Disease Ontology: improving and unifying disease annotations across species.

Model 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\u27s and RGD\u27s disease term annotations identified new terms that enhance DO\u27s representation of human diseases. Expansion of DO term content and cross-references to clinical vocabularies (e.g. OMIM, ORDO, MeSH) has enriched the DO\u27s 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\u27s usability across human data, MGD, RGD and the rest of the model organism database community. Dis Model Mech 2018 Mar 12;11(3):dmm032839

Semantic Ontologies for Complex Healthcare Structures: A Scoping Review

The healthcare environment is made up of highly complicated interactions between many technologies, activities, and people. Ensuring a solid communication between them is vital to ease the healthcare management. Semantic ontologies are knowledge representation tools that implement abstractions to fully describe a given topic in terms of subjects and relations. This scoping review aims to identify and analyse available ontologies which can depict all the available use-cases that describe the hospital environment in relation to the European project ODIN and its future expansion. The review has been conducted on the Scopus database on January 13th, 2023 using the PRISMA extensions for scoping reviews. Two reviewers screened 3,225 documents emerged from the database search. Further filtering led to a final set of 32 articles to be analysed for the results. A set of 34 ontologies extracted by the identified articles has been analysed and discussed as well. The results of this study will lead to the implementation of a common integrated ontology which could hold information about healthcare entities as well as their semantic relationships, strengthen data exchange and interconnections among people, devices and applications in an expanded scenario which include Internet of Things, robots and Artificial Intelligence

ОНТОЛОГО-КЕРОВАНІ ІНФОРМАЦІЙНІ СИСТЕМИ В ЗАБЕЗПЕЧЕННІ БЕЗПЕРЕРВНОГО ПРОФЕСІЙНОГО РОЗВИТКУ ЛІКАРІВ ТА ПРОВІЗОРІВ

The article is devoted to the issue of medical education quality assurance, the improvement of the medical staff qualifications and the continuous professional development of doctors and pharmacists using modern information and communication technologies. The advantages of using the ontological approach to knowledge representation in the process of creation and use of medical information systems in order to provide access to the maximum amount of information through the interoperable integration and aggregation of knowledge-oriented resources and information sources are determined. A brief analysis of existing medical ontologies (from collections of highly specialized thematic ontologies to national terminology health systems), which revealed a number of disadvantages and obstacles to their use in the system of modern medical education in Ukraine is presented. The necessity of creation of a unified interoperable environment with existing ontological solutions by means of unified user interface for increasing the efficiency of continuous professional development of doctors and pharmacists is determined. The main aspects of the development of ontology-driven information systems, which can be used for the medical information systems structure, functionality and interfaces design, but also in the process of using them to solve practical problems, are outlined. The experience of using IT-TODOS cognitive software and information tools that provide interactive temporal and semantic synchronization of information resources, regardless of the format, standards and technologies of their creation, for the design and use of ontology-driven medical information systems is presented. Its functionality and the advantages of using in the process of ensuring the continuous professional development of doctors and pharmacists are described.Стаття присвячена питанню забезпечення якості медичної освіти, підвищення кваліфікації медичних кадрів і безперервного професійного розвитку лікарів та провізорів засобами сучасних інформаційно-комунікаційних технологій. Визна­чені переваги застосування онтологічного підходу до представлення знань у процесі створення і використання медичних інформаційних систем з метою надання доступу до максимально повного обсягу інформації шляхом інтероперабельної інтеграції та агрегації знання-орієнтованих ресурсів та інформаційних джерел. Наведений короткий аналіз існуючих онтологій медичного призначення (від колекцій вузькоспеціалізованих тематичних онтологій до національних термінологічних систем охорони здоров’я), що виявив низку недоліків та перешкод їх використання в системі сучасної медичної освіти в Україні. Визначена необхідність створення єдиного середовища інтероперабельної взаємодії з існуючими онтологічними рішеннями засобами уніфікованого інтерфейсу користувача для підвищення ефективності безперервного професійного розвитку лікарів та провізорів. Викладені основні аспекти розробки онтолого-керованих інформаційних систем, що можуть бути використані не лише при проектуванні і розробці структури, функціоналу та інтерфейсів медичних інформаційних систем, а й у процесі їх використання для вирішення практичних завдань. Представлений досвід застосування ІТ-ТОДОС, когнітивні програмно-інформаційні засоби якої забезпечують інтерактивну інтероперабельну темпоральну та семантичну синхронізацію інформаційних ресурсів незалежно від формату, стандартів і технологій їх створення, для розробки та використання онтолого-керованих медичних інформаційних систем, наведений її функціонал та переваги використання в процесі забезпечення безперервного професійного розвитку лікарів та провізорів

Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics

With the advent of mass spectrometry based proteomics, the identification of thousands of proteins has become commonplace in biology nowadays. Increasingly, efforts have also been invested toward the detection and localization of posttranslational modifications. It is furthermore common practice to quantify the identified entities, a task supported by a panel of different methods. Finally, the results can also be enriched with functional knowledge gained on the proteins, detecting for instance differentially expressed gene ontology terms or biological pathways. In this study, we review the resources, methods and tools available for the researcher to achieve such a quantitative functional analysis. These include statistics for the post-processing of identification and quantification results, online resources and public repositories. With a focus on free but user-friendly software, preferably also open-source, we provide a list of tools designed to help the researcher manage the vast amount of data generated. We also indicate where such applications currently remain lacking. Moreover, we stress the eventual pitfalls of every step of such studies. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.acceptedVersio

