The Plant Ontology facilitates comparisons of plant development stages across species

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

A Knowledge-based Integrative Modeling Approach for <em>In-Silico</em> Identification of Mechanistic Targets in Neurodegeneration with Focus on Alzheimer’s Disease

Dementia is the progressive decline in cognitive function due to damage or disease in the body beyond what might be expected from normal aging. Based on neuropathological and clinical criteria, dementia includes a spectrum of diseases, namely Alzheimer's dementia, Parkinson's dementia, Lewy Body disease, Alzheimer's dementia with Parkinson's, Pick's disease, Semantic dementia, and large and small vessel disease. It is thought that these disorders result from a combination of genetic and environmental risk factors. Despite accumulating knowledge that has been gained about pathophysiological and clinical characteristics of the disease, no coherent and integrative picture of molecular mechanisms underlying neurodegeneration in Alzheimer’s disease is available. Existing drugs only offer symptomatic relief to the patients and lack any efficient disease-modifying effects. The present research proposes a knowledge-based rationale towards integrative modeling of disease mechanism for identifying potential candidate targets and biomarkers in Alzheimer’s disease. Integrative disease modeling is an emerging knowledge-based paradigm in translational research that exploits the power of computational methods to collect, store, integrate, model and interpret accumulated disease information across different biological scales from molecules to phenotypes. It prepares the ground for transitioning from ‘descriptive’ to “mechanistic” representation of disease processes. The proposed approach was used to introduce an integrative framework, which integrates, on one hand, extracted knowledge from the literature using semantically supported text-mining technologies and, on the other hand, primary experimental data such as gene/protein expression or imaging readouts. The aim of such a hybrid integrative modeling approach was not only to provide a consolidated systems view on the disease mechanism as a whole but also to increase specificity and sensitivity of the mechanistic model by providing disease-specific context. This approach was successfully used for correlating clinical manifestations of the disease to their corresponding molecular events and led to the identification and modeling of three important mechanistic components underlying Alzheimer’s dementia, namely the CNS, the immune system and the endocrine components. These models were validated using a novel in-silico validation method, namely biomarker-guided pathway analysis and a pathway-based target identification approach was introduced, which resulted in the identification of the MAPK signaling pathway as a potential candidate target at the crossroad of the triad components underlying disease mechanism in Alzheimer’s dementia

Semantic enrichment for enhancing LAM data and supporting digital humanities. Review article

With the rapid development of the digital humanities (DH) field, demands for historical and cultural heritage data have generated deep interest in the data provided by libraries, archives, and museums (LAMs). In order to enhance LAM data’s quality and discoverability while enabling a self-sustaining ecosystem, “semantic enrichment” becomes a strategy increasingly used by LAMs during recent years. This article introduces a number of semantic enrichment methods and efforts that can be applied to LAM data at various levels, aiming to support deeper and wider exploration and use of LAM data in DH research. The real cases, research projects, experiments, and pilot studies shared in this article demonstrate endless potential for LAM data, whether they are structured, semi-structured, or unstructured, regardless of what types of original artifacts carry the data. Following their roadmaps would encourage more effective initiatives and strengthen this effort to maximize LAM data’s discoverability, use- and reuse-ability, and their value in the mainstream of DH and Semantic Web

Controlled vocabularies and semantics in systems biology

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in structured formats, but there is an increasing need to provide an additional semantic layer. Semantic information adds meaning to components of structured descriptions to help identify and interpret them unambiguously. Ontologies are one of the tools frequently used for this purpose. We describe here three ontologies created specifically to address the needs of the systems biology community. The Systems Biology Ontology (SBO) provides semantic information about the model components. The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of systems biology models, their characterization and interrelationships. The Terminology for the Description of Dynamics (TEDDY) categorizes dynamical features of the simulation results and general systems behavior. The provision of semantic information extends a model's longevity and facilitates its reuse. It provides useful insight into the biology of modeled processes, and may be used to make informed decisions on subsequent simulation experiments

Contextual Analysis of Large-Scale Biomedical Associations for the Elucidation and Prioritization of Genes and their Roles in Complex Disease

