimi, Rou'A · CERN Document Server (European Organization for Nuclear Research) · 2021
The Compact Muon Solenoid (CMS) experiment is one of two large general-purpose particlephysics detectors built on the Large Hardon Collider (LHC) at CERN in Switzerland and France. The goal of the virtual CERN summer student project was to improve the automated workflows (Implement and Test Workflows) to test the usability of CMS open data using ARGO [1] and another tool such as Docker [2] and Minikube [3]. Argo Workflow is an open-source container-native workflow engine for orchestrating parallel jobs on Kubernetes. Argo Workflow is implemented as a Kubernetes CRD (Custom Relation Definition). It defines workflows in which each step in the workflow is a container. It is designed from the ground up for containers without the overhead and limitations of legacy Virtual Machine (VM) and server-based environments. Docker is an open-source containerization platform. It enables developers to package applications into containers combining application source code with the operating system (OS) libraries and dependencies required to run that code in any environment. Kubernetes [4] is a portable, extensible, open-source platform for managing containerized workloads and services that facilitates both declarative configuration and automation. It has a large, rapidly growing ecosystem. Kubernetes services, support, and tools are widely available. Minikube quickly sets up a local Kubernetes cluster on MacOS, Linux, and Windows. Its focuses on helping application developers and new Kubernetes users.Starting the Minikube will create a single-node Kubernetes cluster inside a VM. Minikube start command also creates Minikube context and set it as default. This will reduce the number of incompatibility and portability problems.
Cited by 0Open access
van Horik, M.P.M. · KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) · 2007
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Kim Tallerås · Elsevier eBooks · 2024
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Macanda, Makaba, Bezuidenhout, Ronell · Unisa Institutional Repository (University of South Africa) · 2013
DATA CURATION"[C]uration embraces and goes beyond that of enhanced present-day re-use, and of archival responsibility, to embrace stewardship that adds value through the provision of context and linkage: placing emphasis on publishing data in ways that ease re-use and promoting accountability and integration" Curation
Cited by 0Open access
Rajat Mani Thomas, Dinesh Movva, Sumana Basu et al. · OSF Preprints (OSF Preprints)
Cited by 0
Altamimi, Rou'A · CERN Document Server (European Organization for Nuclear Research) · 2021
The Compact Muon Solenoid (CMS) experiment is one of two large general-purpose particlephysics detectors built on the Large Hardon Collider (LHC) at CERN in Switzerland and France. The goal of the virtual CERN summer student project was to improve the automated workflows (Implement and Test Workflows) to test the usability of CMS open data using ARGO [1] and another tool such as Docker [2] and Minikube [3]. Argo Workflow is an open-source container-native workflow engine for orchestrating parallel jobs on Kubernetes. Argo Workflow is implemented as a Kubernetes CRD (Custom Relation Definition). It defines workflows in which each step in the workflow is a container. It is designed from the ground up for containers without the overhead and limitations of legacy Virtual Machine (VM) and server-based environments. Docker is an open-source containerization platform. It enables developers to package applications into containers combining application source code with the operating system (OS) libraries and dependencies required to run that code in any environment. Kubernetes [4] is a portable, extensible, open-source platform for managing containerized workloads and services that facilitates both declarative configuration and automation. It has a large, rapidly growing ecosystem. Kubernetes services, support, and tools are widely available. Minikube quickly sets up a local Kubernetes cluster on MacOS, Linux, and Windows. Its focuses on helping application developers and new Kubernetes users.Starting the Minikube will create a single-node Kubernetes cluster inside a VM. Minikube start command also creates Minikube context and set it as default. This will reduce the number of incompatibility and portability problems.
Cited by 0
Chen, Yitong · Figshare · 2023
This PowerPoint is the final project material of MLIM7350 at the University of Hong Kong. It covers the contents related to data curation, including data sharing, data reuse, open data, etc. This material aims to help researchers understand the importance of research data curation, and provide guidance on how to achieve it. The content in this material is on a basic level.
Cited by 0Open access
van Horik, M.P.M. · KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) · 2007
Cited by 0
Zain Hasan, Christina Yan, Arindam Banerjee et al. · OSF Preprints (OSF Preprints) · 2023
Information on the data sets being used, pre-processing, access, organization
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Abhay Koushik, prabhant singh, Mark Collier et al. · OSF Preprints (OSF Preprints) · 2023
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Kayla Wheeler · OSF Preprints (OSF Preprints) · 2020
This dataset is used for the LSCI 391 Data Curation class at MSU. This dataset includes analytics on more than 7,000 apps in the Apple App Store.
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Dinesh Movva, Sumana Basu, Derek Yingxuan Zhi et al. · OSF Preprints (OSF Preprints) · 2018
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Rajat Mani Thomas, Dinesh Movva, Sumana Basu et al. · OSF Preprints (OSF Preprints) · 2018
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René van Horik · 2008
Scientific research increasingly creates and uses digital data in many different ways and in a wide range of formats. Data curation activities are required to maintain and preserve the digital research data as well as to facilitate its future reuse. Increasingly science will be carried out through distributed global collaborations enabled by the internet. The Grid infrastructure will provide ‘e-Science’ with powerful large-scale computing resources and dedicated repository management software.
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