Intelligent client for integrating bioinformatics services

Navas‐Delgado, Ismael; Rojano-Muòoz, Maria Del Mar; Ramírez, Salvador Luna; Pérez, A. J.; Andrés-León, Eduardo; Aldana‐Montes, José F.; Trelles, Oswaldo

doi:10.1093/bioinformatics/bti740

Cited by 34 publications

(28 citation statements)

References 10 publications

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“…As the centers' web service models are all based on open standards, their databases and computational resources are expected to be interoperable [75]. Despite the large amount of data in these services, these centers use their own data type definitions, making it harder for end users and developers to utilize these services to create biological analysis workflows [76].…”

Section: Journal/peer Review Perspectivementioning

confidence: 99%

Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results

Alterovitz

Dean

Goble

et al. 2017

Preprint

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Abstract. Precision medicine can be empowered by a personalized approach to patient care based on the patient's unique genomic sequence. T o be used in precision medicine, genomic findings must be robust, reproducible, and experimental data capture should adhere to FAIR Data Guiding Principles. Moreover, precision medicine requires standardization that extends beyond wet lab procedures to computational methods.Rapidly developing standardization technologies improves communication of genomic sequencing by introducing concepts such as error domain, usability domain, validation kit, and provenance information. T hese advancements allow data provenance to be standardized and ensure interoperability. T hus, a resulting bioinformatics computation instance that includes these advancements can be easily communicated, repeated and compared by scientists, regulators, clinicians and others, allowing a greater range of practical applications.Advancing clinical trials, precision medicine, and regulatory submissions requires an umbrella of standards that not only fuses these elements, but also ensures efficient communication and documentation of genomic analyses. T hrough standardized bundling of HT S studies under an umbrella, regulatory agencies (FDA), academic researchers, and clinicians can expand collaboration to drive innovation in precision medicine with the potential for decreasing the time and cost associated with NGS workflow exchange, including FDA regulatory review submissions.

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Section: Journal/peer Review Perspectivementioning

confidence: 99%

Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results

Alterovitz

Dean

Goble

et al. 2017

Preprint

View full text Add to dashboard Cite

show abstract

“…Unfortunately, this approach heavily relies on the provided metadata, which is usually very poor. Other approaches focus on the development of interfaces to assist in the location of web resources; for example (Navas-Delgado et al, 2006) presents a client engine for the automatic and dynamic development of service interfaces built on top of the BioMoby standard.…”

Section: Related Workmentioning

confidence: 99%

A semantic approach for the requirement-driven discovery of web resources in the Life Sciences

et al. 2012

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Abstract. Research in the Life Sciences depends on the integration of large, distributed and heterogeneous web resources (e.g. data sources and web services). The discovery of which of these resources are the most appropriate to solve a given task is a complex research question, since there are many candidate resources and there is little, mostly unstructured, metadata to be able to decide among them.In this paper we contribute with a semi-automatic approach, based on semantic techniques, to assist researchers in the discovery of the most appropriate web resources to fulfill a set of requirements. The main feature of our approach is that it exploits broad knowledge resources in order to annotate the unstructured texts that are available in the emerging web-based repositories of web resource metadata.The results show that the web resource discovery process benefits from a semanticbased approach in several important aspects. One of the advantages is that the user can express her requirements in natural language avoiding the use of specific vocabularies or query languages. Moreover, the discovery exploits not only the categories or tags of web resources, but also their description and documentation.

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“…chain of service invocations) and then execute it over a GRID-based middleware. Other similar Web-based tools have been proposed, for example MOWServ [81], SeaHawk [82] and Remora [83] to mention a few. Recently, some extensions to the BioMOBY protocol have been proposed according to the new requirements arisen from workflow management [84].…”

Section: Workflowsmentioning

confidence: 99%

XML-Based Approaches for the Integration of Heterogeneous Bio-Molecular Data

Mesiti¹,

Jiménez-Ruiz²,

Sanz³

et al. 2011

Recent Advances in Biochemistry

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Intelligent client for integrating bioinformatics services

Abstract: The INB (National Institute for Bioinformatics, Spain) platform is available at www.inab.org/MOWServ

Cited by 34 publications

References 10 publications

Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results

Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results

A semantic approach for the requirement-driven discovery of web resources in the Life Sciences

XML-Based Approaches for the Integration of Heterogeneous Bio-Molecular Data

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