A new approach for publishing workflows: abstractions, standards, and linked data

In recent years, a variety of systems have been developed that export the workflows used to analyze data and make them part of published articles. We argue that the workflows that are published in current approaches are dependent on the specific codes used for execution, the specific workflow system used, and the specific workflow catalogs where they are published. In this paper, we describe a new approach that addresses these shortcomings and makes workflows more reusable through: 1) the use of abstract workflows to complement executable workflows to make them reusable when the execution environment is different, 2) the publication of both abstract and executable workflows using standards such as the Open Provenance Model that can be imported by other workflow systems, 3) the publication of workflows as Linked Data that results in open web accessible workflow repositories. We illustrate this approach using a complex workflow that we re-created from an influential publication that describes the generation of 'drugomes'

Pattern Reification as the Basis for Description-Driven Systems

One of the main factors driving object-oriented software development for information systems is the requirement for systems to be tolerant to change. To address this issue in designing systems, this paper proposes a pattern-based, object-oriented, description-driven system (DDS) architecture as an extension to the standard UML four-layer meta-model. A DDS architecture is proposed in which aspects of both static and dynamic systems behavior can be captured via descriptive models and meta-models. The proposed architecture embodies four main elements - firstly, the adoption of a multi-layered meta-modeling architecture and reflective meta-level architecture, secondly the identification of four data modeling relationships that can be made explicit such that they can be modified dynamically, thirdly the identification of five design patterns which have emerged from practice and have proved essential in providing reusable building blocks for data management, and fourthly the encoding of the structural properties of the five design patterns by means of one fundamental pattern, the Graph pattern. A practical example of this philosophy, the CRISTAL project, is used to demonstrate the use of description-driven data objects to handle system evolution.Comment: 20 pages, 10 figure

A planning approach to the automated synthesis of template-based process models

The design-time specification of flexible processes can be time-consuming and error-prone, due to the high number of tasks involved and their context-dependent nature. Such processes frequently suffer from potential interference among their constituents, since resources are usually shared by the process participants and it is difficult to foresee all the potential tasks interactions in advance. Concurrent tasks may not be independent from each other (e.g., they could operate on the same data at the same time), resulting in incorrect outcomes. To tackle these issues, we propose an approach for the automated synthesis of a library of template-based process models that achieve goals in dynamic and partially specified environments. The approach is based on a declarative problem definition and partial-order planning algorithms for template generation. The resulting templates guarantee sound concurrency in the execution of their activities and are reusable in a variety of partially specified contextual environments. As running example, a disaster response scenario is given. The approach is backed by a formal model and has been tested in experiment

Towards Cloud Application Description Templates Supporting Quality of Service

Typical scientific, industrial and public sector applications require resource scalability and efficient resource utilization in order to serve a variable number of customers. Cloud computing provides an ideal solution to support such applications. However, the dynamic and intelligent utilization of cloud infrastructure resources from the perspective of cloud applications is not trivial. Although there have been several efforts to support the intelligent and coordinated deployment, and to a smaller extent also the run-time orchestration of cloud applications, no comprehensive solution has emerged until now that successfully leverages large scale near operational levels and ease of use. COLA is a European research project to provide a reference implementation of a generic and pluggable framework that supports the optimal and secure deployment and run-time orchestration of cloud applications. Such applications can then be embedded into workflows or science gateway frameworks to support complex application scenarios from user-friendly interfaces. A specific aspect of the cloud orchestration framework developed by COLA is the ability to describe complex application architectures incorporating several services. Besides the description of service components, the framework will also support the definition of various Quality of Service (QoS) parameters related to performance, economic viability and security. This paper concentrates on this latter aspect analysing how such application description templates can be developed based on existing standards and technologies

Automation is Documentation: Functional Documentation of Human-Machine Interaction for Future Software Reuse

Preserving software and providing access to obsolete software is necessary and will become even more important for work with any kind of born-digital artifacts. While usability and availability of emulation in digital curation and preservation workflow has improved significantly, productive (re)use of preserved obsolete software is a growing concern, due to a lack of (future) operational knowledge. In this article we describe solutions to automate and document software usage in a way, such that the result is not only instructive but also productive

Towards workflow ecosystems through standard representations

Workflows are increasingly used to manage and share scientific computations and methods. Workflow tools can be used to design, validate, execute and visualize scientific workflows and their execution results. Other tools manage workflow libraries or mine their contents. There has been a lot of recent work on workflow system integration as well as common workflow interlinguas, but the interoperability among workflow systems remains a challenge. Ideally, these tools would form a workflow ecosystem such that it should be possible to create a workflow with a tool, execute it with another, visualize it with another, and use yet another tool to mine a repository of such workflows or their executions. In this paper, we describe our approach to create a workflow ecosystem through the use of standard models for provenance (OPM and W3C PROV) and extensions (P-PLAN and OPMW) to represent workflows. The ecosystem integrates different workflow tools with diverse functions (workflow generation, execution, browsing, mining, and visualization) created by a variety of research groups. This is, to our knowledge, the first time that such a variety of workflow systems and functions are integrated

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: N

Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data

BACKGROUND: The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating registries, by establishing standards for integration and interoperability. The first practical output of this effort was a set of 16 Common Data Elements (CDEs) that should be implemented by all RD registries. Interoperability, however, requires decisions beyond data elements - including data models, formats, and semantics. Within the European Joint Programme on Rare Diseases (EJP RD), we aim to further the goals of the EU RD Platform by generating reusable RD semantic model templates that follow the FAIR Data Principles. RESULTS: Through a team-based iterative approach, we created semantically grounded models to represent each of the CDEs, using the SemanticScience Integrated Ontology as the core framework for representing the entities and their relationships. Within that framework, we mapped the concepts represented in the CDEs, and their possible values, into domain ontologies such as the Orphanet Rare Disease Ontology, Human Phenotype Ontology and National Cancer Institute Thesaurus. Finally, we created an exemplar, reusable ETL pipeline that we will be deploying over these non-coordinating data repositories to assist them in creating model-compliant FAIR data without requiring site-specific coding nor expertise in Linked Data or FAIR. CONCLUSIONS: Within the EJP RD project, we determined that creating reusable, expert-designed templates reduced or eliminated the requirement for our participating biomedical domain experts and rare disease data hosts to understand OWL semantics. This enabled them to publish highly expressive FAIR data using tools and approaches that were already familiar to them