Designing novel abstraction networks for ontology summarization and quality assurance

Biomedical ontologies are complex knowledge representation systems. Biomedical ontologies support interdisciplinary research, interoperability of medical systems, and Electronic Healthcare Record (EHR) encoding. Ontologies represent knowledge using concepts (entities) linked by relationships. Ontologies may contain hundreds of thousands of concepts and millions of relationships. For users, the size and complexity of ontologies make it difficult to comprehend “the big picture” of an ontology\u27s content. For ontology editors, size and complexity make it difficult to uncover errors and inconsistencies. Errors in an ontology will ultimately affect applications that utilize the ontology. In prior studies abstraction networks (AbNs) were developed to provide a compact summary of an ontology\u27s content and structure. AbNs have been shown to successfully support ontology summarization and quality assurance (QA), e.g., for SNOMED CT and NCIt. Despite the success of these previous studies, several major, unaddressed issues affect the applicability and usability of AbNs. This thesis is broken into five major parts, each addressing one issue. The first part of this dissertation addresses the scalability of AbN-based QA techniques to large SNOMED CT hierarchies. Previous studies focused on relatively small hierarchies. The QA techniques developed for these small hierarchies do not scale to large hierarchies, e.g., Procedure and Clinical finding. A new type of AbN, called a subtaxonomy, is introduced to address this problem. Subtaxonomies summarize a subset of an ontology\u27s content. Several types of subtaxonomies and subtaxonomy-based QA studies are discussed. The second part of this dissertation addresses the need for summarization and QA methods for the twelve SNOMED CT hierarchies with no lateral relationships. Previously developed SNOMED CT AbN derivation methodologies, which require lateral relationships, cannot be applied to these hierarchies. The Tribal Abstraction Network (TAN) is a new type of AbN derived using only hierarchical relationships. A TAN-based QA methodology is introduced and the results of a QA review of the Observable entity hierarchy are reported. The third part focuses on the development of generic AbN derivation methods that are applicable to groups of structurally similar ontologies, e.g., those developed in the Web Ontology Language (OWL) format. Previously, AbN derivation techniques were applicable to only a single ontology at a time. AbNs that are applicable to many OWL ontologies are introduced, a preliminary study on OWL AbN granularity is reported on, and the results of several QA studies are presented. The fourth part describes Diff Abstraction Networks, which summarize and visualize the structural differences between two ontology releases. Diff Area Taxonomy and Diff Partial-area Taxonomy derivation methodologies are introduced and Diff Partial-area taxonomies are derived for three OWL ontologies. The Diff Abstraction Network approach is compared to the traditional ontology diff approach. Lastly, tools for deriving and visualizing AbNs are described. The Biomedical Layout Utility Framework is introduced to support the automatic creation, visualization, and exploration of abstraction networks for SNOMED CT and OWL ontologies

