The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains ...are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
•OwlReady is an ontology-oriented programming module for Python.•It provides automatic classification and high level constructs inspired by medical ontologies.•It has a specific syntax for ...manipulating classes and role-filler constructs.•It supports some form of local closed world reasoning.•These features have been useful for reasoning on drug contraindications.
Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies.
From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated “role-filler” constraints. We also propose an algorithm for performing local closed world reasoning in simple situations.
We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning.
Owlready has been successfully used in a medical research project. It has been published as Open-Source software and then used by many other researchers. Future developments will focus on the support of vagueness and additional non-monotonic reasoning feature, and automatic dialog box generation.
In this paper, we present the current results of the newly formed IEEE-RAS Working Group, named Ontologies for Robotics and Automation. In particular, we introduce a core ontology that encompasses a ...set of terms commonly used in Robotics and Automation along with the methodology we have adopted. Our work uses ISO/FDIS 8373 standard developed by the ISO/TC184/SC2 Working Group as a reference. This standard defines, in natural language, some generic terms which are common in Robotics and Automation such as robot, robotic device, etc. Furthermore, we discuss the ontology development process employed along with the problems and decisions taken.
•We propose a core ontology for the robotics and automation field.•The ontology aims to specify the main notions across robotics subdomains.•In this ontology, a robot is a device composed of many mechanical parts.•A robot is also an agent that interface with the environment.•A robot is also a social entity, which can compose systems with their environment.
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•Address the comprehension of and orientation into the COVID-19 CIDO Ontology.•Weighted aggregate taxonomy provides compact summarization of large ontologies.•Sometimes weighted ...aggregate taxonomies have too many levels to fit a screen.•The child-of layout for weighted aggregate taxonomies provides better visualization.
The current intensive research on potential remedies and vaccinations for COVID-19 would greatly benefit from an ontology of standardized COVID terms. The Coronavirus Infectious Disease Ontology (CIDO) is the largest among several COVID ontologies, and it keeps growing, but it is still a medium sized ontology. Sophisticated CIDO users, who need more than searching for a specific concept, require orientation and comprehension of CIDO.
In previous research, we designed a summarization network called “partial-area taxonomy” to support comprehension of ontologies. The partial-area taxonomy for CIDO is of smaller magnitude than CIDO, but is still too large for comprehension. We present here the “weighted aggregate taxonomy” of CIDO, designed to provide compact views at various granularities of our partial-area taxonomy (and the CIDO ontology). Such a compact view provides a “big picture” of the content of an ontology. In previous work, in the visualization patterns used for partial-area taxonomies, the nodes were arranged in levels according to the numbers of relationships of their concepts. Applying this visualization pattern to CIDO's weighted aggregate taxonomy resulted in an overly long and narrow layout that does not support orientation and comprehension since the names of nodes are barely readable. Thus, we introduce in this paper an innovative visualization of the weighted aggregate taxonomy for better orientation and comprehension of CIDO (and other ontologies). A measure for the efficiency of a layout is introduced and is used to demonstrate the advantage of the new layout over the previous one. With this new visualization, the user can “see the forest for the trees” of the ontology. Benefits of this visualization in highlighting insights into CIDO’s content are provided. Generality of the new layout is demonstrated.
As the core building blocks of the Semantic Web, ontologies provide shared vocabularies and conceptual knowledge for specific application fields. At the same time, ontologies can restrict their ...individuals and relationships through their semantic schema. However, logical conflicts of an ontology are often inevitably unavoidable in actual application scenarios when the ontology contains any form of disjointness or negation. Generally, logical conflicts can be divided into incoherence and inconsistency. Reasoning with incoherent ontologies may obtain many redundant relationships, and incoherence is a potential cause of inconsistency which seriously affects the correctness of semantic reasoning Therefore, handling incoherence is imperative, which mainly involves the fields of conflicts detection, ontology repair and justification computation. Various incoherent ontologies are indispensable to evaluate the proposed methods for handling incoherence. We provide a survey of relevant research works to study the proposed construction methods of incoherent ontologies. It is observed that incoherent ontologies in existing works still have the following limitations: (1) Lots of web pages used to download ontologies were temporarily constructed are now inaccessible; (2) Most of the existing incoherent ontologies were constructed in a simple way such as randomly adding disjointness axioms or merging ontologies through their alignments without considering all possible incoherence cases. To address the limitations, we propose a general framework to construct incoherent ontologies and design a hybrid algorithm to instantiate this framework. With the implemented construction methods, a comprehensive benchmark containing 116 ontologies is constructed. In our evaluations, incoherent ontologies in the benchmark are measured with 11 classic metrics. We then compare 5 representative ontology debugging systems and 3 repair methods. The evaluation results reveal that these ontologies could reflect different characteristics of each ontology system and repair method. All observations could guide researchers to select incoherent ontologies. The availability of our benchmark makes a contribution to the community of ontology debugging and repair fields.
•The first work studies construction methods of incoherent ontologies.•Propose a framework of existing methods to construct incoherent ontologies.•Construct a benchmark of incoherent ontologies for ontology debugging community.•Conduct abundant experiments to compare ontology debugging systems.
