Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

Since Turing proposed the first test of intelligence, several modifications have been proposed with the aim of making Turing’s proposal more realistic and applicable in the search for artificial intelligence. In the modern context, it turns out that some of these definitions of intelligence and the corresponding tests merely measure computational power. Furthermore, in the framework of the original Turing test, for a system to prove itself to be intelligent, a certain amount of deceit is implicitly required which can have (...) serious security implications for future human societies. In this article, we propose a unified framework for developing intelligence tests which takes care of important ethical and practical issues. Our proposed framework has several important consequences. Firstly, it results in the suggestion that it is not possible to construct a single, context independent, intelligence test. Secondly, any measure of intelligence must have access to the process by which a problem is solved by the system under consideration and not merely the final solution. Finally, it requires an intelligent agent to be evolutionary in nature with the flexibility to explore new algorithms on its own. (shrink)

In this paper, we employ bibliometric analysis to empirically analyse the research on social entrepreneurship published between 1996 and 2017. By employing methods of citation analysis, document co-citation analysis, and social network analysis, we analyse 1296 papers containing 74,237 cited references and uncover the structure, or intellectual base, of research on social entrepreneurship. We identify nine distinct clusters of social entrepreneurship research that depict the intellectual structure of the field. The results provide an overall perspective of the social entrepreneurship field, (...) identifying its influential works and analysing scholarly communication between these works. The results further aid in clarifying the overall centrality features of the social entrepreneurship research network. We also examine the integration of ethics into social entrepreneurship literature. We conclude with a discussion on the structure and evolution of the social entrepreneurship field. (shrink)

Studies on the conservation of the inferred transcriptional regulatory network of prokaryotes have suggested that specific transcription factors are less‐widely conserved in comparison to their target genes. This observation implied that, at large evolutionary distances, the turnover of specific transcription factors through loss and non‐orthologous displacement might be a major factor in the adaptive radiation of prokaryotes. However, the recent work of Hershberg and Margalit1 suggests that, at shorter phylogenetic scales, the evolutionary dynamics of the bacterial transcriptional regulatory network might (...) exhibit distinct patterns. The authors find previously unnoticed relationships between the regulatory mode (activation or repression), the number of regulatory interactions and their conservation patterns in γ‐proteobacteria. These relationships might be shaped by the differences in the adaptive value and mode of operation of different regulatory interactions. BioEssays 29:625–629, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

The insulin/insulin‐like growth factor‐1 (IGF‐1) signaling (IIS) pathway is a pivotal genetic program regulating cell growth, tissue development, metabolic physiology, and longevity of multicellular organisms. IIS integrates a fine‐tuned cascade of signaling events induced by insulin/IGF‐1, which is precisely controlled by post‐translational modifications. The ubiquitin/proteasome‐system (UPS) influences the functionality of IIS through inducible ubiquitylation pathways that regulate internalization of the insulin/IGF‐1 receptor, the stability of downstream insulin/IGF‐1 signaling targets, and activity of nuclear receptors for control of gene expression. An age‐related (...) decline in UPS activity is often associated with an impairment of IIS, contributing to pathologies such as cancer, diabetes, cardiovascular, and neurodegenerative disorders. Recent findings identified a key role of diverse ubiquitin modifications in insulin signaling decisions, which governs dynamic adaption upon environmental and physiological changes. In this review, we discuss the mutual crosstalk between ubiquitin and insulin signaling pathways in the context of cellular and organismal homeostasis. (shrink)

Evolution of cities is a subject of research for over a hundred years in the organization of urban knowledge systems. Locating five key methodological approaches used by urban scholars and practitioners, this paper demonstrates different relationships between urban studies and classification. Five significant themes form the background of urban studies literature. The first theme sources and literature explore organizing urban materials into sources and literature with a unique dimension of spatiality. The second theme discusses three important facets: scale as a (...) geographic unit of analysis and space as an abstract entity and system as a set of interdependent parts of urban places. The third theme, known as “other” urban, argued for the poor treatment of global south and how it builds inclusivity. The fourth theme, classification and retrieval, investigates the relationship between urban materials and user needs. The last theme, classification schemes, highlights subject treatment of urban in the existing library classification schemes. This paper concludes that the five themes discussed point to a model of urban studies classification. However, this model is not just concerned with urban methods, facets and formats, but explores how each theme interconnects with various sets of people-urbanists, practitioners and librarians-and through studying these actors, established boundaries of urban theories, urban librarianship and knowledge organization are crossed. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

In this paper we take a fresh look at the information retrieval problem of balancing recall with precision in electronic document extraction. We examine the IR constructs of uncertainty, context and relevance, proposing a new process model for context learning, and introducing a new IT artifact designed to support user driven learning by leveraging explicit knowledge to discover implicit knowledge within a corpus of documents. The IT artifact is a prototype designed to present a small set of extracted documents from (...) a targeted corpus based upon user inputted criteria. The prototype provides the user with the opportunity to balance exploration and exploitation, via iterative relevance feedback to address the problem of imprecision resulting from uncertainty. We model the problem as an exploration–exploitation dilemma and apply it to a specific case of IR called eDiscovery. We conduct a series of behavioral experiments to evaluate the model and the artifact. Our initial findings indicate that the proposed model and the artifact improve performance in the IR result. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Coreference resolution is a challenging natural language processing task, and it is difficult to identify the correct mentions of an entity that can be any noun or noun phrase. In this article, a semisupervised, two-stage pattern-based bootstrapping approach is proposed for the coreference resolution task. During Stage 1, the possible mentions are identified using word-based features, and during Stage 2, the correct mentions are identified by filtering the non-coreferents of an entity using statistical measures and graph-based features. Whereas the existing (...) approaches use morphosyntactic and number/gender agreement features, the proposed approach uses semantic graph-based context-level semantics and nested noun phrases in the correct mentions identification. Moreover, mentions without the number/gender information are identified, using the context-based features of the semantic graph. The evaluation performed for the coreference resolution shows significant improvements, when compared with the word association-based bootstrapping systems. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

This paper explains conceptual modeling within the framework of Frame-Based Terminology (Faber, 2012; 2015; 2022), as applied to EcoLexicon (ecolexicon.ugr.es), a specialized knowledge base on the environment (León-Araúz, Reimerink &, Faber, 2019; Faber & León-Araúz, 2021). It describes how a frame-based terminological resource is currently being restructured and reengineered as an initial step towards its formalization and subsequent transformation into an ontology. It also explains how the information in EcoLexicon can be integrated in environmental ontologies such as ENVO (Buttigieg, Morrison, (...) Smith, Mungall & Lewis, 2013; Buttigieg, Pafilis, Lewis, Schildhauer, Walls & Mungall, 2016), particularly at the bottom tiers of the Ontology Learning Layer Cake (Cimiano, 2006; Cimiano, Maedche, Staab & Volker, 2009). The assumption is that frames, as a conceptual modeling tool, and information extracted from corpora can be used to represent the conceptual structure of a specialized domain. (shrink)