Using structural and semantic methodologies to enhance biomedical terminologies

Biomedical terminologies and ontologies underlie various Health Information Systems (HISs), Electronic Health Record (EHR) Systems, Health Information Exchanges (HIEs) and health administrative systems. Moreover, the proliferation of interdisciplinary research efforts in the biomedical field is fueling the need to overcome terminological barriers when integrating knowledge from different fields into a unified research project. Therefore well-developed and well-maintained terminologies are in high demand. Most of the biomedical terminologies are large and complex, which makes it impossible for human experts to manually detect and correct all errors and inconsistencies. Automated and semi-automated Quality Assurance methodologies that focus on areas that are more likely to contain errors and inconsistencies are therefore important. In this dissertation, structural and semantic methodologies are used to enhance biomedical terminologies. The dissertation work is divided into three major parts. The first part consists of structural auditing techniques for the Semantic Network of the Unified Medical Language System (UMLS), which serves as a vocabulary knowledge base for biomedical research in various applications. Research techniques are presented on how to automatically identify and prevent erroneous semantic type assignments to concepts. The Web-based adviseEditor system is introduced to help UMLS editors to make correct multiple semantic type assignments to concepts. It is made available to the National Library of Medicine for future use in maintaining the UMLS. The second part of this dissertation is on how to enhance the conceptual content of SNOMED CT by methods of semantic harmonization. By 2015, SNOMED will become the standard terminology for EH R encoding of diagnoses and problem lists. In order to enrich the semantics and coverage of SNOMED CT for clinical and research applications, the problem of semantic harmonization between SNOMED CT and six reference terminologies is approached by 1) comparing the vertical density of SNOM ED CT with the reference terminologies to find potential concepts for export and import; and 2) categorizing the relationships between structurally congruent concepts from pairs of terminologies, with SNOMED CT being one terminology in the pair. Six kinds of configurations are observed, e.g., alternative classifications, and suggested synonyms. For each configuration, a corresponding solution is presented for enhancing one or both of the terminologies. The third part applies Quality Assurance techniques based on “Abstraction Networks” to biomedical ontologies in BioPortal. The National Center for Biomedical Ontology provides B ioPortal as a repository of over 350 biomedical ontologies covering a wide range of domains. It is extremely difficult to design a new Quality Assurance methodology for each ontology in BioPortal. Fortunately, groups of ontologies in BioPortal share common structural features. Thus, they can be grouped into families based on combinations of these features. A uniform Quality Assurance methodology design for each family will achieve improved efficiency, which is critical with the limited Quality Assurance resources available to most ontology curators. In this dissertation, a family-based framework covering 186 BioPortal ontologies and accompanying Quality Assurance methods based on abstraction networks are presented to tackle this problem

Applications of big knowledge summarization

Advanced technologies have resulted in the generation of large amounts of data ( Big Data ). The Big Knowledge derived from Big Data could be beyond humans\u27 ability of comprehension, which will limit the effective and innovative use of Big Knowledge repository. Biomedical ontologies, which play important roles in biomedical information systems, constitute one kind of Big Knowledge repository. Biomedical ontologies typically consist of domain knowledge assertions expressed by the semantic connections between tens of thousands of concepts. Without some high-level visual representation of Big Knowledge in biomedical ontologies, humans cannot grasp the big picture of those ontologies. Such Big Knowledge orientation is required for the proper maintenance of ontologies and their effective use. This dissertation is addressing the Big Knowledge challenge - How to enable humans to use Big Knowledge correctly and effectively (referred to as the Big Knowledge to Use (BK2U) problem) - with a focus on biomedical ontologies. In previous work, Abstraction Networks (AbNs) have been demonstrated successful for the summarization, visualization and quality assurance (QA) of biomedical ontologies. Based on the previous research, this dissertation introduces new AbNs of various granularities for Big Knowledge summarization and extends the applications of AbNs. This dissertation consists of three main parts. The first part introduces two advanced AbNs. One is the weighted aggregate partial-area taxonomy with a parameter to flexibly control the summarization granularity. The second is the Ingredient Abstraction Network (IAbN) for the National Drug File - Reference Terminology (NDF-RT) Chemical Ingredients hierarchy, for which the previously developed AbNs for hierarchies with outgoing relationships, are not applicable. Since NDF-RT\u27s Chemical Ingredients hierarchy has no outgoing relationships. The second part describes applications of the two advanced AbNs. A study utilizing the weighted aggregate partial-area taxonomy for the identification of major topics in SNOMED CT\u27s Specimen hierarchy is reported. A multi-layer interactive visualization system of required granularity for ontology comprehension, based on the weighted aggregate partial-area taxonomy, is demonstrated to comprehend the Neoplasm subhierarchy of National Cancer Institute thesaurus (NCIt). The IAbN is applied for drug-drug interaction (DDI) discovery. The third part reports eight family-based QA studies on NCIt\u27s Neoplasm, Gene, and Biological Process hierarchies, SNOMED CT\u27s Infectious disease hierarchy, the Chemical Entities of Biological Interest ontology, and the Chemical Ingredients hierarchy in NDF-RT. There is no one-size-fits-all QA method and it is impossible to find a QA method for each individual ontology. Hence, family-based QA is an effective way, i.e., one QA technique could be applicable to a whole family of structurally similar ontologies. The results of these studies demonstrate that complex concepts and uncommonly modeled concepts are more likely to have errors. Furthermore, the three studies on overlapping concepts in partial-area taxonomies reported in this dissertation combined with previous three studies prove the success of overlapping concepts as a QA methodology for a whole family of 76 similar ontologies in BioPortal

