Thesauri on the Web: current developments and trends

This article provides an overview of recent developments relating to the application of thesauri in information organisation and retrieval on the World Wide Web. It describes some recent thesaurus projects undertaken to facilitate resource description and discovery and access to wide-ranging information resources on the Internet. Types of thesauri available on the Web, thesauri integrated in databases and information retrieval systems, and multiple-thesaurus systems for cross-database searching are also discussed. Collective efforts and events in addressing the standardisation and novel applications of thesauri are briefly reviewed

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Desiderata for an ontology of diseases for the annotation of biological datasets.

There is a plethora of disease ontologies available, all potentially useful for the annotation of biological datasets. We define seven desirable features for such ontologies and examine whether or not these features are supported by eleven disease ontologies. The four ontologies most closely aligned with our desiderata are Disease Ontology, SNOMED CT, NCI thesaurus and UMLS

The Potential of the Digital Anatomist Foundational Model for Assuring Consistency in UMLS Sources

Inconsistent anatomical concept representation can be identified in anatomy textbooks and hard copy term lists, as well as in UMLS source vocabularies and other controlled medical terminologies. In this report we select some examples of inconsistent representations of anatomical concepts, and illustrate how these inconsistencies can be explained and reconciled by the Digital Anatomist Foundational Model1. We use this process for gaining a measure of the validity of the logic-based Model

Revising the UMLS Semantic Network

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration

Terminologia Anatomica; Considered from the Perspective of Next-Generation Knowledge Sources

This report examines the semantic structure of Terminologia Anatomica, taking one randomly selected page as an example. The focus of analysis is the meaning imparted to an anatomical term by virtue of its location within the structured list. Terminologia’s structure expressed through hierarchies of headings, varied typographical styles, indentations and an alphanumeric code implies specific relationships between the terms embedded in the list. Together, terms and relationships can potentially capture essential elements of anatomical knowledge. The analysis focuses on these knowledge elements and evaluates the consistency and logic in their representation. Most critical of these elements are class inclusion and part-whole relationships, which are implied, rather than explicitly modeled by Terminologia. This limits the use of the term list to those who have some knowledge of anatomy and excludes computer programs from navigating through the terminology. Assuring consistency in the explicit representation of anatomical relationships would facilitate adoption of Terminologia as the anatomical standard by the various controlled medical terminology (CMT) projects. These projects are motivated by the need for computerizing the patient record, and their aim is to generate machineunderstandable representations of biomedical concepts, including anatomy. Because of the lack of a consistent and explicit representation of anatomy, each of these CMTs has generated it own anatomy model. None of these models is compatible with each other, yet each is consistent with textbook descriptions of anatomy. The analysis of the semantic structure of Terminologia Anatomica leads to some suggestions for enhancing the term list in ways that would facilitate its adoption as the standard for anatomical knowledge representation in biomedical informatics

Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

Applications of the ACGT Master Ontology on Cancer

In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within the ACGT project thus far

Knowledge Organization Systems (KOS) in the Semantic Web: A Multi-Dimensional Review

Since the Simple Knowledge Organization System (SKOS) specification and its SKOS eXtension for Labels (SKOS-XL) became formal W3C recommendations in 2009 a significant number of conventional knowledge organization systems (KOS) (including thesauri, classification schemes, name authorities, and lists of codes and terms, produced before the arrival of the ontology-wave) have made their journeys to join the Semantic Web mainstream. This paper uses "LOD KOS" as an umbrella term to refer to all of the value vocabularies and lightweight ontologies within the Semantic Web framework. The paper provides an overview of what the LOD KOS movement has brought to various communities and users. These are not limited to the colonies of the value vocabulary constructors and providers, nor the catalogers and indexers who have a long history of applying the vocabularies to their products. The LOD dataset producers and LOD service providers, the information architects and interface designers, and researchers in sciences and humanities, are also direct beneficiaries of LOD KOS. The paper examines a set of the collected cases (experimental or in real applications) and aims to find the usages of LOD KOS in order to share the practices and ideas among communities and users. Through the viewpoints of a number of different user groups, the functions of LOD KOS are examined from multiple dimensions. This paper focuses on the LOD dataset producers, vocabulary producers, and researchers (as end-users of KOS).Comment: 31 pages, 12 figures, accepted paper in International Journal on Digital Librarie