Ontology Development Life Cycle Research Articles

PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data.

Disease ontologies facilitate the semantic organization and representation of domain-specific knowledge. In the case of prostate cancer (PCa), large volumes of research results and clinical data have been accumulated and needed to be standardized for sharing and translational researches. A formal representation of PCa-associated knowledge will be essential to the diverse data standardization, data sharing and the future knowledge graph extraction, deep phenotyping and explainable artificial intelligence developing. In this study, we constructed an updated PCa ontology (PCAO2) based on the ontology development life cycle. An online information retrieval system was designed to ensure the usability of the ontology. The PCAO2 with a subclass-based taxonomic hierarchy covers the major biomedical concepts for PCa-associated genotypic, phenotypic and lifestyle data. The current version of the PCAO2 contains 633 concepts organized under three biomedical viewpoints, namely, epidemiology, diagnosis and treatment. These concepts are enriched by the addition of definition, synonym, relationship and reference. For the precision diagnosis and treatment, the PCa-associated genes and lifestyles are integrated in the viewpoint of epidemiological aspects of PCa. PCAO2 provides a standardized and systematized semantic framework for studying large amounts of heterogeneous PCa data and knowledge, which can be further, edited and enriched by the scientific community. The PCAO2 is freely available at https://bioportal.bioontology.org/ontologies/PCAO, http://pcaontology.net/ and http://pcaontology.net/mobile/.

Comprehensive Ontology of Fibroproliferative Diseases: Protocol for a Semantic Technology Study.

Fibroproliferative or fibrotic diseases (FDs), which represent a significant proportion of age-related pathologies and account for over 40% of mortality in developed nations, are often underrepresented in focused research. Typically, these conditions are studied individually, such as chronic obstructive pulmonary disease or idiopathic pulmonary fibrosis (IPF), rather than as a collective entity, thereby limiting the holistic understanding and development of effective treatments. To address this, we propose creating and publicizing a comprehensive fibroproliferative disease ontology (FDO) to unify the understanding of FDs. This paper aims to delineate the study protocol for the creation of the FDO, foster transparency and high quality standards during its development, and subsequently promote its use once it becomes publicly available. We aim to establish an ontology encapsulating the broad spectrum of FDs, constructed in the Web Ontology Language format using the Protégé ontology editor, adhering to ontology development life cycle principles. The modeling process will leverage Protégé in accordance with a methodologically defined process, involving targeted scoping reviews of MEDLINE and PubMed information, expert knowledge, and an ontology development process. A hybrid top-down and bottom-up strategy will guide the identification of core concepts and relations, conducted by a team of domain experts based on systematic iterations of scientific literature reviews. The result will be an exhaustive FDO accommodating a wide variety of crucial biomedical concepts, augmented with synonyms, definitions, and references. The FDO aims to encapsulate diverse perspectives on the FD domain, including those of clinicians, health informaticians, medical researchers, and public health experts. The FDO is expected to stimulate broader and more in-depth FD research by enabling reasoning, inference, and the identification of relationships between concepts for application in multiple contexts, such as developing specialized software, fostering research communities, and enhancing domain comprehension. A common vocabulary and understanding of relationships among medical professionals could potentially expedite scientific progress and the discovery of innovative solutions. The publicly available FDO will form the foundation for future research, technological advancements, and public health initiatives. PRR1-10.2196/48645.

STO: Stroke Ontology for Accelerating Translational Stroke Research.

IntroductionOntology-based annotation of evidence, using disease-specific ontologies, can accelerate analysis and interpretation of the knowledge domain of diseases. Although many domain-specific disease ontologies have been developed so far, in the area of cardiovascular diseases, there is a lack of ontological representation of the disease knowledge domain of stroke.MethodsThe stroke ontology (STO) was created on the basis of the ontology development life cycle and was built using Protégé ontology editor in the ontology web language format. The ontology was evaluated in terms of structural and functional features, expert evaluation, and competency questions.ResultsThe stroke ontology covers a broad range of major biomedical and risk factor concepts. The majority of concepts are enriched by synonyms, definitions, and references. The ontology attempts to incorporate different users’ views on the stroke domain such as neuroscientists, molecular biologists, and clinicians. Evaluation of the ontology based on natural language processing showed a high precision (0.94), recall (0.80), and F-score (0.78) values, indicating that STO has an acceptable coverage of the stroke knowledge domain. Performance evaluation using competency questions designed by a clinician showed that the ontology can be used to answer expert questions in light of published evidence.ConclusionsThe stroke ontology is the first, multiple-view ontology in the domain of brain stroke that can be used as a tool for representation, formalization, and standardization of the heterogeneous data related to the stroke domain. Since this is a draft version of the ontology, the contribution of the stroke scientific community can help to improve the usability of the current version.

ROBOT: A Tool for Automating Ontology Workflows

BackgroundOntologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as running automated reasoners and quality control checks, extracting dependencies and application-specific subsets, generating standard reports, and generating release files in multiple formats. Similar to more general software development, automation is the key to executing and managing these tasks effectively and to releasing more robust products in standard forms.For ontologies using the Web Ontology Language (OWL), the OWL API Java library is the foundation for a range of software tools, including the Protégé ontology editor. In the Open Biological and Biomedical Ontologies (OBO) community, we recognized the need to package a wide range of low-level OWL API functionality into a library of common higher-level operations and to make those operations available as a command-line tool.ResultsROBOT (a recursive acronym for “ROBOT is an OBO Tool”) is an open source library and command-line tool for automating ontology development tasks. The library can be called from any programming language that runs on the Java Virtual Machine (JVM). Most usage is through the command-line tool, which runs on macOS, Linux, and Windows. ROBOT provides ontology processing commands for a variety of tasks, including commands for converting formats, running a reasoner, creating import modules, running reports, and various other tasks. These commands can be combined into larger workflows using a separate task execution system such as GNU Make, and workflows can be automatically executed within continuous integration systems.ConclusionsROBOT supports automation of a wide range of ontology development tasks, focusing on OBO conventions. It packages common high-level ontology development functionality into a convenient library, and makes it easy to configure, combine, and execute individual tasks in comprehensive, automated workflows. This helps ontology developers to efficiently create, maintain, and release high-quality ontologies, so that they can spend more time focusing on development tasks. It also helps guarantee that released ontologies are free of certain types of logical errors and conform to standard quality control checks, increasing the overall robustness and efficiency of the ontology development lifecycle.