Enrichment of ontologies using machine learning and summarization

Biomedical ontologies are structured knowledge systems in biomedicine. They play a major role in enabling precise communications in support of healthcare applications, e.g., Electronic Healthcare Records (EHR) systems. Biomedical ontologies are used in many different contexts to facilitate information and knowledge management. The most widely used clinical ontology is the SNOMED CT. Placing a new concept into its proper position in an ontology is a fundamental task in its lifecycle of curation and enrichment. A large biomedical ontology, which typically consists of many tens of thousands of concepts and relationships, can be viewed as a complex network with concepts as nodes and relationships as links. This large-size node-link diagram can easily become overwhelming for humans to understand or work with. Adding concepts is a challenging and time-consuming task that requires domain knowledge and ontology skills. IS-A links (aka subclass links) are the most important relationships of an ontology, enabling the inheritance of other relationships. The position of a concept, represented by its IS-A links to other concepts, determines how accurately it is modeled. Therefore, considering as many parent candidate concepts as possible leads to better modeling of this concept. Traditionally, curators rely on classifiers to place concepts into ontologies. However, this assumes the accurate relationship modeling of the new concept as well as the existing concepts. Since many concepts in existing ontologies, are underspecified in terms of their relationships, the placement by classifiers may be wrong. In cases where the curator does not manually check the automatic placement by classifier programs, concepts may end up in wrong positions in the IS-A hierarchy. A user searching for a concept, without knowing its precise name, would not find it in its expected location. Automated or semi-automated techniques that can place a concept or narrow down the places where to insert it, are highly desirable. Hence, this dissertation is addressing the problem of concept placement by automatically identifying IS-A links and potential parent concepts correctly and effectively for new concepts, with the assistance of two powerful techniques, Machine Learning (ML) and Abstraction Networks (AbNs). Modern neural networks have revolutionized Machine Learning in vision and Natural Language Processing (NLP). They also show great promise for ontology-related tasks, including ontology enrichment, i.e., insertion of new concepts. This dissertation presents research using ML and AbNs to achieve knowledge enrichment of ontologies. Abstraction networks (AbNs), are compact summary networks that preserve a significant amount of the semantics and structure of the underlying ontologies. An Abstraction Network is automatically derived from the ontology itself. It consists of nodes, where each node represents a set of concepts that are similar in their structure and semantics. Various kinds of AbNs have been previously developed by the Structural Analysis of Biomedical Ontologies Center (SABOC) to support the summarization, visualization, and quality assurance (QA) of biomedical ontologies. Two basic kinds of AbNs are the Area Taxonomy and the Partial-area Taxonomy, which have been developed for various biomedical ontologies (e.g., SNOMED CT of SNOMED International and NCIt of the National Cancer Institute). This dissertation presents four enrichment studies of SNOMED CT, utilizing both ML and AbN-based techniques

A Visual Analytics Framework Case Study: Understanding Colombia’s National Administrative Department of Statistics Datasets

In a world filled with data, it is expected for a nation to take decisions informed by data. However, countries need to first collect and publish such data in a way meaningful for both citizens and policy makers. A good thematic classification could be instrumental in helping users to navigate and find the right resources on a rich data repository, such as the one collected by the DANE (Departamento Administrativo Nacional de Estadística, i.e. the Colombia’s National Administrative Department of Statistics). The Visual Analytics Framework is a methodology for conducting visual analysis developed by T. Munzner et al.1 that could help with this task. This paper presents a case study applying such framework conducted to help the DANE to better visualize their data repository, and also to understand it better by using another classification extracted from its metadata. It describes the three main analysis tasks identified and the proposed solutions. Usability testing results during the process helped to correct the visualizations and make them adapted to decision-making. Finally, we explained the collection of insights generated from them

Towards increased business model comprehension – principles for an advanced business model tool