Cyber-physical systems (CPSs) in the manufacturing domain can be deployed to support monitoring and analysis of production systems of a factory in order to improve, support, or automate processes, ...such as maintenance or scheduling. When a network of CPS is subject to frequent changes, the semantic interoperability between the CPSs is of special interest in order to avoid manual, tedious, and error-prone information model alignments at runtime. Ontologies are a suitable technology to enable semantic interoperability, as they allow the building of information models that lank machine-readable meaning to information, thus enabling CPSs to mutually understand the shared information. The contribution of this article is twofold. First, we present an ontology building method that is tailored toward the needs of CPSs in the manufacturing domain. For this purpose, we introduce the requirements regarding this method and discuss related research concerning ontology building. The method itself is designed to begin with ontological requirements and to yield a formal ontology. As the reuse of ontologies and other information resources (IRs) is crucial to the success of ontology building projects, we put special emphasis on how to reuse IRs in the CPS domain. Second, we present a reusable set of ontology design patterns that have been developed with the aforementioned method in an industrial use case and illustrate their application in the considered industrial environment. The contribution of this article extends the method introduced, as a postconference paper, by a detailed industrial application. Note to Practitioners -With growing digitalization in industry, the exchange and use of manufacturing-related data are becoming increasingly important to improve, support, or automate processes. Thus, it is necessary to combine information from different data sources that have been designed by different vendors and may, therefore, be heterogeneous in structure and semantics. A system that plans a maintenance worker's daily schedule, for instance, requires information about the status of machines, production plans, and inventory, which resides in other systems, such as programmable logic controllers (PLCs) or databases. When creating such information systems, accessing, searching, and understanding the different data sources is a time-intensive and error-prone procedure due to the heterogeneities of the data sources. Even worse, this procedure has to be repeated for every newly built system and for every newly introduced data source. To allow for eased access, searching, and understanding of these heterogeneous data sources, ontology can be used to integrate all heterogeneous data sources in one schema. This article contributes a method for building such ontologies in the manufacturing domain. Furthermore, a set of ontology design patterns is presented, which can be reused when building ontologies for a domain.
After years of research on ontology matching, it is reasonable to consider several questions: is the field of ontology matching still making progress? Is this progress significant enough to pursue ...further research? If so, what are the particularly promising directions? To answer these questions, we review the state of the art of ontology matching and analyze the results of recent ontology matching evaluations. These results show a measurable improvement in the field, the speed of which is albeit slowing down. We conjecture that significant improvements can be obtained only by addressing important challenges for ontology matching. We present such challenges with insights on how to approach them, thereby aiming to direct research into the most promising tracks and to facilitate the progress of the field.
In order to model a context and adapt it to any domain, it is necessary an ontology that captures generic concepts to a higher level. The context model must provide mechanisms to extend the specific ...information of a context in a hierarchical manner. In this paper, we propose CAMeOnto, an ontology with these characteristics, based on the principles of 5Ws: who, when, what, where and why. CAMeOnto is used by CARMiCLOC, a reflective middleware for context-aware applications, and is instantiated in several case studies, in order to test how CAMeOnto works correctly and can reason to infer information about the context.
Audio event recognition, the human-like ability to identify and relate sounds from audio, is a nascent problem in machine perception. Comparable problems such as object detection in images have ...reaped enormous benefits from comprehensive datasets - principally ImageNet. This paper describes the creation of Audio Set, a large-scale dataset of manually-annotated audio events that endeavors to bridge the gap in data availability between image and audio research. Using a carefully structured hierarchical ontology of 632 audio classes guided by the literature and manual curation, we collect data from human labelers to probe the presence of specific audio classes in 10 second segments of YouTube videos. Segments are proposed for labeling using searches based on metadata, context (e.g., links), and content analysis. The result is a dataset of unprecedented breadth and size that will, we hope, substantially stimulate the development of high-performance audio event recognizers.
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•Ontology evaluation is an integral part of ontology development and maintenance.•We assessed the ontology evaluation practice of a sample of 200 BioPortal ontologies.•We reviewed ...recent ontology quality assurance and auditing techniques.•We identified the gaps between ontology evaluation and quality assurance.
With the proliferation of heterogeneous health care data in the last three decades, biomedical ontologies and controlled biomedical terminologies play a more and more important role in knowledge representation and management, data integration, natural language processing, as well as decision support for health information systems and biomedical research. Biomedical ontologies and controlled terminologies are intended to assure interoperability. Nevertheless, the quality of biomedical ontologies has hindered their applicability and subsequent adoption in real-world applications. Ontology evaluation is an integral part of ontology development and maintenance. In the biomedicine domain, ontology evaluation is often conducted by third parties as a quality assurance (or auditing) effort that focuses on identifying modeling errors and inconsistencies. In this work, we first organized four categorical schemes of ontology evaluation methods in the existing literature to create an integrated taxonomy. Further, to understand the ontology evaluation practice in the biomedicine domain, we reviewed a sample of 200 ontologies from the National Center for Biomedical Ontology (NCBO) BioPortal—the largest repository for biomedical ontologies—and observed that only 15 of these ontologies have documented evaluation in their corresponding inception papers. We then surveyed the recent quality assurance approaches for biomedical ontologies and their use. We also mapped these quality assurance approaches to the ontology evaluation criteria. It is our anticipation that ontology evaluation and quality assurance approaches will be more widely adopted in the development life cycle of biomedical ontologies.
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