Vast amounts of biomedical associations are easily accessible in public resources, spanning gene-disease associations, tissue-specific gene expression, gene function and pathway annotations, and many other data types. Despite this mass of data, information most relevant to the study of a particular disease remains loosely coupled and difficult to incorporate into ongoing research. Current public databases are difficult to navigate and do not interoperate well due to the plethora of interfaces and varying biomedical concept identifiers used. Because no coherent display of data within a specific problem domain is available, finding the latent relationships associated with a disease of interest is impractical. This research describes a method for extracting the contextual relationships embedded within associations relevant to a disease of interest. After applying the method to a small test data set, a large-scale integrated association network is constructed for application of a network propagation technique that helps uncover more distant latent relationships. Together these methods are adept at uncovering highly relevant relationships without any a priori knowledge of the disease of interest. The combined contextual search and relevance methods power a tool which makes pertinent biomedical associations easier to find, easier to assimilate into ongoing work, and more prominent than currently available databases. Increasing the accessibility of current information is an important component to understanding high-throughput experimental results and surviving the data deluge

Semantic technologies: from niche to the mainstream of Web 3? A comprehensive framework for web Information modelling and semantic annotation

Context: Web information technologies developed and applied in the last decade have considerably changed the way web applications operate and have revolutionised information management and knowledge discovery. Social technologies, user-generated classification schemes and formal semantics have a far-reaching sphere of influence. They promote collective intelligence, support interoperability, enhance sustainability and instigate innovation. Contribution: The research carried out and consequent publications follow the various paradigms of semantic technologies, assess each approach, evaluate its efficiency, identify the challenges involved and propose a comprehensive framework for web information modelling and semantic annotation, which is the thesis’ original contribution to knowledge. The proposed framework assists web information modelling, facilitates semantic annotation and information retrieval, enables system interoperability and enhances information quality. Implications: Semantic technologies coupled with social media and end-user involvement can instigate innovative influence with wide organisational implications that can benefit a considerable range of industries. The scalable and sustainable business models of social computing and the collective intelligence of organisational social media can be resourcefully paired with internal research and knowledge from interoperable information repositories, back-end databases and legacy systems. Semantified information assets can free human resources so that they can be used to better serve business development, support innovation and increase productivity

