Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

The Computer Science Ontology: A Large-Scale Taxonomy of Research Areas

Ontologies of research areas are important tools for characterising, exploring, and analysing the research landscape. Some fields of research are comprehensively described by large-scale taxonomies, e.g., MeSH in Biology and PhySH in Physics. Conversely, current Computer Science taxonomies are coarse-grained and tend to evolve slowly. For instance, the ACM classification scheme contains only about 2K research topics and the last version dates back to 2012. In this paper, we introduce the Computer Science Ontology (CSO), a large-scale, automatically generated ontology of research areas, which includes about 26K topics and 226K semantic relationships. It was created by applying the Klink-2 algorithm on a very large dataset of 16M scientific articles. CSO presents two main advantages over the alternatives: i) it includes a very large number of topics that do not appear in other classifications, and ii) it can be updated automatically by running Klink-2 on recent corpora of publications. CSO powers several tools adopted by the editorial team at Springer Nature and has been used to enable a variety of solutions, such as classifying research publications, detecting research communities, and predicting research trends. To facilitate the uptake of CSO we have developed the CSO Portal, a web application that enables users to download, explore, and provide granular feedback on CSO at different levels. Users can use the portal to rate topics and relationships, suggest missing relationships, and visualise sections of the ontology. The portal will support the publication of and access to regular new releases of CSO, with the aim of providing a comprehensive resource to the various communities engaged with scholarly data

Ontology and medical terminology: Why description logics are not enough

Ontology is currently perceived as the solution of first resort for all problems related to biomedical terminology, and the use of description logics is seen as a minimal requirement on adequate ontology-based systems. Contrary to common conceptions, however, description logics alone are not able to prevent incorrect representations; this is because they do not come with a theory indicating what is computed by using them, just as classical arithmetic does not tell us anything about the entities that are added or subtracted. In this paper we shall show that ontology is indeed an essential part of any solution to the problems of medical terminology – but only if it is understood in the right sort of way. Ontological engineering, we shall argue, should in every case go hand in hand with a sound ontological theory

Semantic units: organizing knowledge graphs into semantically meaningful units of representation

Background In today’s landscape of data management, the importance of knowledge graphs and ontologies is escalating as critical mechanisms aligned with the FAIR Guiding Principles—ensuring data and metadata are Findable, Accessible, Interoperable, and Reusable. We discuss three challenges that may hinder the effective exploitation of the full potential of FAIR knowledge graphs. Results We introduce “semantic units” as a conceptual solution, although currently exemplified only in a limited prototype. Semantic units structure a knowledge graph into identifiable and semantically meaningful subgraphs by adding another layer of triples on top of the conventional data layer. Semantic units and their subgraphs are represented by their own resource that instantiates a corresponding semantic unit class. We distinguish statement and compound units as basic categories of semantic units. A statement unit is the smallest, independent proposition that is semantically meaningful for a human reader. Depending on the relation of its underlying proposition, it consists of one or more triples. Organizing a knowledge graph into statement units results in a partition of the graph, with each triple belonging to exactly one statement unit. A compound unit, on the other hand, is a semantically meaningful collection of statement and compound units that form larger subgraphs. Some semantic units organize the graph into different levels of representational granularity, others orthogonally into different types of granularity trees or different frames of reference, structuring and organizing the knowledge graph into partially overlapping, partially enclosed subgraphs, each of which can be referenced by its own resource. Conclusions Semantic units, applicable in RDF/OWL and labeled property graphs, offer support for making statements about statements and facilitate graph-alignment, subgraph-matching, knowledge graph profiling, and for management of access restrictions to sensitive data. Additionally, we argue that organizing the graph into semantic units promotes the differentiation of ontological and discursive information, and that it also supports the differentiation of multiple frames of reference within the graph

Combining link and content-based information in a Bayesian inference model for entity search

An architectural model of a Bayesian inference network to support entity search in semantic knowledge bases is presented. The model supports the explicit combination of primitive data type and object-level semantics under a single computational framework. A flexible query model is supported capable to reason with the availability of simple semantics in querie

A Review on Information Accessing Systems Based on Fuzzy Linguistic Modelling

This paper presents a survey of some fuzzy linguistic information access systems. The review shows information retrieval systems, filtering systems, recommender systems, and web quality evaluation tools, which are based on tools of fuzzy linguistic modelling. The fuzzy linguistic modelling allows us to represent and manage the subjectivity, vagueness and imprecision that is intrinsic and characteristic of the processes of information searching, and, in such a way, the developed systems allow users the access to quality information in a flexible and user-adapted way.European Union (EU) TIN2007-61079 PET2007-0460Ministry of Public Works 90/07Excellence Andalusian Project TIC529

Sensemaking on the Pragmatic Web: A Hypermedia Discourse Perspective

The complexity of the dilemmas we face on an organizational, societal and global scale forces us into sensemaking activity. We need tools for expressing and contesting perspectives flexible enough for real time use in meetings, structured enough to help manage longer term memory, and powerful enough to filter the complexity of extended deliberation and debate on an organizational or global scale. This has been the motivation for a programme of basic and applied action research into Hypermedia Discourse, which draws on research in hypertext, information visualization, argumentation, modelling, and meeting facilitation. This paper proposes that this strand of work shares a key principle behind the Pragmatic Web concept, namely, the need to take seriously diverse perspectives and the processes of meaning negotiation. Moreover, it is argued that the hypermedia discourse tools described instantiate this principle in practical tools which permit end-user control over modelling approaches in the absence of consensus

Mental distress detection and triage in forum posts: the LT3 CLPsych 2016 shared task system

This paper describes the contribution of LT3 for the CLPsych 2016 Shared Task on automatic triage of mental health forum posts. Our systems use multiclass Support Vector Machines (SVM), cascaded binary SVMs and ensembles with a rich feature set. The best systems obtain macro-averaged F-scores of 40% on the full task and 80% on the green versus alarming distinction. Multiclass SVMs with all features score best in terms of F-score, whereas feature filtering with bi-normal separation and classifier ensembling are found to improve recall of alarming posts