Adapters, shims, and glue—service interoperability for <i>in silico</i> experiments

Radetzki, U.; Leser, Ulf; Schulze-Rauschenbach, Svenja; Zimmermann, Július; Lüssem, J.; Bode, Thomas; Cremers, Armin B.

doi:10.1093/bioinformatics/btl054

Cited by 32 publications

(20 citation statements)

References 16 publications

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“…They are domain preserving mappings: their inputs and outputs belong to the same semantic domain, e.g., IPIAC TO UniprotAC consumes a protein accession and outputs a protein accession. These kind of service operations are commonly used in scientific workflows to deal with representation mismatch [4], [5] and are known in the literature of scientific workflows as Shims [20], [10]. The resulting workflow can be used to substitute the operation GetHomologous in the protein identification workflow.…”

Section: Replacing Missing Operation With a Workflowmentioning

confidence: 99%

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Fostering Scientific Workflow Preservation through Discovery of Substitute Services

Belhajjame

Goble

Soiland‐Reyes

et al. 2011

2011 IEEE Seventh International Conference on eScience

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Abstract-Scientific workflows are increasingly gaining momentum as the new paradigm for modeling and enacting scientific experiments. The value of a workflow specification does not end once it is enacted. Indeed, workflow specifications encapsulate knowledge that documents scientific experiments, and are, therefore, worth preserving.Our experience suggests that workflow preservation is frequently hampered by the volatility of the constituent service operations when these operations are supplied by third-party providers. To deal with this issue, we propose a heuristic for locating substitutes that are able to replace unavailable service operations within workflows. The proposed method uses the data links connecting inputs and outputs of service operations in existing workflow specifications to locate operations with parameters compatible with those of the missing operations. Furthermore, it exploits provenance traces collected from past executions of workflows to ensure that candidate substitutes perform tasks similar to those of the missing operations. The effectiveness of the proposed method has been empirically assessed.

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Section: Replacing Missing Operation With a Workflowmentioning

confidence: 99%

“…In the same lines, Radetzki et al [20] developed a method for discovering shims, which are service operations the are used for resolving mismatches within scientific workflows. In doing so, they rely on similarity techniques to infer semantic information about web services, and use the derived semantic annotations to match web services.…”

Section: Related Workmentioning

confidence: 99%

Fostering Scientific Workflow Preservation through Discovery of Substitute Services

Belhajjame

Goble

Soiland‐Reyes

et al. 2011

2011 IEEE Seventh International Conference on eScience

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“…IETF's CRISP [48] should not be confused with [54]. Similarly, IETF's IRIS [49] should not be confused with the Interoperability and Reusability of Internet Services [55] or the International Rice Information System [56].…”

Section: Domain Naming and Registering Systemsmentioning

confidence: 99%

DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing

Taswell

2008

IEEE Trans. Inform. Technol. Biomed.

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Abstract-The semantic web remains in the early stages of development. It has not yet achieved the goals envisioned by its founders as a pervasive web of distributed knowledge and intelligence. Success will be attained when a dynamic synergism can be created between people and a sufficient number of infrastructure systems and tools for the semantic web in analogy with those for the original web. The domain name system (DNS), web browsers, and the benefits of publishing web pages motivated many people to register domain names and publish web sites on the original web. An analogous resource label system, semantic search applications, and the benefits of collaborative semantic networks will motivate people to register resource labels and publish resource descriptions on the semantic web. The Domain Ontology Oriented Resource System (DOORS) and Problem Oriented Registry of Tags and Labels (PORTAL) are proposed as infrastructure systems for resource metadata within a paradigm that can serve as a bridge between the original web and the semantic web. Registers domain names while DNS publishes domain addresses with mapping of names to addresses for the original web. Analogously, POR-TAL registers resource labels and tags while DOORS publishes resource locations and descriptions with mapping of labels to locations for the semantic web. BioPORT is proposed as a prototype PORTAL registry specific for the problem domain of biomedical computing.

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“…Other approaches combine matchmaking and information retrieval (IR) techniques. Service information based on WSDL is analyzed and service profiles are extracted which are matched against user requirements [12]. These profiles can contain, beside syntactic information, context information about location of services etc.…”

Section: Registries In B2b Collaborationsmentioning

confidence: 99%

Contextualized B2B Registries

Radetzki¹,

Boniface²,

Surridge³

2007

Service-Oriented Computing – ICSOC 2007

Self Cite

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Abstract. Service discovery is a fundamental concept underpinning the move towards dynamic service-oriented business partnerships. The business process for integrating service discovery and underlying registry technologies into business relationships, procurement and project management functions has not been examined and hence existing Web Service registries lack capabilities required by business today. In this paper we present a novel contextualized B2B registry that supports dynamic registration and discovery of resources within management contexts to ensure that the search space is constrained to the scope of authorized and legitimate resources only. We describe how the registry has been deployed in three case studies from important economic sectors (aerospace, automotive, pharmaceutical) showing how contextualized discovery can support distributed product development processes.

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Adapters, shims, and glue—service interoperability for in silico experiments

Cited by 32 publications

References 16 publications

Fostering Scientific Workflow Preservation through Discovery of Substitute Services

Fostering Scientific Workflow Preservation through Discovery of Substitute Services

DOORS to the Semantic Web and Grid With a PORTAL for Biomedical Computing

Contextualized B2B Registries

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