The &lt;SUP align=right&gt;my&lt;/SUP&gt;Grid ontology: bioinformatics service discovery

Wolstencroft, Katy; Alper, Pinar; Hull, Duncan; Wroe, Chris; Lord, Phillip; Stevens, Robert; Goble, Carole

doi:10.1504/ijbra.2007.015005

Cited by 73 publications

(38 citation statements)

References 22 publications

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“…Besides, we find "myGrid" ontology [18] the most promising ontology to use, but it can be too big and complex for our purpose. Therefore, we use "myGrid" ontology as a reference and build our own domain ontology only covering the data and analysis required.…”

Section: A Worklet Services Selectionmentioning

confidence: 99%

A Novel Approach for Bioinformatics Workflow Discovery

Nagy¹,

Hoda²

2014

ijacsa

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Abstract-Workflow systems are typical fit for in the explorative research of bioinformaticians. These systems can help bioinformaticians to design and run their experiments and to automatically capture and store the data generated at runtime. On the other hand, Web services are increasingly used as the preferred method for accessing and processing the information coming from the diverse life science sources. In this work we provide an efficient approach for creating bioinformatic workflow for all-service architecture systems (i.e., all system components are services ). This architecture style simplifies the user interaction with workflow systems and facilitates both the change of individual components, and the addition of new components to adopt to other workflow tasks if required. We finally present a case study for the bioinformatics domain to elaborate the applicability of our proposed approach.

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Section: A Worklet Services Selectionmentioning

confidence: 99%

A Novel Approach for Bioinformatics Workflow Discovery

Nagy¹,

Hoda²

2014

ijacsa

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“…Built upon the my Grid ontology (Wolstencroft et al, 2007), a bioinformatics service and domain ontology, FETA (Lord et al, 2005) is a service discovery framework characterized by a light-weight semantic support and a semi-automatic approach. Three main actors are distinguished in this framework: both knowledge engineers and service annotators provide semantic enhanced web services consumed by scientists.…”

Section: Semantic Workflow Environmentsmentioning

confidence: 99%

Characterizing Semantic Service Parameters With Role Concepts to Infer Domain-Specific Knowledge at Runtime

Gaignard

Montagnat

Wali

et al. 2011

Proceedings of the International Conference on Knowledge Engineering and Ontology Development

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Abstract:E-Science platforms leverage Service Oriented Architecture (SOA) principles to deliver large catalogs of data processing services and experiments description workflows. In spite of their growing success, the usability of these platforms is hampered by their catalogs size and the domain-specific knowledge needed to manipulate the services provided. Relying on domain ontologies and semantic services to enhance the understanding and usability of e-Science platforms, our contribution is twofold. First, we propose to delineate role concepts from natural concepts at domain ontology design time which leads to a neuroimaging role taxonomy, making explicit how neuroimaging datasets are related to the data analysis services. Then we propose to exploit, at workflow runtime, provenance information extended with these domain roles, to infer new meaningful semantic annotations. Platform semantic repositories are thus transparently populated, with newly inferred annotations, through the execution of e-Science workflows. A concrete example in the area of neurosciences illustrates the use of role concepts to create reusable inference rules.

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“…bioinformatics data resource, (3) the types of input data it accepts and of output data it produces (protein structure, for example), and more. The terms used in the annotations belong to the myGrid ontology [13], a controlled ontology of terms for the bioinformatics domain.…”

Section: Support For Service Discoverymentioning

confidence: 99%

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

Tan

Missier

Madduri

et al. 2009

Service-Oriented Computing – ICSOC 2007

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Abstract. 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 of a scientific workflow, including service discovery, service composition, workflow execution, and workflow result analysis. We determine that BPEL offers a comprehensive set of primitives for modeling processes of all flavors, while Taverna provides a more compact set of primitives and a functional programming model that eases data flow modeling. We hope that our analysis not only helps researchers choose a tool that meets their needs, but also provides some insight on how a workflow language and tool can fulfill the requirement of scientists.

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The <SUP align=right>my</SUP>Grid ontology: bioinformatics service discovery

Cited by 73 publications

References 22 publications

A Novel Approach for Bioinformatics Workflow Discovery

A Novel Approach for Bioinformatics Workflow Discovery

Characterizing Semantic Service Parameters With Role Concepts to Infer Domain-Specific Knowledge at Runtime

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

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