Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an ...increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.
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•A UML Profile for the OBO Core Relations Ontology.•A graphical editor for the development UML conceptual models using the profile.•Methodological support for the OBOFFF knowledge ...reuse in UML.•A command-line tool to transform an OBOFFF ontology into a shareable UML model.
A conceptual model abstractly defines a number of concepts and their relationships for the purposes of understanding and communication. Once a conceptual model is available, it can also be used as a starting point for the development of a software system. The development of conceptual models using the Unified Modeling Language (UML) facilitates the representation of modeled concepts and allows software developers to directly reuse these concepts in the design of a software system. The OBO Foundry represents the most relevant collaborative effort towards the development of ontologies in the biomedical domain. The development of UML conceptual models in the biomedical domain may benefit from the use of domain-specific semantics and notation. Further, the development of these models may also benefit from the reuse of knowledge contained in OBO ontologies. This paper investigates the support for the development of conceptual models in the biomedical domain using UML as a conceptual modeling language and using the support provided by the OBO Foundry for the development of biomedical ontologies, namely entity kind and relationship types definitions provided by the Basic Formal Ontology (BFO) and the OBO Core Relations Ontology (OBO Core), respectively. Further, the paper investigates the support for the reuse of biomedical knowledge currently available in OBOFFF ontologies in the development these conceptual models. The paper describes a UML profile for the OBO Core Relations Ontology, which basically defines a number of stereotypes to represent BFO entity kinds and OBO Core relationship types definitions. The paper also presents a support toolset consisting of a graphical editor named OBO-RO Editor, which directly supports the development of UML models using the extensions defined by our profile, and a command-line tool named OBO2UML, which directly converts an OBOFFF ontology into a UML model.
Abstract Patterns have been widely used in Computer Science. A pattern describes a generic solution to an existing problem in a more readable and accessible form. A pattern-oriented process ...specification consists of a generic and abstract description of a process. This paper presents a pattern-oriented specification of a genetic regulatory network inference process performed from microarray data and prior biological knowledge. The proposed specification was conceived based on prior work on gene inference networks. The adequacy of the proposed solution was then evaluated with respect to modern tendencies of the genes network inference literature.
A UML profile for the OBO relation ontology Guardia, Gabriela D A; Vêncio, Ricardo Z N; de Farias, Cléver R G
BMC genomics,
2012, Letnik:
13 Suppl 5, Številka:
Suppl 5
Journal Article
Recenzirano
Odprti dostop
Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and ...Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain.
The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge ...associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heterogeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data.
We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data.
The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.
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•A novel approach to support the semantic composition of functional genomics services.•A composition platform named SemanticSCo that implements the proposed approach.•Semi-automatic ...support for the definition and execution of analysis workflows.•Support for the development and management of (complex) services.
Gene expression studies often require the combined use of a number of analysis tools. However, manual integration of analysis tools can be cumbersome and error prone. To support a higher level of automation in the integration process, efforts have been made in the biomedical domain towards the development of semantic web services and supporting composition environments. Yet, most environments consider only the execution of simple service behaviours and requires users to focus on technical details of the composition process.
We propose a novel approach to the semantic composition of gene expression analysis services that addresses the shortcomings of the existing solutions. Our approach includes an architecture designed to support the service composition process for gene expression analysis, and a flexible strategy for the (semi) automatic composition of semantic web services. Finally, we implement a supporting platform called SemanticSCo to realize the proposed composition approach and demonstrate its functionality by successfully reproducing a microarray study documented in the literature.
The SemanticSCo platform provides support for the composition of RESTful web services semantically annotated using SAWSDL. Our platform also supports the definition of constraints/conditions regarding the order in which service operations should be invoked, thus enabling the definition of complex service behaviours. Our proposed solution for semantic web service composition takes into account the requirements of different stakeholders and addresses all phases of the service composition process. It also provides support for the definition of analysis workflows at a high-level of abstraction, thus enabling users to focus on biological research issues rather than on the technical details of the composition process. The SemanticSCo source code is available at https://github.com/usplssb/SemanticSCo.
Bioinformatics data obtained using different molecular biology techniques must be processed through different analysis tools to discover new biological knowledge. Since plain processed data have no ...explicit semantic value, the extraction of additional knowledge through data exploration would benefit from the transformation of bioinformatics data into Linked Open Data (LOD). Different approaches have been proposed to support the transformation of different types of biomedical data into LOD. However, these approaches are not flexible enough so they can be easily adapted for the transformation of semi-structured bioinformatics data into LOD. Thus, this paper proposes a novel approach to support such transformation. According to this approach, a set of competency questions drive not only the definition of transformation rules, but also the data transformation and exploration afterwards. The paper also presents a support toolset and describes the successful application of the proposed approach in the functional genomics domain.
•Transformation of semi-structured data (SSD) into linked open data (LOD).•Stepwise, competency question-oriented approach.•Language for specifying data item to ontology concept semantic equivalence.•Support toolset for the transformation of SSD into LOD.
An Architectural Model for Component Groupware de Farias, Cléver R. G.; Gonçalves, Carlos E.; Rosatelli, Marta C. ...
Groupware: Design, Implementation, and Use,
2005
Book Chapter, Conference Proceeding
Recenzirano
This paper proposes an architectural model to facilitate the design of component-based groupware systems. This architectural model has been defined based on (1) three pre-defined component types, (2) ...a refinement strategy that relies on these component types, (3) the identification of layers of collaboration concerns, and (4) rules for the coupling and distribution of the components that implement these concerns. Our architectural model is beneficial for controlling the complexity of the development process, since it gives concrete guidance on the concerns to be considered and decomposition disciplines to be applied in each development step. The paper illustrates the application of this architectural model with an example of an electronic voting system.
Web services have become increasingly important for software development. In order to facilitate the search, composition, and reuse of web services, their descriptions can be semantically annotated ...using definitions provided by an ontology, thus creating the so-called semantic web services. A semantic web service is developed according to different approaches and standards recommended by W3C, such as OWL-S, SAWSDL, and WSMO-Lite. A limited number of tools are available to support the development of semantic annotations using SAWSDL, such as Radiant, Iridescent, and EasyWSDL. However, these tools support the annotation process at a low abstraction level, therefore requiring from users an extensive technical knowledge on XML/WSDL, among other technologies. The semantic annotation task could be facilitated if the semantic annotation process were carried at a higher abstraction level using graphical notations. Additionally, the semantic annotation could also benefit from a collaborative approach. Different people from different backgrounds could individually contribute with the semantic web services creation, regardless of their geographic locations. In that sense, this paper presents a visual notation to represent the main elements of a WSDL 2.0 especification focused on the semantic annotation using SAWSDL. The paper also describes a graphical collaborative semantic annotation support tool.
Context-aware mobile applications are increasingly attracting interest of the research community. To facilitate the development of this class of applications, it is necessary that both applications ...and support platforms share a common context metamodel. This paper presents a metamodel defined using the OMG Meta Object Facility (MOF). This metamodel has been used as basis for the development of context-aware applications and an associated service platform.
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