Business modelling is recognized as an important concept to make company strategies more explicit and to compare alternatives combined with their translation to the operational layer. Typically, busi-ness modelling is performed by a group of experts building on established frameworks like the Busi-ness Model Canvas. In a subsequent step, different stakeholders in a company should build upon and work with the defined business models, thus, comprehension is critical. However, this is challenging from a practical point of view and existing research has not addressed the issue of business model comprehension. In order to close this research gap and to increase users’ business model comprehen-sion, we propose an advanced business model tool and an experimental design in this research-in-progress paper. Following the design science approach, we derive a first set of meta-requirements and design principles and present an advanced business model tool instantiation. The presented tool should contribute to an increased business model comprehension by providing semantic relationships and extended business performance indicators. Finally, we present a set of testable hypotheses and the research design for an experimental tool evaluation. With this research we intend to provide a solu-tion to the problem of business model comprehension and contribute to the design knowledge base of business model tools

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: N

Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

Contextual Social Networking

The thesis centers around the multi-faceted research question of how contexts may be detected and derived that can be used for new context aware Social Networking services and for improving the usefulness of existing Social Networking services, giving rise to the notion of Contextual Social Networking. In a first foundational part, we characterize the closely related fields of Contextual-, Mobile-, and Decentralized Social Networking using different methods and focusing on different detailed aspects. A second part focuses on the question of how short-term and long-term social contexts as especially interesting forms of context for Social Networking may be derived. We focus on NLP based methods for the characterization of social relations as a typical form of long-term social contexts and on Mobile Social Signal Processing methods for deriving short-term social contexts on the basis of geometry of interaction and audio. We furthermore investigate, how personal social agents may combine such social context elements on various levels of abstraction. The third part discusses new and improved context aware Social Networking service concepts. We investigate special forms of awareness services, new forms of social information retrieval, social recommender systems, context aware privacy concepts and services and platforms supporting Open Innovation and creative processes. This version of the thesis does not contain the included publications because of copyrights of the journals etc. Contact in terms of the version with all included publications: Georg Groh, [email protected] zentrale Gegenstand der vorliegenden Arbeit ist die vielschichtige Frage, wie Kontexte detektiert und abgeleitet werden können, die dazu dienen können, neuartige kontextbewusste Social Networking Dienste zu schaffen und bestehende Dienste in ihrem Nutzwert zu verbessern. Die (noch nicht abgeschlossene) erfolgreiche Umsetzung dieses Programmes führt auf ein Konzept, das man als Contextual Social Networking bezeichnen kann. In einem grundlegenden ersten Teil werden die eng zusammenhängenden Gebiete Contextual Social Networking, Mobile Social Networking und Decentralized Social Networking mit verschiedenen Methoden und unter Fokussierung auf verschiedene Detail-Aspekte näher beleuchtet und in Zusammenhang gesetzt. Ein zweiter Teil behandelt die Frage, wie soziale Kurzzeit- und Langzeit-Kontexte als für das Social Networking besonders interessante Formen von Kontext gemessen und abgeleitet werden können. Ein Fokus liegt hierbei auf NLP Methoden zur Charakterisierung sozialer Beziehungen als einer typischen Form von sozialem Langzeit-Kontext. Ein weiterer Schwerpunkt liegt auf Methoden aus dem Mobile Social Signal Processing zur Ableitung sinnvoller sozialer Kurzzeit-Kontexte auf der Basis von Interaktionsgeometrien und Audio-Daten. Es wird ferner untersucht, wie persönliche soziale Agenten Kontext-Elemente verschiedener Abstraktionsgrade miteinander kombinieren können. Der dritte Teil behandelt neuartige und verbesserte Konzepte für kontextbewusste Social Networking Dienste. Es werden spezielle Formen von Awareness Diensten, neue Formen von sozialem Information Retrieval, Konzepte für kontextbewusstes Privacy Management und Dienste und Plattformen zur Unterstützung von Open Innovation und Kreativität untersucht und vorgestellt. Diese Version der Habilitationsschrift enthält die inkludierten Publikationen zurVermeidung von Copyright-Verletzungen auf Seiten der Journals u.a. nicht. Kontakt in Bezug auf die Version mit allen inkludierten Publikationen: Georg Groh, [email protected]