Ontology Project Research Articles

Ingeniería ontológica aplicada a la gestión de interesados de un proyecto

La gestión de proyectos (vista desde los diferentes estándares y entidades que promueven las buenas prácticas en esta disciplina) refleja que un factor determinante en el éxito o fracaso en la ejecución de proyectos radica en el talento humano que interviene durante el ciclo de vida de este, ya que de acuerdo con su rol y momento de intervención, puede impactar positiva o negativamente el proyecto. Dicha problemática resalta la importancia de contar con un instrumento que permita la identificación, clasificación y seguimiento efectivo de los interesados del proyecto, de tal manera que la toma decisiones frente a este recurso permita hacer una gestión preventiva antes que correctiva, mitigando así el riesgo que pueda generar la desinformación o mala comunicación entre los mismos. Por lo anterior, el objetivo de este artículo, es modelar una ontología que sirva como instrumento de gestión de interesados con elementos semánticos y conceptuales dentro del dominio de la gestión de proyectos, construido a partir de las técnicas de la ingeniería ontológica, la cual permite resolver preguntas puntuales respecto a información concerniente a este recurso de manera ágil, precisa y efectiva, facilitando así su gestión en las fases que componen el ciclo de vida del proyecto. Esta investigación contribuirá con la integración de la ingeniería ontológica y la gestión de proyectos, posibilitando la construcción de una estructura de información de los interesados con componentes semánticos que la habilitan para ser insumo de un modelo de gestión de conocimiento más complejo.

Formal representation of immunology related data with ontologies

Abstract The Human Immunology Project Consortium (HIPC) is a multicenter collaboration between research centers performing large-scale human immunology studies that focus on profiling the human immune response to natural infection and vaccination. “Immune exposures” are events such as natural infection and vaccination whereby the immune system may or may not respond to the exposure. Many of the HIPC studies investigate the response of specific cell populations after a variety of immune exposures. In order to cross-compare results from the many different centers and projects, we established a standardized representation of immune exposures and cell descriptions that simplifies data collection. By standardizing how this data is collected and stored, the vast amount of data collected by these diverse projects is made significantly more useful and interoperable. The data collected by the HIPC projects is stored in the National Institute of Health, Division of Allergy, Immunology and Transplantation funded resource, the Immunology Database and Analysis Portal (ImmPort). ImmPort was modified to provide the necessary structured data fields to capture our standardized representation of immune exposures and studied cell populations with a set of data fields that primarily utilize formal ontology terms. We will discuss the process of modeling immune exposures and cell populations via ontology terms, including real life scenarios from HIPC projects, as well as collaborations with existing ontology projects in order to meet the specific needs of immunologists.

Merab Mamardashvili: Event of Thought and Pedagogic Practice

The concept of event has been widely disseminated in various fields of human sciences, including the psychology of education and pedagogics. If one seeks to explore the full heuristic potential of the concept, it is necessary to take into account its essential affiliation with non-classical ontology. The article presents an attempt to analyze the inner structure of Merab Mamardashvili’s oral philosophical speech, that can be considered a distinctive feature of the series of lection courses, which he held in the late 70-ies – beginning of 80-ies mainly for the audience of non-philosophers. The article deals with the research of essential connection between form and content of Mamardashvili’s philosophy. In the light of this connection the article reviews the project of the non-classical ontology of cognition, that Mamardashvili develops in some of his main works.The first part of the article contains an exposition of the problem field of “event” in the context of history and ontology of cognition, as well as reconstruction of the genesis of this theme in Mamardashvili’s philosophy. Mamardashvili describes the classical type of rationality and its “blind spots” – that is, historicity and “evental” character of phenomena of cognition, which cannot be seen in the objectifying gaze of the classical observer. An attempt is made to analyze Mamardashvili’s concept of conscience in the context of his phenomenology of event. The term “epiphany” is interpreted as a key characteristic of events of cognition.The second part of the article deals with the uniqueness of Merab Mamardashvili’s oral philosophical speech, that is interpreted as one of the strategies of indirect communication. Indirect communication is distinguished from direct communication of knowledge, the central model of classical pedagogics. The article studies several different approaches to interpretation of Merab Mamardashvili’s teaching strategy and proposes the approach that is based on the concept of indirect communication of event of cognition.

