Common motifs in scientific workflows: An empirical analysis

Workflow technology continues to play an important role as a means for specifying and enacting computational experiments in modern science. Reusing and re-purposing workflows allow scientists to do new experiments faster, since the workflows capture useful expertise from others. As workflow libraries grow, scientists face the challenge of finding workflows appropriate for their task, understanding what each workflow does, and reusing relevant portions of a given workflow.We believe that workflows would be easier to understand and reuse if high-level views (abstractions) of their activities were available in workflow libraries. As a first step towards obtaining these abstractions, we report in this paper on the results of a manual analysis performed over a set of real-world scientific workflows from Taverna, Wings, Galaxy and Vistrails. Our analysis has resulted in a set of scientific workflow motifs that outline (i) the kinds of data-intensive activities that are observed in workflows (Data-Operation motifs), and (ii) the different manners in which activities are implemented within workflows (Workflow-Oriented motifs). These motifs are helpful to identify the functionality of the steps in a given workflow, to develop best practices for workflow design, and to develop approaches for automated generation of workflow abstractions.

Leveraging Semantics to Improve Reproducibility in Scientific Workflows

Reproducibility of published results is a cornerstone in scientific publishing and progress. Therefore, the scientific community has been encouraging authors and editors to publish their contributions in a verifiable and understandable way. Efforts such as the Reproducibility Initiative [1], or the Reproducibility Projects on Biology [2] and Psychology [3] domains, have been defining standards and patterns to assess whether an experimental result is reproducible.

A formalism and method for representing and reasoning with process models authored by subject matter experts

Enabling Subject Matter Experts (SMEs) to formulate knowledge without the intervention of Knowledge Engineers (KEs) requires providing SMEs with methods and tools that abstract the underlying knowledge representation and allow them to focus on modeling activities. Bridging the gap between SME-authored models and their representation is challenging, especially in the case of complex knowledge types like processes, where aspects like frame management, data, and control flow need to be addressed. In this paper, we describe how SME-authored process models can be provided with an operational semantics and grounded in a knowledge representation language like F-logic in order to support process-related reasoning. The main results of this work include a formalism for process representation and a mechanism for automatically translating process diagrams into executable code following such formalism. From all the process models authored by SMEs during evaluation 82% were well-formed, all of which executed correctly. Additionally, the two optimizations applied to the code generation mechanism produced a performance improvement at reasoning time of 25% and 30% with respect to the base case, respectively.

Integrating geographical information in the Linked Digital Earth

Many progresses have been made since the Digital Earth notion was envisioned thirteen years ago. However, the mechanism for integrating geographic information into the Digital Earth is still quite limited. In this context, we have developed a process to generate, integrate and publish geospatial Linked Data from several Spanish National data-sets. These data-sets are related to four Infrastructure for Spatial Information in the European Community (INSPIRE) themes, specifically with Administrative units, Hydrography, Statistical units, and Meteorology. Our main goal is to combine different sources (heterogeneous, multidisciplinary, multitemporal, multiresolution, and multilingual) using Linked Data principles. This goal allows the overcoming of current problems of information integration and driving geographical information toward the next decade scenario, that is, ?Linked Digital Earth.?

A workflow PROV-corpus based on taverna and wings

We describe a corpus of provenance traces that we have collected by executing 120 real world scientific workflows. The workflows are from two different workflow systems: Taverna [5] and Wings [3], and 12 different application domains (see Figure 1). Table 1 provides a summary of this PROV-corpus.

Towards concept identification using a knowledge-intensive approach

This paper presents a method for identifying concepts in microposts and classifying them into a predefined set of categories. The method relies on the DBpedia knowledge base to identify the types of the concepts detected in the messages. For those concepts that are not classified in the ontology we infer their types via the ontology properties which characterise the type.