Creation, Enrichment and Application of Knowledge Graphs

The world is in constant change, and so is the knowledge about it. Knowledge-based systems - for example, online encyclopedias, search engines and virtual assistants - are thus faced with the constant challenge of collecting this knowledge and beyond that, to understand it and make it accessible to their users. Only if a knowledge-based system is capable of this understanding - that is, it is capable of more than just reading a collection of words and numbers without grasping their semantics - it can recognise relevant information and make it understandable to its users. The dynamics of the world play a unique role in this context: Events of various kinds which are relevant to different communities are shaping the world, with examples ranging from the coronavirus pandemic to the matches of a local football team. Vital questions arise when dealing with such events: How to decide which events are relevant, and for whom? How to model these events, to make them understood by knowledge-based systems? How is the acquired knowledge returned to the users of these systems? A well-established concept for making knowledge understandable by knowledge-based systems are knowledge graphs, which contain facts about entities (persons, objects, locations, ...) in the form of graphs, represent relationships between these entities and make the facts understandable by means of ontologies. This thesis considers knowledge graphs from three different perspectives: (i) Creation of knowledge graphs: Even though the Web offers a multitude of sources that provide knowledge about the events in the world, the creation of an event-centric knowledge graph requires recognition of such knowledge, its integration across sources and its representation. (ii) Knowledge graph enrichment: Knowledge of the world seems to be infinite, and it seems impossible to grasp it entirely at any time. Therefore, methods that autonomously infer new knowledge and enrich the knowledge graphs are of particular interest. (iii) Knowledge graph interaction: Even having all knowledge of the world available does not have any value in itself; in fact, there is a need to make it accessible to humans. Based on knowledge graphs, systems can provide their knowledge with their users, even without demanding any conceptual understanding of knowledge graphs from them. For this to succeed, means for interaction with the knowledge are required, hiding the knowledge graph below the surface. In concrete terms, I present EventKG - a knowledge graph that represents the happenings in the world in 15 languages - as well as Tab2KG - a method for understanding tabular data and transforming it into a knowledge graph. For the enrichment of knowledge graphs without any background knowledge, I propose HapPenIng, which infers missing events from the descriptions of related events. I demonstrate means for interaction with knowledge graphs at the example of two web-based systems (EventKG+TL and EventKG+BT) that enable users to explore the happenings in the world as well as the most relevant events in the lives of well-known personalities.Die Welt befindet sich im steten Wandel, und mit ihr das Wissen über die Welt. Wissensbasierte Systeme - seien es Online-Enzyklopädien, Suchmaschinen oder Sprachassistenten - stehen somit vor der konstanten Herausforderung, dieses Wissen zu sammeln und darüber hinaus zu verstehen, um es so Menschen verfügbar zu machen. Nur wenn ein wissensbasiertes System in der Lage ist, dieses Verständnis aufzubringen - also zu mehr in der Lage ist, als auf eine unsortierte Ansammlung von Wörtern und Zahlen zurückzugreifen, ohne deren Bedeutung zu erkennen -, kann es relevante Informationen erkennen und diese seinen Nutzern verständlich machen. Eine besondere Rolle spielt hierbei die Dynamik der Welt, die von Ereignissen unterschiedlichster Art geformt wird, die für unterschiedlichste Bevölkerungsgruppe relevant sind; Beispiele hierfür erstrecken sich von der Corona-Pandemie bis hin zu den Spielen lokaler Fußballvereine. Doch stellen sich hierbei bedeutende Fragen: Wie wird die Entscheidung getroffen, ob und für wen derlei Ereignisse relevant sind? Wie sind diese Ereignisse zu modellieren, um von wissensbasierten Systemen verstanden zu werden? Wie wird das angeeignete Wissen an die Nutzer dieser Systeme zurückgegeben? Ein bewährtes Konzept, um wissensbasierten Systemen das Wissen verständlich zu machen, sind Wissensgraphen, die Fakten über Entitäten (Personen, Objekte, Orte, ...) in der Form von Graphen sammeln, Zusammenhänge zwischen diesen Entitäten darstellen, und darüber hinaus anhand von Ontologien verständlich machen. Diese Arbeit widmet sich der Betrachtung von Wissensgraphen aus drei aufeinander aufbauenden Blickwinkeln: (i) Erstellung von Wissensgraphen: Auch wenn das Internet eine Vielzahl an Quellen anbietet, die Wissen über Ereignisse in der Welt bereithalten, so erfordert die Erstellung eines ereigniszentrierten Wissensgraphen, dieses Wissen zu erkennen, miteinander zu verbinden und zu repräsentieren. (ii) Anreicherung von Wissensgraphen: Das Wissen über die Welt scheint schier unendlich und so scheint es unmöglich, dieses je vollständig (be)greifen zu können. Von Interesse sind also Methoden, die selbstständig das vorhandene Wissen erweitern. (iii) Interaktion mit Wissensgraphen: Selbst alles Wissen der Welt bereitzuhalten, hat noch keinen Wert in sich selbst, vielmehr muss dieses Wissen Menschen verfügbar gemacht werden. Basierend auf Wissensgraphen, können wissensbasierte Systeme Nutzern ihr Wissen darlegen, auch ohne von diesen ein konzeptuelles Verständis von Wissensgraphen abzuverlangen. Damit dies gelingt, sind Möglichkeiten der Interaktion mit dem gebotenen Wissen vonnöten, die den genutzten Wissensgraphen unter der Oberfläche verstecken. Konkret präsentiere ich EventKG - einen Wissensgraphen, der Ereignisse in der Welt repräsentiert und in 15 Sprachen verfügbar macht, sowie Tab2KG - eine Methode, um in Tabellen enthaltene Daten anhand von Hintergrundwissen zu verstehen und in Wissensgraphen zu wandeln. Zur Anreicherung von Wissensgraphen ohne weiteres Hintergrundwissen stelle ich HapPenIng vor, das fehlende Ereignisse aus den vorliegenden Beschreibungen ähnlicher Ereignisse inferiert. Interaktionsmöglichkeiten mit Wissensgraphen demonstriere ich anhand zweier web-basierter Systeme (EventKG+TL und EventKG+BT), die Nutzern auf einfache Weise die Exploration von Geschehnissen in der Welt sowie der wichtigsten Ereignisse in den Leben bekannter Persönlichkeiten ermöglichen

Semantic adaptability for the systems interoperability

In the current global and competitive business context, it is essential that enterprises adapt their knowledge resources in order to smoothly interact and collaborate with others. However, due to the existent multiculturalism of people and enterprises, there are different representation views of business processes or products, even inside a same domain. Consequently, one of the main problems found in the interoperability between enterprise systems and applications is related to semantics. The integration and sharing of enterprises knowledge to build a common lexicon, plays an important role to the semantic adaptability of the information systems. The author proposes a framework to support the development of systems to manage dynamic semantic adaptability resolution. It allows different organisations to participate in a common knowledge base building, letting at the same time maintain their own views of the domain, without compromising the integration between them. Thus, systems are able to be aware of new knowledge, and have the capacity to learn from it and to manage its semantic interoperability in a dynamic and adaptable way. The author endorses the vision that in the near future, the semantic adaptability skills of the enterprise systems will be the booster to enterprises collaboration and the appearance of new business opportunities