The Ontographic Turn: From Cubism to the Surrealist Object

Abstract The practice of Ontography deployed by OOO, clarified and expanded in this essay, produces a highly productive framework for analyzing Salvador Dalí’s ontological project between 1928 and 1935. Through the careful analysis of paintings and original texts from this period, we establish the antecedents for Dalí’s theorization of Surrealist objects in Cubism and Italian Metaphysical art, which we collectively refer to as ‘Ontographic art,’ drawing parallels with the tenets of Graham Harman’s and Ian Bogost’s object-oriented philosophical programmes. We respond to the question raised by Roger Rothman concerning Object-Oriented Idealism in Dalí’s work by showing pivotal changes to Dalí’s ontological outlook, from Idealism to Realism, across the aforementioned period, positing the Ontographic intentionality of Dalí’s ontological project in Surrealist art.

The Presuppositions of Being and Time

It is often remarked that Heidegger’s Being and Time was originally proposed as a book on Aristotle, and that formative work for this initial expression of Heidegger’s existential ontology was developed through the early 1920s in a series of lecture courses and seminars on Aristotle’s practical philosophy. This paper examines select details from Heidegger’s 1924 summer course in order to question the presuppositions of Heidegger’s decision to found the project of fundamental ontology on a purely philological reading of Aristotle. At stake is the method of investigation which permitted Heidegger to think politics through ontology in his most controversial writings from the 1930s—and ultimately the meaning of philosophy itself.

Theodor W. Adorno. Actuality of philosophy (Translation from German)

A young philosopher neo-marxist Theodor Adorno read his work «Actuality of Philosophy» in the summer of 1931 as a іnaugural lecture of privatdozent of the Goethe University of Frankfurt am Main. In this lecture young Adorno critically analyzed to the philosophy of positivism, neo-kantianism, the philosophy of life and the phenomenological learning of Edmund Husserl, theoretically influential currents and schools of German philosophy, which had the status of dominant theoretical knowledge in society. Adorno also carried out the neo-marxist critique of the ontological projects of such German philosophers as Max Scheler and Martin Heidegger, who were subjected to the theoretically influence of the Husserl’s learning. According to Adorno these ontological projects through the primary presence in itself an irrational elements of human existence, form the kind of subjective thinking that can not effectively combine its subject with external reality. Another object of Adorno's critique was the philosophy of the Vienna Circle, which, in his conviction, although he was concerned with the consideration of man as the subject of empirical knowledge, but she did not notice the true essence of his existence as a historical creature. Neo-marxist Adorno proposed to see the joint scientism of phenomenology, the philosophy of empirio criticism and the Vienna circle such a theoretical tendency that could not provide apodictic answers to the basic and substantive questions of human existence as historically fluid. So this theory proves its ideological imperfection and historical untopicality. After this critique, Adorno proposed his neo-marxist vision of a theory that should replace the previous theory as dominant in society. This new materialist philosophy has a being-dialectic relationship with social practice and should facilitate to independent interpretation by the subject to being senses and historical images. This philosophy forms with the help of concepts the understanding of social reality as a historical and to abolish the claims of any philosophy to the status of official theory. In this lecture Adorno also presented the ideological conception of his learning of human being, whose essence in a modified form was later explored in the Negative Dialectics (1966), in his main philosophical work.

