Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework

This paper describes a pilot query interface that has been constructed to help us explore a "concept-based" approach for searching the Neuroscience Information Framework (NIF). The query interface is concept-based in the sense that the search terms submitted through the interface are selected from a standardized vocabulary of terms (concepts) that are structured in the form of an ontology. The NIF contains three primary resources: the NIF Resource Registry, the NIF Document Archive, and the NIF Database Mediator. These NIF resources are very different in their nature and therefore pose challenges when designing a single interface from which searches can be automatically launched against all three resources simultaneously. The paper first discusses briefly several background issues involving the use of standardized biomedical vocabularies in biomedical information retrieval, and then presents a detailed example that illustrates how the pilot concept-based query interface operates. The paper concludes by discussing certain lessons learned in the development of the current version of the interface

Developing Human Functioning and Rehabilitation Research from the comprehensive perspective.

With the International Classification of Functioning, Disability and Health (ICF) the World Health Organization (WHO) has prepared the ground for a comprehensive understanding of Human Functioning and Rehabilitation Research, integrating the biomedical perspective on impairment with the social model of disability. This poses a number of old and new challenges regarding the enhancement of adequate research capacity. Here we will summarize approaches to address these challenges with respect to 3 areas: the organization of Human Functioning and Rehabilitation Research into distinct scientific fields, the development of suitable academic training programmes and the building of university centres and collaboration networks

Participatory design of a continuous care ontology : towards a user-driven ontology engineering methodology

The patient room of the future would be able to sense the needs and preferences of the patients and nurses and adapt itself accordingly by combining all the heterogeneous data offered by the different technologies. This goal can be achieved by developing a context-aware framework, which exploits and integrates the heterogeneous data by utilizing a continuous care ontology. The existing ontology engineering methodologies are rather extreme in their choices to include domain experts. On the one hand, there are methodologies that only discuss the scope, use and requirements of the ontology with the domain experts. On the other hand, there are approaches in which the ontology is completely constructed by the domain experts by providing them with user-friendly and collaborative tools. In this paper, a participatory ontology engineering methodology is presented that finds a middle ground between these two extremes. The methodology actively involves social scientists, ontology engineers and stakeholders. The stakeholders participate in each step of the ontology life cycle without having to construct the ontology themselves or attribute a large amount of their time. The applicability of the methodology is illustrated by presenting the co-created continuous care ontology

Bioinformatics and the politics of innovation in the life sciences: Science and the state in the United Kingdom, China, and India

The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific community itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation

Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based Tools for Representation and Integration of Event-related Brain Potentials

We describe a first-generation ontology for
representation and integration of event-related brain potentials (ERPs). The ontology is designed following OBO “best practices” and is augmented with tools to perform ontology-based labeling and annotation of ERP data, and a database that enables semantically based reasoning over these data. Because certain high-level concepts in the ERP domain are illdefined, we have developed methods to support coordinated updates to each of these three components. This approach consists of “top-down” (knowledge-driven) design and implementation, followed by “bottom-up” (data-driven) validation and refinement. Our goal is to build an ERP ontology that is logically valid, empirically sound, robust in application, and transparent to users. This ontology will be used to support sharing and meta-analysis of EEG and MEG data collected within our Neural Electromagnetic Ontologies (NEMO) project

Hypotheses, evidence and relationships: The HypER approach for representing scientific knowledge claims

Biological knowledge is increasingly represented as a collection of (entity-relationship-entity) triplets. These are queried, mined, appended to papers, and published. However, this representation ignores the argumentation contained within a paper and the relationships between hypotheses, claims and evidence put forth in the article. In this paper, we propose an alternate view of the research article as a network of 'hypotheses and evidence'. Our knowledge representation focuses on scientific discourse as a rhetorical activity, which leads to a different direction in the development of tools and processes for modeling this discourse. We propose to extract knowledge from the article to allow the construction of a system where a specific scientific claim is connected, through trails of meaningful relationships, to experimental evidence. We discuss some current efforts and future plans in this area

An ontology co-design method for the co-creation of a continuous care ontology

Ontology engineering methodologies tend to emphasize the role of the knowledge engineer or require a very active role of domain experts. In this paper, a participatory ontology engineering method is described that holds the middle ground between these two 'extremes'. After thorough ethnographic research, an interdisciplinary group of domain experts closely interacted with ontology engineers and social scientists in a series of workshops. Once a preliminary ontology was developed, a dynamic care request system was built using the ontology. Additional workshops were organized involving a broader group of domain experts to ensure the applicability of the ontology across continuous care settings. The proposed method successfully actively engaged domain experts in constructing the ontology, without overburdening them. Its applicability is illustrated by presenting the co-created continuous care ontology. The lessons learned during the design and execution of the approach are also presented

Ontology as Product-Service System: Lessons Learned from GO, BFO and DOLCE

This paper defends a view of the Gene Ontology (GO) and of Basic Formal Ontology (BFO) as examples of what the manufacturing industry calls product-service systems. This means that they are products (the ontologies) bundled with a range of ontology services such as updates, training, help desk, and permanent identifiers. The paper argues that GO and BFO are contrasted in this respect with DOLCE, which approximates more closely to a scientific theory or a scientific publication. The paper provides a detailed overview of ontology services and concludes with a discussion of some implications of the product-service system approach for the understanding of the nature of applied ontology. Ontology developer communities are compared in this respect with developers of scientific theories and of standards (such as W3C). For each of these we can ask: what kinds of products do they develop and what kinds of services do they provide for the users of these products

A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

Integration of ontologies with decentralized autonomous organizations development: A systematic literature review

This paper presents a systematic literature review of the integration of ontologies into the Decentralized Autonomous Organization (DAO) development process. The review extracted data from 34 primary studies dealing with ontologies in the blockchain domain. DAO has become a key concept for the development of blockchain-based decentralized software systems. DAOs are seen as a positive alternative for organizations interested in the adoption of decentralized, reliable and transparent governance, as well as attracting the interest of academic research. However, there is no common understanding or generally accepted formal definition of a DAO, and the guidelines that provide support for the adoption and development of DAOs are limited to a few key references that lack the computational semantics needed to enable their automated validation, simulation or execution. Thus, the objective of this paper is to provide an unbiased and up-to-date review related to the integration of ontologies within DAOs which helps to identify new research opportunities and take advantage of this integration from a blockchain-based decentralized perspective