Digital libraries for the preservation of research methods and associated artifacts

New digital artifacts are emerging in data-intensive science. For example, scientific workflows are executable descriptions of scientific procedures that define the sequence of computational steps in an automated data analysis, supporting reproducible research and the sharing and replication of best-practice and know-how through reuse. Workflows are specified at design time and interpreted through their execution in a variety of situations, environments, and domains. Hence it is essential to preserve both their static and dynamic aspects, along with the research context in which they are used. To achieve this, we propose the use of multidimensional digital objects (Research Objects) that aggregate the resources used and/or produced in scientific investigations, including workflow models, provenance of their executions, and links to the relevant associated resources, along with the provision of technological support for their preservation and efficient retrieval and reuse. In this direction, we specified a software architecture for the design and implementation of a Research Object preservation system, and realized this architecture with a set of services and clients, drawing together practices in digital libraries, preservation systems, workflow management, social networking and Semantic Web technologies. In this paper, we describe the backbone system of this realization, a digital library system built on top of dLibra.

On correctness in RDF stream processor benchmarking

Two complementary benchmarks have been proposed so far for the evaluation and continuous improvement of RDF stream processors: SRBench and LSBench. They put a special focus on different features of the evaluated systems, including coverage of the streaming extensions of SPARQL supported by each processor, query processing throughput, and an early analysis of query evaluation correctness, based on comparing the results obtained by different processors for a set of queries. However, none of them has analysed the operational semantics of these processors in order to assess the correctness of query evaluation results. In this paper, we propose a characterization of the operational semantics of RDF stream processors, adapting well-known models used in the stream processing engine community: CQL and SECRET. Through this formalization, we address correctness in RDF stream processor benchmarks, allowing to determine the multiple answers that systems should provide. Finally, we present CSRBench, an extension of SRBench to address query result correctness verification using an automatic method.

Towards a systematic benchmarking of ontology-based query rewriting systems

Query rewriting is one of the fundamental steps in ontologybased data access (OBDA) approaches. It takes as inputs an ontology and a query written according to that ontology, and produces as an output a set of queries that should be evaluated to account for the inferences that should be considered for that query and ontology. Different query rewriting systems give support to different ontology languages with varying expressiveness, and the rewritten queries obtained as an output do also vary in expressiveness. This heterogeneity has traditionally made it difficult to compare different approaches, and the area lacks in general commonly agreed benchmarks that could be used not only for such comparisons but also for improving OBDA support. In this paper we compile data, dimensions and measurements that have been used to evaluate some of the most recent systems, we analyse and characterise these assets, and provide a unified set of them that could be used as a starting point towards a more systematic benchmarking process for such systems. Finally, we apply this initial benchmark with some of the most relevant OBDA approaches in the state of the art.

Demo paper: tablet-based visualization of transportation data in Madrid using SPARQLStream

In this demo paper we describe an iOS-based application that allows visualizing live bus transport data in Madrid from static and streaming RDF endpoints, reusing the Web services provided by the bus transport authority in the city and wrapping them using SPARQLStream

Federating queries in SPARQL 1.1: syntax, semantics and evaluation

Given the sustained growth that we are experiencing in the number of SPARQL endpoints available, the need to be able to send federated SPARQL queries across these has also grown. To address this use case, the W3C SPARQL working group is defining a federation extension for SPARQL 1.1 which allows for combining graph patterns that can be evaluated over several endpoints within a single query. In this paper, we describe the syntax of that extension and formalize its semantics. Additionally, we describe how a query evaluation system can be implemented for that federation extension, describing some static optimization techniques and reusing a query engine used for data-intensive science, so as to deal with large amounts of intermediate and final results. Finally we carry out a series of experiments that show that our optimizations speed up the federated query evaluation process.

Caracterización productiva de los alcornocales catalanes

En este trabajo se analizan, para Cataluña, los principales parámetros que afectan a la producción de corcho: densidad superficial, calidad y precio medio del corcho, turno de descorche. Los resultados reflejan la elevada variabilidad en la edad del corcho, la homogeneidad de la densidad superficial y la mayor calidad del corcho procedente de los alcornocales del litoral.