Correlation: Registers of Change

Chapter 4 analyses how Correlation approaches maintain a knowing human subject and a world of patterned regularity amenable to policy intervention. Here, the island emerges as a ‘correlational technology’ where changes are seen as early indicators of climate change. Central however, is an (onto)epistemology of inter-relation and correlation rather than one of linear cause-and-effect: we move from a temporal and spatial line of movement to one of synchronicity. Correlational modes are deployed for sensing global warming, rising sea levels and other shifting planetary conditions. As islands are reinterpellated as ‘living laboratories’, the authors argue that the island is seen as enabling the generation of onto-epistemologies operating on correlative not causal principles. In addition to such correlational practices as the evolutionary patterns of island life, there is the widespread celebration of Indigenous islanders’ correlational abilities, useful in the ‘forecasting of extreme weather conditions’. Such approaches have received a high-tech boost in the Anthropocene, taking the algorithmic form of the, ‘if this … then that’ logic associated with Big Data, the Internet of Things and the trope of the ‘smart island’. Here, prolific use of Big Data combined with extensive networks of sensors or tracking social media on islands enables rapid policy responsiveness. The authors demonstrate how working with islands as sites for understanding relational entanglements and feedbacks plays an important role in the generation and exponential development of Correlational onto-epistemologies in broader Anthropocene thinking

Training of Crisis Mappers and Map Production from Multi-sensor Data: Vernazza Case Study (Cinque Terre National Park, Italy)

This aim of paper is to presents the development of a multidisciplinary project carried out by the cooperation between Politecnico di Torino and ITHACA (Information Technology for Humanitarian Assistance, Cooperation and Action). The goal of the project was the training in geospatial data acquiring and processing for students attending Architecture and Engineering Courses, in order to start up a team of "volunteer mappers". Indeed, the project is aimed to document the environmental and built heritage subject to disaster; the purpose is to improve the capabilities of the actors involved in the activities connected in geospatial data collection, integration and sharing. The proposed area for testing the training activities is the Cinque Terre National Park, registered in the World Heritage List since 1997. The area was affected by flood on the 25th of October 2011. According to other international experiences, the group is expected to be active after emergencies in order to upgrade maps, using data acquired by typical geomatic methods and techniques such as terrestrial and aerial Lidar, close-range and aerial photogrammetry, topographic and GNSS instruments etc.; or by non conventional systems and instruments such us UAV, mobile mapping etc. The ultimate goal is to implement a WebGIS platform to share all the data collected with local authorities and the Civil Protectio

Ubiquitous Semantic Applications

As Semantic Web technology evolves many open areas emerge, which attract more research focus. In addition to quickly expanding Linked Open Data (LOD) cloud, various embeddable metadata formats (e.g. RDFa, microdata) are becoming more common. Corporations are already using existing Web of Data to create new technologies that were not possible before. Watson by IBM an artificial intelligence computer system capable of answering questions posed in natural language can be a great example. On the other hand, ubiquitous devices that have a large number of sensors and integrated devices are becoming increasingly powerful and fully featured computing platforms in our pockets and homes. For many people smartphones and tablet computers have already replaced traditional computers as their window to the Internet and to the Web. Hence, the management and presentation of information that is useful to a user is a main requirement for today’s smartphones. And it is becoming extremely important to provide access to the emerging Web of Data from the ubiquitous devices. In this thesis we investigate how ubiquitous devices can interact with the Semantic Web. We discovered that there are five different approaches for bringing the Semantic Web to ubiquitous devices. We have outlined and discussed in detail existing challenges in implementing this approaches in section 1.2. We have described a conceptual framework for ubiquitous semantic applications in chapter 4. We distinguish three client approaches for accessing semantic data using ubiquitous devices depending on how much of the semantic data processing is performed on the device itself (thin, hybrid and fat clients). These are discussed in chapter 5 along with the solution to every related challenge. Two provider approaches (fat and hybrid) can be distinguished for exposing data from ubiquitous devices on the Semantic Web. These are discussed in chapter 6 along with the solution to every related challenge. We conclude our work with a discussion on each of the contributions of the thesis and propose future work for each of the discussed approach in chapter 7

An Indoor Positioning System Based on Wearables for Ambient-Assisted Living

The urban population is growing at such a rate that by 2050 it is estimated that 84% of the world’s population will live in cities, with flats being the most common living place. Moreover, WiFi technology is present in most developed country urban areas, with a quick growth in developing countries. New Ambient-Assisted Living applications will be developed in the near future having user positioning as ground technology: elderly tele-care, energy consumption, security and the like are strongly based on indoor positioning information. We present an indoor positioning system for wearable devices based on WiFi fingerprinting. Smart-watch wearable devices are used to acquire the WiFi strength signals of the surrounding Wireless Access Points used to build an ensemble of Machine Learning classification algorithms. Once built, the ensemble algorithm is used to locate a user based on the WiFi strength signals provided by the wearable device. Experimental results for five different urban flats are reported, showing that the system is robust and reliable enough for locating a user at room level into his/her home. Another interesting characteristic of the presented system is that it does not require deployment of any infrastructure, and it is unobtrusive, the only device required for it to work is a smart-watch.This work has been partially funded by the Spanish Ministry of Economy and Competitiveness through the “Proyectos I + D Excelencia” programme (TIN2015-70202-P) and the “Redes de Excelencia” programme (TEC2015-71426-REDT), and from the Regional Government of Valencia (‘Proyectos de I + D para Grupos de Investigación Emergentes’ GV/2016/159). Special thanks to Víctor, Maricarmen, Inma and Daniel who lent their houses for performing the experiments