Ontology Engineering and Development Aspects: A Survey

Ontology can be defined as hierarchical representation of classes, sub classes, their properties and instances. It has led to understanding the concepts of given domain, deriving relationships and representing them in machine interpretable language. Ontologies are associated with different languages that are used in mapping of multiple ontologies. Several applications of ontologies have led towards realization of semantic web. The current web (2.0) is approaching towards semantic web (3.0) that performs intelligent search and stores results in distributed databases. The paper makes readers aware of various aspects of ontology like types of ontology, ontology development life cycle phases, activities involved in ontology development and ontology engineering tools. Ontology engineering contributes to meaningful search and provides with open source tools for deploying and building ontologies.

Overview and Analysis of Ontology Studies Supporting Development of the Construction Industry

AbstractBeing information-intensive, the construction industry has the feature of multiagents, including multiparticipants from different disciplines, multiprocesses with a long-span timeline, and multidocuments generated by various systems. The multistakeholder context of the construction industry creates problems such as poor information interoperability and low productivity arising from difficulties in information reuse. Many researchers have explored the use of ontology to address these issues. This study aims to review ontology research to explore its trends, gaps, and opportunities in the construction industry. A systematic process employing three-phase search method, objective analysis and subjective analysis, helps to provide enough potential articles related to construction ontology research, and to reduce arbitrariness and subjectivity involved in research topic analysis. As a result, three main research topics aligned with the ontology development lifecycle were derived as follows: information ...

A Comparative Study on Ontology Development Methodologies towards Building Semantic Conflicts Detection Ontology for Heterogeneous Web Services

Semantic conflicts detection is considered to be one of the essential steps that should be carried out effectively, in order to pave the way towards establishing semantic interoperability between heterogeneous Web services. To achieve that, ontology plays the backbone of the detection process, which required to be implemented in a high quality manner. However, choosing a methodology to build this ontology is very difficult, since a considerable number of methodologies have been emerged to guide the ontology development process. Therefore, this study aims at reviewing and comparing the most accepted and used methodologies, with the aim of choosing an effective methodology from ontology engineering perspective to be recommended and used for building semantic conflicts detection ontology. Furthermore, to provide some useful insights for both theoretical and practical purposes to help ontology developers to choose the right methodology and to advance the state of the art. The comparison was performed against the common ontology development life cycle. The result of this survey and comparison recommend a methodology called METHONTOLOGY to be used for implementing semantic conflicts detection ontology.

OIntEd: online ontology instance editor enabling a new approach to ontology development

SUMMARYOntology development involves people with different background knowledge and expertise. It is an elaborate process, where sophisticated tools for experienced knowledge engineers are available. However, domain experts need simple tools that they can use to focus on ontology instantiation. In this paper, we propose a methodology with a separation of concern between domain experts and knowledge engineers. This separation allows domain experts to focus on information processing and ontology instantiation while providing immediate feedback to the knowledge engineers on usability of the ontology being developed. We have designed and implemented OINTED, an adaptive online ontology instance editor that supports this methodology. We present usage examples of OINTED that highlight three main features: the intuitive visualization of concepts, instances, and relationships within an ontology; the seamless integration in pre‐existing problem solving environment; and the assistance in ontology evolution. OINTED complements existing tools suited for knowledge engineers by enabling immediate feedback and a shorter ontology development life cycle. Copyright © 2012 John Wiley & Sons, Ltd.

Developing ontologies in decentralised settings

AbstractThis paper addresses two research questions: “How should a well-engineered methodology facilitate the development of ontologies within communities of practice?” and “What methodology should be used?” If ontologies are to be developed by communities then the ontology development life cycle should be better understood within this context. This paper presents the Melting Point (MP), a proposed new methodology for developing ontologies within decentralized settings. It describes how MP was developed by taking best practices from other methodologies, provides details on recommended steps and recommended processes, and compares MP with alternatives. The methodology presented here is the product of direct first-hand experience and observation of biological communities of practice in which some of the authors have been involved. The Melting Point is a methodology engineered for decentralised communities of practice for which the designers of technology and the users may be the same group. As such, MP provides a potential foundation for the establishment of standard practices for ontology engineering.

The roles of scenario use in ontology development

With the recent focus on knowledge management and knowledge-based systems, the proper development of ontologies, that is, conceptual structures underlying these systems, has become critical. Also recently, the benefits of using scenarios in the development of artifacts have received much attention in multiple disciplines. This paper examines the roles that scenarios can play in ontology development. It presents a set of claims about why scenarios are useful and how they can be used to support each phase of the ontology development lifecycle. These claims are drawn from, supported by, and illustrated with the lessons from a 5-year ontology design project that led to a NIST specification of the process ontology that is on the way to become an International Standard Organisation (ISO) standard. Based on the analysis of these claims, an overall picture relating the roles of scenario use in ontology development is presented in an effort to help ontology developers better understand why, when and how to use scenarios. The results of this study are also related to the earlier studies of the scenario uses in other related disciplines such as software engineering, human–computer interaction and management. Copyright © 2006 John Wiley & Sons, Ltd.