Document clustering is a text mining technique used to provide better document search and browsing in digital libraries or online corpora. A lot of research has been done on biomedical document clustering that is based on using existing ontology. But, associations and co-occurrences of the medical concepts are not well represented by using ontology. In this research, a vector representation of concepts of diseases and similarity measurement between concepts are proposed. They identify the closest concepts of diseases in the context of a corpus. Each document is represented by using the vector space model. A weight scheme is proposed to consider both local content and associations between concepts. A Self-Organizing Map is used as document clustering algorithm. The vector projection and visualization features of SOM enable visualization and analysis of the clusters distributions and relationships on the two dimensional space. The experimental results show that the proposed document clustering framework generates meaningful clusters and facilitate visualization of the clusters based on the concepts of diseases.

In 1992 Tom Gruber proposed the following definition "An ontology is a specification of a conceptualization" [4]. Several variants exist that usually add adjectives further describing the specification (e.g., "formal", "explicit") or the conceptualization (e.g., "shared") (see discussion of related work in Section 5). These definitions are not helpful because they violate one of the basic rules for good definitions: the defining statement (the definiens) should be clearer than the term that is defined (the definiendum). As long as "conceptualization" is murkier than "ontology", any attempt of defining "ontology" as a kind of "specification of a conceptualization" is an intellectual placebo: it makes us feel like it provides a better grasp of the nature of ontologies, but there is no intellectual progress, because it lacks explanatory value (see Section 2 for details). Given the difficulties in defining "ontology" one may come to the conclusion that a proper definition is not really needed.

The sharing of ontologies between diverse communities of discourse allows them to compare their own information structures with that of other communities that share a common terminology and semantics - ontology sharing facilitates interoperability between online knowledge organizations. This paper demonstrates how ontology sharing is formalizable within the conceptual knowledge model of Information Flow (IF). Information Flow indirectly represents sharing through a specifiable, ontology extension hierarchy augmented with synonymic type equivalencing - two ontologies share terminology and meaning through a common generic ontology that each extends. Using the paradigm of participant community ontologies formalized as IF logics, a common shared extensible ontology formalized as an IF theory, participant community specification links from the common ontology to the participating community ontology formalizable as IF theory interpretations, this paper argues that ontology sharing is concentrated in a virtual ontology of community connections, and demonstrates how this virtual ontology is computable as the fusion of the participant ontologies - the quotient of the sum of the participant ontologies modulo the ontological sharing structure.

It is crucial to provide compatible treatment schemes for a disease according to various symptoms at different stages. However, most classification methods might be ineffective in accurately classifying a disease that holds the characteristics of multiple treatment stages, various symptoms, and multi-pathogenesis. Moreover, there are limited exchanges and cooperative actions in disease diagnoses and treatments between different departments and hospitals. Thus, when new diseases occur with atypical symptoms, inexperienced doctors might have difficulty in identifying them promptly and accurately. Therefore, to maximize the utilization of the advanced medical technology of developed hospitals and the rich medical knowledge of experienced doctors, a Disease Diagnosis and Treatment Recommendation System (DDTRS) is proposed in this paper. First, to effectively identify disease symptoms more accurately, a Density-Peaked Clustering Analysis (DPCA) algorithm is introduced for disease-symptom clustering. In addition, association analyses on Disease-Diagnosis (D-D) rules and Disease-Treatment (D-T) rules are conducted by the Apriori algorithm separately. The appropriate diagnosis and treatment schemes are recommended for patients and inexperienced doctors, even if they are in a limited therapeutic environment. Moreover, to reach the goals of high performance and low latency response, we implement a parallel solution for DDTRS using the Apache Spark cloud platform. Extensive experimental results demonstrate that the proposed DDTRS realizes disease-symptom clustering effectively and derives disease treatment recommendations intelligently and accurately.

This chapter discusses the institutional approach for organizing and maintaining ontologies. The theory of institutions was named and initially developed by Joseph Goguen and Rod Burstall. This theory, a metatheory based on category theory, regards ontologies as logical theories or local logics. The theory of institutions uses the category-theoretic ideas of fibrations and indexed categories to develop logical theories. Institutions unite the lattice approach of Formal Concept Analysis of Ganter and Wille with the distributed logic of Information Flow of Barwise and Seligman. The institutional approach incorporates locally the lattice of theories idea of Sowa from the theory of knowledge representation. The Information Flow Framework, which was initiated within the IEEE Standard Upper Ontology project, uses the institutional approach in its applied aspect for the comparison, semantic integration and maintenance of ontologies. This chapter explains the central ideas of the institutional approach to ontologies in a careful and detailed manner.