A Semantic-Based Approach to Attain Reproducibility of Computational Environments in Scientic Work ows: A Case Study

Reproducible research in scientic work ows is often addressed by tracking the provenance of the produced results. While this approach allows inspecting intermediate and nal results, improves understanding, and permits replaying a work ow execution, it does not ensure that the computational environment is available for subsequent executions to reproduce the experiment. In this work, we propose describing the resources involved in the execution of an experiment using a set of semantic vocabularies, so as to conserve the computational environment. We dene a process for documenting the work ow application, management system, and their dependencies based on 4 domain ontologies. We then conduct an experimental evaluation sing a real work ow application on an academic and a public Cloud platform. Results show that our approach can reproduce an equivalent execution environment of a predened virtual machine image on both computing platforms.

Gestión de ideas innovadoras

El trabajo de fin de grado que se va a definir detalladamente en esta memoria, trata de poner de manifiesto muchos de los conocimientos que he adquirido a lo largo de la carrera, aplicándolos en un proyecto real. Se ha desarrollado una plataforma capaz de albergar ideas, escritas por personas de todo el mundo que buscan compartirlas con los demás, para que estas sean comentadas, valoradas y entre todos poder mejorarlas. Estas ideas pueden ser de cualquier ámbito, por tanto, se da la posibilidad de clasificarlas en las categorías que mejor encajen con la idea. La aplicación ofrece una API RESTful muy descriptiva, en la que se ha identificado y estructurado cada recurso, para que a través de los “verbos http” se puedan gestionar todos los elementos de una forma fácil y sencilla, independientemente del cliente que la utilice. La arquitectura está montada siguiendo el patrón de diseño modelo vista-controlador, utilizando las últimas tecnologías del mercado como Spring, Liferay, SmartGWT y MongoDB (entre muchas otras) con el objetivo de crear una aplicación segura, escalable y modulada, por lo que se ha tenido que integrar todos estos frameworks. Los datos de la aplicación se hacen persistentes en dos tipos de bases de datos, una relacional (MySQL) y otra no relacional (MongoDB), aprovechando al máximo las características que ofrecen cada una de ellas. El cliente propuesto es accesible mediante un navegador web, se basa en el portal de Liferay. Se han desarrollado varios “Portlets o Widgets”, que componen la estructura de contenido que ve el usuario final. A través de ellos se puede acceder al contenido de la aplicación, ideas, comentarios y demás contenidos sociales, de una forma agradable para el usuario, ya que estos “Portlets” se comunican entre sí y hacen peticiones asíncronas a la API RESTful sin necesidad de recargar toda la estructura de la página. Además, los usuarios pueden registrarse en el sistema para aportar más contenidos u obtener roles que les dan permisos para realizar acciones de administración. Se ha seguido una metodología “Scrum” para la realización del proyecto, con el objetivo de dividir el proyecto en tareas pequeñas y desarrollarlas de una forma ágil. Herramientas como “Jenkins” me han ayudado a una integración continua y asegurando mediante la ejecución de los test de prueba, que todos los componentes funcionan. La calidad ha sido un aspecto principal en el proyecto, se han seguido metodologías software y patrones de diseño para garantizar un diseño de calidad, reutilizable, óptimo y modulado. El uso de la herramienta “Sonar” ha ayudado a este cometido. Además, se ha implementado un sistema de pruebas muy completo de todos los componentes de la aplicación. En definitiva, se ha diseñado una aplicación innovadora de código abierto, que establece unas bases muy definidas para que si algún día se pone en producción, sirva a las personas para compartir pensamientos o ideas ayudando a mejorar el mundo en el que vivimos. ---ABSTRACT---The Final Degree Project, described in detail in this report, attempts to cover a lot of the knowledge I have acquired during my studies, applying it to a real project. The objective of the project has been to develop a platform capable of hosting ideas from people all over the world, where users can share their ideas, comment on and rate the ideas of others and together help improving them. Since these ideas can be of any kind, it is possible to classify them into suitable categories. The application offers a very descriptive API RESTful, where each resource has been identified and organized in a way that makes it possible to easily manage all the elements using the HTTP verbs, regardless of the client using it. The architecture has been built following the design pattern model-view-controller, using the latest market technologies such as Spring, Liferay, Smart GWT and MongoDB (among others) with the purpose of creating a safe, scalable and adjustable application. The data of the application are persistent in two different kinds of databases, one relational (MySQL) and the other non-relational (MongoDB), taking advantage of all the different features each one of them provides. The suggested client is accessible through a web browser and it is based in Liferay. Various “Portlets" or "Widgets” make up the final content of the page. Thanks to these Portlets, the user can access the application content (ideas, comments and categories) in a pleasant way as the Portlets communicate with each other making asynchronous requests to the API RESTful without the necessity to refresh the whole page. Furthermore, users can log on to the system to contribute with more contents or to obtain administrator privileges. The Project has been developed following a “Scrum” methodology, with the main objective being that of dividing the Project into smaller tasks making it possible to develop each task in a more agile and ultimately faster way. Tools like “Jenkins” have been used to guarantee a continuous integration and to ensure that all the components work correctly thanks to the execution of test runs. Quality has been one of the main aspects in this project, why design patterns and software methodologies have been used to guarantee a high quality, reusable, modular and optimized design. The “Sonar” technology has helped in the achievement of this goal. Furthermore, a comprehensive proofing system of all the application's components has been implemented. In conclusion, this Project has consisted in developing an innovative, free source application that establishes a clearly defined basis so that, if it someday will be put in production, it will allow people to share thoughts and ideas, and by doing so, help them to improve the World we live in.

