RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

Background: Biomedical translational science is increasingly leveraging computational reasoning on large repositories of structured knowledge (such as the Unified Medical Language System (UMLS), the Semantic Medline Database (SemMedDB), ChEMBL, DrugBank, and the Small Molecule Pathway Database (SMPDB)) and data in order to facilitate discovery of new therapeutic targets and modalities. Since 2016, the NCATS Biomedical Data Translator project has been working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and within the field more broadly, there is an urgent need for an open-source framework that can efficiently and reproducibly build an integrated, standards-compliant, and comprehensive biomedical knowledge graph that can be either downloaded in standard serialized form or queried via a public application programming interface (API) that accords with the FAIR data principles. Results: To create a knowledge provider system within the Translator project, we have developed RTX-KG2, an open-source software system for building—and hosting a web API for querying—a biomedical knowledge graph that uses an Extract-Transform-Load (ETL) approach to integrate 70 knowledge sources (including the aforementioned sources) into a single knowledge graph. The semantic layer and schema for RTX-KG2 follow the standard Biolink metamodel to maximize interoperability within Translator. RTX-KG2 is currently being used by multiple Translator reasoning agents, both in its downloadable form and via its SmartAPI-registered web interface. JavaScript Object Notation (JSON) serializations of RTX-KG2 are available for download of RTX-KG2 in both the pre-canonicalized form and in canonicalized form (in which synonym concepts are merged). The current canonicalized version (KG2.7.3) of RTX-KG2 contains 6.4M concept nodes and 39.3M relationship edges with a rich set of 77 relationship types. Conclusion: RTX-KG2 is the first open-source knowledge graph of which we are aware that integrates UMLS, SemMedDB, ChEMBL, DrugBank, SMPDB, and 65 additional knowledge sources within a knowledge graph that conforms to the Biolink standard for its semantic layer and schema at the intersections of these databases. RTX-KG2 is publicly available for querying via its (API) at arax.ncats.io/api/rtxkg2/v1.2/openapi.json. The code to build RTX-KG2 is publicly available at github:RTXteam/RTX-KG2.

Building the Semantic Layer of the Józef Piłsudski Digital Archive With an Ontology-Based Approach

Using semantic web technologies is becoming an efficient way to overcome metadata storage and data integration problems in digital archives, thus enhancing the accuracy of the search process and leading to the retrieval of more relevant results. In this paper, the results of the implementation of the semantic layer of the Józef Piłsudski Institute of America digital archive are presented. In order to represent and integrate data about the archival collections housed by the institute, the authors developed arkivo, an ontology that accommodates the archival description of records but also provides a reference schema for publishing linked data. The authors describe the application of arkivo to the digitized archival collections of the institute, with emphasis on how these resources have been linked to external datasets in the linked data cloud. They also show the results of an experiment focused on the query answering task involving a state-of-the-art triple store system. The dataset related to the Piłsudski Institute archival collections has been made available for ontology benchmarking purposes.

The Influence of the Lotus Flower Theme on the Perception of Contemporary Urban Architecture

We live in the visual culture times, when images continuously and daily are transferring some information. A visual message is also an indispensable element of architecture, in the semantic layer as an aesthetic value, sometimes fulfilling a narrative function by means of a symbol, which is an international visual code. Most of the symbols, hidden in painting, sculpture, or architecture, are elements of nature. The article discusses examples of architecture whose form is based on a lotus flower. Unification of urban landscapes leads to a decrease in the value of aesthetic impressions; therefore, the unique architecture builds the unique identity of the place.

Symphonic Volume in the Symphony-Requiem by Bohdana Frolyak “Pravednaya Dushe”