This paper summarizes some of the technical background, research ideas, and possible development strategies for achieving machine common sense. Machine common sense has long been a critical-but-missing component of Artificial Intelligence (AI). Recent advances in machine learning have resulted in new AI capabilities, but in all of these applications, machine reasoning is narrow and highly specialized. Developers must carefully train or program systems for every situation. General commonsense reasoning remains elusive. The absence of common sense prevents intelligent systems from understanding their world, behaving reasonably in unforeseen situations, communicating naturally with people, and learning from new experiences. Its absence is perhaps the most significant barrier between the narrowly focused AI applications we have today and the more general, human-like AI systems we would like to build in the future. Machine common sense remains a broad, potentially unbounded problem in AI. There are a wide range of strategies that could be employed to make progress on this difficult challenge. This paper discusses two diverse strategies for focusing development on two different machine commonsense services: (1) a service that learns from experience, like a child, to construct computational models that mimic the core domains of child cognition for objects (intuitive physics), agents (intentional actors), and places (spatial navigation); and (2) service that learns from reading the Web, like a research librarian, to construct a commonsense knowledge repository capable of answering natural language and image-based questions about commonsense phenomena.

Conceptual Knowledge Markup Language (CKML) is an application of XML. Earlier versions of CKML followed rather exclusively the philosophy of Conceptual Knowledge Processing (CKP), a principled approach to knowledge representation and data analysis that "advocates methods and instruments of conceptual knowledge processing which support people in their rational thinking, judgment and acting and promote critical discussion." The new version of CKML continues to follow this approach, but also incorporates various principles, insights and techniques from Information Flow (IF), the logical design of distributed systems. Among other things, this allows diverse communities of discourse to compare their own information structures, as coded in logical theories, with that of other communities that share a common generic ontology. CKML incorporates the CKP ideas of concept lattice and formal context, along with the IF ideas of classification (= formal context), infomorphism, theory, interpretation and local logic. Ontology Markup Language (OML), a subset of CKML that is a self-sufficient markup language in its own right, follows the principles and ideas of Conceptual Graphs (CG). OML is used for structuring the specifications and axiomatics of metadata into ontologies. OML incorporates the CG ideas of concept, conceptual relation, conceptual graph, conceptual context, participants and ontology. The link from OML to CKML is the process of conceptual scaling, which is the interpretive transformation of ontologically structured knowledge to conceptual structured knowledge.

We introduce an extension to the Protégé ontology editor, which allows for discovering concept definitions, which are not explicitly present in axioms, but are logically implied by an ontology. The plugin supports ontologies formulated in the Description Logic EL, which underpins the OWL 2 EL profile of the Web Ontology Language and despite its limited expressiveness captures most of the biomedical ontologies published on the Web. The developed tool allows to verify whether a concept can be defined using a vocabulary of interest specified by a user. In particular, it allows to decide whether some vocabulary items can be omitted in a formulation of a complex concept. The corresponding definitions are presented to the user and are provided with explanations generated by an ontology reasoner.

This paper discusses an axiomatic approach for the integration of ontologies, an approach that extends to first order logic a previous approach (Kent 2000) based on information flow. This axiomatic approach is represented in the Information Flow Framework (IFF), a metalevel framework for organizing the information that appears in digital libraries, distributed databases and ontologies (Kent 2001). The paper argues that the integration of ontologies is the two-step process of alignment and unification. Ontological alignment consists of the sharing of common terminology and semantics through a mediating ontology. Ontological unification, concentrated in a virtual ontology of community connections, is fusion of the alignment diagram of participant community ontologies - the quotient of the sum of the participant portals modulo the ontological alignment structure.

This paper presents a novel SHOI tableau calculus which incorporates algebraic reasoning for deciding ontology consistency. Numerical restrictions imposed by nominals, existential and universal restrictions are encoded into a set of linear inequalities. Column generation and branch-and-price algorithms are used to solve these inequalities. Our preliminary experiments indicate that this calculus performs better on SHOI ontologies than standard tableau methods.