Semantic Annotation of RESTful and WFS OGC services

Actualmente, la Web provee un inmenso conjunto de servicios (WS-*, RESTful, OGC WFS), los cuales están normalmente expuestos a través de diferentes estándares que permiten localizar e invocar a estos servicios. Estos servicios están, generalmente, descritos utilizando información textual, sin una descripción formal, es decir, la descripción de los servicios es únicamente sintáctica. Para facilitar el uso y entendimiento de estos servicios, es necesario anotarlos de manera formal a través de la descripción de los metadatos. El objetivo de esta tesis es proponer un enfoque para la anotación semántica de servicios Web en el dominio geoespacial. Este enfoque permite automatizar algunas de las etapas del proceso de anotación, mediante el uso combinado de recursos ontológicos y servicios externos. Este proceso ha sido evaluado satisfactoriamente con un conjunto de servicios en el dominio geoespacial. La contribución principal de este trabajo es la automatización parcial del proceso de anotación semántica de los servicios RESTful y WFS, lo cual mejora el estado del arte en esta área. Una lista detallada de las contribuciones son: • Un modelo para representar servicios Web desde el punto de vista sintáctico y semántico, teniendo en cuenta el esquema y las instancias. • Un método para anotar servicios Web utilizando ontologías y recursos externos. • Un sistema que implementa el proceso de anotación propuesto. • Un banco de pruebas para la anotación semántica de servicios RESTful y OGC WFS. Abstract The Web contains an immense collection of Web services (WS-*, RESTful, OGC WFS), normally exposed through standards that tell us how to locate and invocate them. These services are usually described using mostly textual information and without proper formal descriptions, that is, existing service descriptions mostly stay on a syntactic level. If we want to make such services potentially easier to understand and use, we may want to annotate them formally, by means of descriptive metadata. The objective of this thesis is to propose an approach for the semantic annotation of services in the geospatial domain. Our approach automates some stages of the annotation process, by using a combination of thirdparty resources and services. It has been successfully evaluated with a set of geospatial services. The main contribution of this work is the partial automation of the process of RESTful and WFS semantic annotation services, what improves the current state of the art in this area. The more detailed list of contributions are: • A model for representing Web services. • A method for annotating Web services using ontological and external resources. • A system that implements the proposed annotation process. • A gold standard for the semantic annotation of RESTful and OGC WFS services, and algorithms for evaluating the annotations.