Relevance of the study. The article is relevant as it studies the works of Bogdana Frolyak, who is a popular contemporary Ukrainian composer. Her music attracts the attention of performers and researchers and reflects the current trends of contemporary art such as musical language, new forms of choral sound, synthesis of genres. The Requiem Symphony “Righteous Ssoul” (lyrics by T. Shevchenko) is an example of a complex multidimensional nature genre renewal. Therefore, lack of research devoted to this work outlines a scientific novelty of this article. The objective of the study is to identify the features of symphony in the symphonyrequiem “Righteous Soul” by B. Frolyak. The research methodology is based on the interpretation analysis method proposed by V. Moskalenko. The concept of A. Adamyan is used to study symphonic principles. Results. Analysing the requiem symphony “Righteous Soul”, it was determined that the leading role is devoted to chorus, which serves as a main mean of expression. The choir is regarded as a symbol of collegiality and stands in as an active participant in the formation of musical thought and sounds through almost the entire opus (except for two vocal episodes). T. Shevchenko’s poetic lines are entrusted to mixed chorus and embody a main idea of the work. Choral fragments serve various functions starting from the creation of a harmonic background to being a main storyteller. At the same time, B. Frolyak’s composition realizes symphonic principles, which display themselves at different levels of organization of musical material. Symphonic patterns are expressed in timbre-textured and thematic connections, cross-cutting development, national instrumentation color and intonation transformations of themes. The composer’s principle of artistic thinking reveals parallels with the symphonic concept developed by A. Adamyan. Conclusion. A special genre multidimensionality is expressed in the symphony-requiem “Pravednaya Dushe”. B. Frolyak enriches the semantic layer of the work due to the features of the requiem. Composer takes an advantage of the cathedral’s choral sonority rich possibilities and uses the symphonic intonation and dramatic basis. At the intonation level, she unites all these features with the help of solospiv (solosining) — a musical symbol of Ukrainian nation. Finally, unique synthesis of supersubstantial spiritual and philosophic ideas with universal (symphony, requiem) and national characteristic (solospiv) genres makes B. Frolyak’s work one of the most original in the series of Ukrainian choral symphonies.

SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks

A comprehensible representation of a molecular network is key to communicating and understanding scientific results in systems biology. The Systems Biology Graphical Notation (SBGN) has emerged as the main standard to represent such networks graphically. It has been implemented by different software tools, and is now largely used to communicate maps in scientific publications. However, learning the standard, and using it to build large maps, can be tedious. Moreover, SBGN maps are not grounded on a formal semantic layer and therefore do not enable formal analysis. Here, we introduce a new set of patterns representing recurring concepts encountered in molecular networks, called SBGN bricks. The bricks are structured in a new ontology, the Bricks Ontology (BKO), to define clear semantics for each of the biological concepts they represent. We show the usefulness of the bricks and BKO for both the template-based construction and the semantic annotation of molecular networks. The SBGN bricks and BKO can be freely explored and downloaded at sbgnbricks.org.

Semantic and Blockchain Technology

Blockchain is a distributed ledger with the ability of keeping up the uprightness of exchanges by decentralizing the record among participating clients. The key advancement is that it enables its users to exchange resources over the internet without the requirement for a centralised third party. Also, each 'block' is exceptionally associated with the past blocks by means of digital signature which implies that creation a change to a record without exasperating the previous records in the chain is beyond the realm of imagination, in this way rendering the data tamper-proof. A semantic layer based upon a blockchain framework would join the advantages of adaptable administration disclosure and approval by consensus. This chapter examines the engineering supporting the blockchain and portrays in detail how the information distribution is done, the structure of the block itself, the job of the block header, the block identifier, and the idea of the Genesis block.

"Galáxias", de Haroldo de Campos, é um livro de artista?

In the fifty text fragments that compose Galáxias, by Haroldo de Campos, the dominance of the cogito is constantly broken. In this way, the reader’s attention, generally inclined to turn only to the semantic layer of the text, to look for what the text means, is led to perceive there also the pulse of a living materiality. If the word is not just a vehicle for the message, the body of the book is not merely a support for the texts, but an important element for the production of meaning. With a strange graphic design, could Haroldo’s work be considered an artist’s book? This is what this article investigates.

Linguistic peculiarities of functionality of authorial commentaries in the English literary text (based on the English-language novel “Sister Carrie” by Theodore Dreiser)

This article is dedicated to examination of verbal means of expression of authorial commentaries in English fiction. The relevance of the selected topic is defined by the fact that the question of characteristics of authorial commentaries remain an insufficiently studied area within the framework of interpretation of a literary work. Such linguists as R. Posner in the “Theory of Commentaries”, I. V. Arnold in the “Stylistics of Decoding”, and N. D. Arutyunova in her work “On the Problems of Structural Linguistics” have been dealing the topic at hand. Examination of the authorial commentaries allows assessing the depth and wholeness of the literary work. The article presents the analysis of linguistic means of functionality of authorial commentaries in the English-language novel “Sister Carrie” by Theodore Dreiser. Authorial commentaries manifest as one of the means for explication of dialogical nature of the literary text. Linguistic means emphasize the expressiveness of authorial commentaries within the framework of progression of a storyline. Most of the authorial commentaries in T. Dreiser's novel “Sister Carry” represent the contrasting contexts, reflected in the development of two thematic lines. To the first theme includes the associative series: beast – nature – the forces of life. The second semantic layer is demonstrated in the line: human – man – free will. Contrasting contexts originate the oppositions not only on the level of meaningful-logical information, but also on the level of subtext.