Философия информации, проект нарративной онтологии и современная картина мира

Философия информации, проект нарративной онтологии и современная картина мира

TRIQ: a new method to evaluate triclusters

BackgroundTriclustering has shown to be a valuable tool for the analysis of microarray data since its appearance as an improvement of classical clustering and biclustering techniques. The standard for validation of triclustering is based on three different measures: correlation, graphic similarity of the patterns and functional annotations for the genes extracted from the Gene Ontology project (GO).ResultsWe propose TRIQ, a single evaluation measure that combines the three measures previously described: correlation, graphic validation and functional annotation, providing a single value as result of the validation of a tricluster solution and therefore simplifying the steps inherent to research of comparison and selection of solutions. TRIQ has been applied to three datasets already studied and evaluated with single measures based on correlation, graphic similarity and GO terms. Triclusters have been extracted from this three datasets using two different algorithms: TriGen and OPTricluster.ConclusionsTRIQ has successfully provided the same results as a the three single evaluation measures. Furthermore, we have applied TRIQ to results from another algorithm, OPTRicluster, and we have shown how TRIQ has been a valid tool to compare results from different algorithms in a quantitative straightforward manner. Therefore, it appears as a valid measure to represent and summarize the quality of tricluster solutions. It is also feasible for evaluation of non biological triclusters, due to the parametrization of each component of TRIQ.

Apis mellifera (Rilke, Leśmian, Valéry, Miłosz)

The article concerns Paul Valéry’s sonet The Bee, a fragment of Rainer Maria Rilke’s letter to Witold Hulewicz, Boleslaw Lesmian’s poem The Bees and a fragment of Czeslaw Milosz’s poem Orpheus and Eurydice. The analysis of the semantic connotations and symbolic meanings of the bee, which appears in these texts, shows them as elements of a larger ontological project: an attempt to answer the question of the relation between being and non-being. In essence, this project denies the division into being and non- -being, proposing the concept of a greater whole instead the entrenched opposition.

Vom Symptom zum Syndrom mit moderner Softwareunterstützung

Diagnosing rare diseases can be challenging for clinicians. This article gives an overview on novel approaches, which enable automated phenotype-driven analyses of differential diagnoses for rare diseases as well as genomic variation data of affected individuals. The focus lies on reliable methods for collating clinical phenotypic data and new algorithms for precise and robust assessment of the similarity between phenotypic profiles. The Human Phenotype Ontology project (HPO; www.human-phenotype-ontology.org ) provides an ontology for collating symptoms and clinical phenotypic abnormalities. Using ontologies makes it possible to capture these data in aprecise and comprehensive fashion as well as to apply reliable and robust automated analyses. Tools, such as the Phenomizer, enable the algorithmic calculation of similarity values amongst patients or between patients and disease descriptions. Such digital tools represent asolid foundation for differential diagnostic applications. Many rare diseases have astrong genetic component but the analysis of the coding DNA variants in rare disease patients is an enormously complex procedure, which often impedes successful molecular diagnostics. In this situation acombined analysis of the patients HPO-coded phenotypic features and the genomic characteristics of the variants can be of substantial help. In this case the HPO project and the associated algorithms are helpful: it is therefore an important component for phenotype-driven translational research and prioritization of disease-relavant genomic variations.

Against Conservatism in Metaphysics

AbstractIn his recent book, Daniel Korman contrasts ontological conservatives with permissivists and eliminativists about ontology. Roughly speaking, conservatives admit the existence of ‘ordinary objects' like trees, dogs, and snowballs, but deny the existence of ‘extraordinary objects', like composites of trees and dogs (‘trogs'). Eliminativists, on the other hand, deny many or all ordinary objects, while permissivists accept both ordinary and extraordinary objects. Our aim in this paper is to outline some of our reasons for being drawn to permissivism, as well as some of our misgivings about conservative metaphysics. In the first section, we discuss a tempting epistemic line of argument against conservatism. This isn’t a line of argument we find especially promising. Our most basic complaint against conservatism is not that conservatism has poor epistemic standing even if true, but instead that conservatism is weird. We develop this thought in the second part of the paper. In the final section we discuss some larger methodological issues about the project of ontology.

