An Editorial Workflow Approach For Collaborative Ontology Development

The widespread use of ontologies in the last years has raised new challenges for their development and maintenance. Ontology development has transformed from a process normally performed by one ontology engineer into a process performed collaboratively by a team of ontology engineers, who may be geographically distributed and play different roles. For example, editors may propose changes, while authoritative users approve or reject them following a well defined process. This process, however, has only been partially addressed by existing ontology development methods, methodologies, and tool support. Furthermore, in a distributed environment where ontology editors may be working on local copies of the same ontology, strategies should be in place to ensure that changes in one copy are reflected in all of them. In this paper, we propose a workflow-based model for the collaborative development of ontologies in distributed environments and describe the components required to support them. We illustrate our model with a test case in the fishery domain from the United Nations Food and Agriculture Organisation (FAO)

Context-Aware Information Retrieval for Enhanced Situation Awareness

In the coalition forces, users are increasingly challenged with the issues of information overload and correlation of information from heterogeneous sources. Users might need different pieces of information, ranging from information about a single building, to the resolution strategy of a global conflict. Sometimes, the time, location and past history of information access can also shape the information needs of users. Information systems need to help users pull together data from disparate sources according to their expressed needs (as represented by system queries), as well as less specific criteria. Information consumers have varying roles, tasks/missions, goals and agendas, knowledge and background, and personal preferences. These factors can be used to shape both the execution of user queries and the form in which retrieved information is packaged. However, full automation of this daunting information aggregation and customization task is not possible with existing approaches. In this paper we present an infrastructure for context-aware information retrieval to enhance situation awareness. The infrastructure provides each user with a customized, mission-oriented system that gives access to the right information from heterogeneous sources in the context of a particular task, plan and/or mission. The approach lays on five intertwined fundamental concepts, namely Workflow, Context, Ontology, Profile and Information Aggregation. The exploitation of this knowledge, using appropriate domain ontologies, will make it feasible to provide contextual assistance in various ways to the work performed according to a user’s taskrelevant information requirements. This paper formalizes these concepts and their interrelationships

Enhancing Workflow with a Semantic Description of Scientific Intent

Peer reviewedPreprin

The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web

Research in life sciences is increasingly being conducted in a digital and online environment. In particular, life scientists have been pioneers in embracing new computational tools to conduct their investigations. To support the sharing of digital objects produced during such research investigations, we have witnessed in the last few years the emergence of specialized repositories, e.g., DataVerse and FigShare. Such repositories provide users with the means to share and publish datasets that were used or generated in research investigations. While these repositories have proven their usefulness, interpreting and reusing evidence for most research results is a challenging task. Additional contextual descriptions are needed to understand how those results were generated and/or the circumstances under which they were concluded. Because of this, scientists are calling for models that go beyond the publication of datasets to systematically capture the life cycle of scientific investigations and provide a single entry point to access the information about the hypothesis investigated, the datasets used, the experiments carried out, the results of the experiments, the people involved in the research, etc. In this paper we present the Research Object (RO) suite of ontologies, which provide a structured container to encapsulate research data and methods along with essential metadata descriptions. Research Objects are portable units that enable the sharing, preservation, interpretation and reuse of research investigation results. The ontologies we present have been designed in the light of requirements that we gathered from life scientists. They have been built upon existing popular vocabularies to facilitate interoperability. Furthermore, we have developed tools to support the creation and sharing of Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page

Automatic annotation of bioinformatics workflows with biomedical ontologies

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014 conference), 15 pages, 4 figure

Clinical guidelines as plans: An ontological theory

Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of are realized through the actions of individuals organized into teams. We provide various levels of implementation representing different levels of conformity on the part of health care organizations. Implementations built in conformity with our framework are marked by two dimensions of flexibility that are designed to make them more likely to be accepted by health care professionals than standard guideline-based management systems. They do justice to the fact 1) that responsibilities within a health care organization are widely shared, and 2) that health care professionals may on different occasions be non-compliant with guidelines for a variety of well justified reasons. The advantage of the framework lies in its built-in flexibility, its sensitivity to clinical context, and its ability to use inference tools based on a robust ontology. One disadvantage lies in its complicated implementation

Initiating organizational memories using ontology-based network analysis as a bootstrapping tool

An important problem for many kinds of knowledge systems is their initial set-up. It is difficult to choose the right information to include in such systems, and the right information is also a prerequisite for maximizing the uptake and relevance. To tackle this problem, most developers adopt heavyweight solutions and rely on a faithful continuous interaction with users to create and improve content. In this paper, we explore the use of an automatic, lightweight ontology-based solution to the bootstrapping problem, in which domain-describing ontologies are analysed to uncover significant yet implicit relationships between instances. We illustrate the approach by using such an analysis to provide content automatically for the initial set-up of an organizational memory

Expressing the tacit knowledge of a digital library system as linked data

Library organizations have enthusiastically undertaken semantic web initiatives and in particular the data publishing as linked data. Nevertheless, different surveys report the experimental nature of initiatives and the consumer difficulty in re-using data. These barriers are a hindrance for using linked datasets, as an infrastructure that enhances the library and related information services. This paper presents an approach for encoding, as a Linked Vocabulary, the "tacit" knowledge of the information system that manages the data source. The objective is the improvement of the interpretation process of the linked data meaning of published datasets. We analyzed a digital library system, as a case study, for prototyping the "semantic data management" method, where data and its knowledge are natively managed, taking into account the linked data pillars. The ultimate objective of the semantic data management is to curate the correct consumers' interpretation of data, and to facilitate the proper re-use. The prototype defines the ontological entities representing the knowledge, of the digital library system, that is not stored in the data source, nor in the existing ontologies related to the system's semantics. Thus we present the local ontology and its matching with existing ontologies, Preservation Metadata Implementation Strategies (PREMIS) and Metadata Objects Description Schema (MODS), and we discuss linked data triples prototyped from the legacy relational database, by using the local ontology. We show how the semantic data management, can deal with the inconsistency of system data, and we conclude that a specific change in the system developer mindset, it is necessary for extracting and "codifying" the tacit knowledge, which is necessary to improve the data interpretation process

Semantically Resolving Type Mismatches in Scientific Workflows

Scientists are increasingly utilizing Grids to manage large data sets and execute scientific experiments on distributed resources. Scientific workflows are used as means for modeling and enacting scientific experiments. Windows Workflow Foundation (WF) is a major component of Microsoft’s .NET technology which offers lightweight support for long-running workflows. It provides a comfortable graphical and programmatic environment for the development of extended BPEL-style workflows. WF’s visual features ease the syntactic composition of Web services into scientific workflows but do nothing to assure that information passed between services has consistent semantic types or representations or that deviant flows, errors and compensations are handled meaningfully. In this paper we introduce SAWSDL-compliant annotations for WF and use them with a semantic reasoner to guarantee semantic type correctness in scientific workflows. Examples from bioinformatics are presented