Disease Ontology: improving and unifying disease annotations across species.

ABSTRACTModel organisms are vital to uncovering the mechanisms of human disease and developing new therapeutic tools. Researchers collecting and integrating relevant model organism and/or human data often apply disparate terminologies (vocabularies and ontologies), making comparisons and inferences difficult. A unified disease ontology is required that connects data annotated using diverse disease terminologies, and in which the terminology relationships are continuously maintained. The Mouse Genome Database (MGD, http://www.informatics.jax.org), Rat Genome Database (RGD, http://rgd.mcw.edu) and Disease Ontology (DO, http://www.disease-ontology.org) projects are collaborating to augment DO, aligning and incorporating disease terms used by MGD and RGD, and improving DO as a tool for unifying disease annotations across species. Coordinated assessment of MGD's and RGD's disease term annotations identified new terms that enhance DO's representation of human diseases. Expansion of DO term content and cross-references to clinical vocabularies (e.g. OMIM, ORDO, MeSH) has enriched the DO's domain coverage and utility for annotating many types of data generated from experimental and clinical investigations. The extension of anatomy-based DO classification structure of disease improves accessibility of terms and facilitates application of DO for computational research. A consistent representation of disease associations across data types from cellular to whole organism, generated from clinical and model organism studies, will promote the integration, mining and comparative analysis of these data. The coordinated enrichment of the DO and adoption of DO by MGD and RGD demonstrates DO's usability across human data, MGD, RGD and the rest of the model organism database community.

SYMBOLIC LANDSCAPE OF CONSCIOUSNESS: MAN BETWEEN REPRESENTATIONALISM, FUNCTIONALISM AND RELATIVISM

Purpose. The aim of the study is to clarify the changed interpretation of symbol in the context of the ontological turn in cultural anthropology and philosophical anthropology and their correlation with the functioning of the semantic field of culture, and in particular with religious symbols. The paper also considers an epistemological-ideological positions of representationalism, functionalism and relativism with respect to philosopheme of symbol. Methodology. The authors implemented theoretical and conceptual analysis in synchronic and diachronic aspects, the methodology of comparative consideration of the character within the analytical and existential paradigms in the 20th century philosophy. Originality. The work presents the study of correlation between aspect consideration of the nature and specific character in representationalism, functionalism and relativism within the philosophical projects of the cognitive position. The authors substantiated the position of symbol ontologization in the contemporary cultural and philosophical anthropology and the importance of convergence of the symbol concept and philosopheme with the concepts of an object and a thing. They fixed the value of the ontological turn in cultural anthropology for philosophical anthropology. The authors specifically examined the correlation between the declared symbol interpretation, project of object-oriented ontology and the modern philosophy of science. They substantiated ontological concept of symbolic landscape of modern philosophical anthropology, social philosophy and philosophy of mind. The symbol and religious symbolism have the significant importance for human identity, the symbol is considered to be the tool of human’s self-knowledge. Conclusions. The paper outlines the specific character of existence of symbol philosopheme in communicative field of modern man, the social media space, in particular the role of religious symbols for the construction of identity and self-positioning of modern man.

WormBase 2017: molting into a new stage.

WormBase (http://www.wormbase.org) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive knowledge about Caenorhabditis elegans, and genomic information about other nematodes and parasitic flatworms. Recent notable enhancements include user-directed submission of data, such as micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query tools, such as SimpleMine, Gene Enrichment Analysis; new data displays, such as the Person Lineage browser and the Summary of Ontology-based Annotations. Anticipating more rapid data growth ahead, WormBase continues the process of migrating to a cutting-edge database technology to achieve better stability, scalability, reproducibility and a faster response time. To better serve the broader research community, WormBase, with five other Model Organism Databases and The Gene Ontology project, have begun to collaborate formally as the Alliance of Genome Resources.

Негативная гносеология в греческом аристотелизме XVII века

The article studies the project of critical epistemology on the periphery of Europe, which is considered as an alternative to the project of critical ontology in the center of Europe. It is proved that this critical, or negative epistemology was based on two presumptions: on the concept of power as not decision-making, but as making control over the variety of decisions, and on the representation of speech not as a statement but as an establishment of the boundaries of consciousness. These presumptions date back to the unique social and political situation in the Orthodox world, which transformed the conventions of classical rhetoric into epistemological tools. In the struggle of various political forces to master this instrumentation, the concept of power as internal speech or intellectual attitude in relation to the diversity of events was developed, and the realization of power was understood as negative epistemology, allowing facts to be established not as simple events but as true and right events. The classical concepts of Aristotle were turned into topoi, describing reality not as an aggregate of ontological statuses, but as a set of epistemological problems. The study of this phenomenon based on the works by Theophilos Corydalleus and Gerasimos Vlakhos allows to explain common origins of the key problems of Eastern European religious philosophy (such as iconicity, personalism, and philosophy of the Divine name), which are otherwise perceived as fragmented and anomalous.

Preaxial polydactyly of the foot

Background and purpose — Preaxial polydactyly of the foot is a rare malformation and clinicians are often unfamiliar with the associated malformations and syndromes. In order to give guidelines for diagnostics and referral to a clinical geneticist, we provide an overview of the presentation using a literature review and our own patient population.Patients and methods — The literature review was based on the Human Phenotype Ontology (HPO) project. From the HPO dataset, all phenotypes describing preaxial polydactyly were obtained and related diseases were identified and selected. An overview was generated in a heatmap, in which the phenotypic contribution of 12 anatomical groups to each disease is displayed. Clinical cases were obtained from our hospital database and were reviewed in terms of phenotype, genotype, heredity, and diagnosed syndromes.Results — From the HPO dataset, 21 diseases were related to preaxial polydactyly of the foot. The anatomical groups with the highest phenotypic contribution were lower limb, upper limb, and craniofacial. From our clinical database, we included 76 patients with 9 different diseases, of which 27 had a GLI3 mutation. Lower limb malformations (n = 55), upper limb malformations (n = 59), and craniofacial malformations (n = 32) were most frequently observed. Malformations in other anatomical groups were observed in 27 patients.Interpretation — Preaxial polydactyly of the foot often presents with other upper and lower limb malformations. In patients with isolated preaxial polydactyly of the foot, referral to a clinical geneticist is not mandatory. In patients with additional malformations, consultation with a clinical geneticist is recommended. When additional limb malformations are present, analysis of GLI3 is most feasible.

Heidegger’s Black Notebooks and the Logic of a History of Being

Abstract Interpretations of the so-called Black Notebooks have emphasized the interaction between Heidegger’s philosophy, particularly his notion of a “history of being” (Seinsgeschichte), on the one hand, and his affiliation with National Socialism and his anti-Semitic views on the other. The paper proposes to understand this interaction as in part determined by the inherent logic of Heidegger’s ontological reasoning: Heidegger takes power (Macht), violence (Gewalt) and brutality (Brutalität) as the key for understanding his present day and turns to these phenomena as confirmation of the ontology he envisages at the time. But the notes published so far, ranging from 1931 to 1948 (Gesamtausgabe vols. 94–97), document Heidegger’s incapacity to assign to the events of these years a plausible position in his ontology. This failure deepens a trauma both personal and philosophical. Rather than reject the notion of a history of being altogether, I propose an alternative understanding of its logic motivated by Heidegger’s failure to bring his ontological project to the anticipated completion.

Cambridge Social Ontology: Clarification, Development and Deployment

Social ontology—the study of the nature and basic structure of the social realm—is currently enjoying a period of sustained growth and development, both as a field of study in its own right and as a project concerned with under-labouring for a variety of different social scientific disciplines including economics. One of the most active streams in this area emanates from Cambridge and a group of researchers operating at the interface between social ontology and heterodox economics whose work is sometimes identified as Cambridge Social Ontology. The central figure in this project is Tony Lawson, whose work has provided much of the impetus for Cambridge Social Ontology over the last thirty years. This Special Issue of the Cambridge Journal of Economics is intended to mark the contribution Lawson has made to the study of social ontology and to the application of its results to economics and the social sciences more widely. It does so by presenting a range of new papers whose authors were invited to engage with the work of Lawson and his colleagues in the Cambridge Social Ontology project. The intention was to encourage new work, whether it be critical or constructive in orientation, and thereby hopefully to advance the themes that Lawson has pursued over the course of his career.

Screening disrupted molecular functions and pathways associated with clear cell renal cell carcinoma using Gibbs sampling

ObjectiveTo explore the disturbed molecular functions and pathways in clear cell renal cell carcinoma (ccRCC) using Gibbs sampling. MethodsGene expression data of ccRCC samples and adjacent non-tumor renal tissues were recruited from public available database. Then, molecular functions of expression changed genes in ccRCC were classed to Gene Ontology (GO) project, and these molecular functions were converted into Markov chains. Markov chain Monte Carlo (MCMC) algorithm was implemented to perform posterior inference and identify probability distributions of molecular functions in Gibbs sampling. Differentially expressed molecular functions were selected under posterior value more than 0.95, and genes with the appeared times in differentially expressed molecular functions ≥5 were defined as pivotal genes. Functional analysis was employed to explore the pathways of pivotal genes and their strongly co-regulated genes. ResultsIn this work, we obtained 396 molecular functions, and 13 of them were differentially expressed. Oxidoreductase activity showed the highest posterior value. Gene composition analysis identified 79 pivotal genes, and survival analysis indicated that these pivotal genes could be used as a strong independent predictor of poor prognosis in patients with ccRCC. Pathway analysis identified one pivotal pathway − oxidative phosphorylation. ConclusionsWe identified the differentially expressed molecular functions and pivotal pathway in ccRCC using Gibbs sampling. The results could be considered as potential signatures for early detection and therapy of ccRCC.

Identification of Associated Genes and Diseases in Patients With Congenital Upper-Limb Anomalies: A Novel Application of the OMT Classification

Congenital upper-limb anomalies (CULA) can present as a part of a syndrome or association. There is a wide spectrum of CULA, each of which might be related to different diseases. The structure provided by the Oberg, Manske, and Tonkin (OMT) classification could aid in differential diagnosis formulation in patients with CULA. The aims of this study were to review the Human Phenotype Ontology (HPO) project database for diseases and causative genes related to the CULA described in the OMT classification and to develop a methodology for differential diagnosis formulation based on the observed congenital anomalies, CulaPhen. We reviewed the HPO database for all diseases, including causative genes related to CULA. All CULA were classified according to the OMT classification; associated non-hand phenotypes were classified into 12 anatomical groups. We analyzed the contribution of each anatomical group to a given disease and developed a tool for differential diagnosis formulation based on these contributions. We compared our results with cases from the literature and with a current HPO tool, Phenomizer. In total, 514 hand phenotypes were obtained, 384 of which could be classified in the OMT classification. A total of 1,403 diseases could be related to those CULA. A comparison with 10 recently published cases with CULA revealed that the presented phenotype matched the descriptions in our dataset. The differential diagnosis produced using our methodology was more accurate than Phenomizer in 4 of 5 examples. The OMT classification can be used to describe hand anomalies that may present in over 1,400 diseases. CulaPhen was developed to provide a (hand) phenotype-based differential diagnosis. Differential diagnosis formulation based on the proposed system outperforms the system in current use. This study illustrates that the OMT diagnoses, either individually or combined, can be cross-referenced with different diseases and syndromes. Therefore, use of the OMT classification can aid differential diagnosis formulation for CULA patients.