Natalya F. Noy

Bio: Natalya F. Noy is an academic researcher from Stanford University. The author has contributed to research in topics: Ontology (information science) & Open Biomedical Ontologies. The author has an hindex of 56, co-authored 166 publications receiving 23427 citations. Previous affiliations of Natalya F. Noy include Pennsylvania State University & Google.

Ontology Development 101: A Guide to Creating Your First Ontology

Abstract: 1 Why develop an ontology? In recent years the development of ontologies—explicit formal specifications of the terms in the domain and relations among them (Gruber 1993)—has been moving from the realm of ArtificialIntelligence laboratories to the desktops of domain experts. Ontologies have become common on the World-Wide Web. The ontologies on the Web range from large taxonomies categorizing Web sites (such as on Yahoo!) to categorizations of products for sale and their features (such as on Amazon.com). The WWW Consortium (W3C) is developing the Resource Description Framework (Brickley and Guha 1999), a language for encoding knowledge on Web pages to make it understandable to electronic agents searching for information. The Defense Advanced Research Projects Agency (DARPA), in conjunction with the W3C, is developing DARPA Agent Markup Language (DAML) by extending RDF with more expressive constructs aimed at facilitating agent interaction on the Web (Hendler and McGuinness 2000). Many disciplines now develop standardized ontologies that domain experts can use to share and annotate information in their fields. Medicine, for example, has produced large, standardized, structured vocabularies such as SNOMED (Price and Spackman 2000) and the semantic network of the Unified Medical Language System (Humphreys and Lindberg 1993). Broad general-purpose ontologies are emerging as well. For example, the United Nations Development Program and Dun & Bradstreet combined their efforts to develop the UNSPSC ontology which provides terminology for products and services (www.unspsc.org). An ontology defines a common vocabulary for researchers who need to share information in a domain. It includes machine-interpretable definitions of basic concepts in the domain and relations among them. Why would someone want to develop an ontology? Some of the reasons are:

The evolution of Protégé: an environment for knowledge-based systems development

Abstract: The Protege project has come a long way since Mark Musen first built the Protege meta-tool for knowledge-based systems in 1987. The original tool was a small application, aimed at building knowledge-acquisition tools for a few specialized programs in medical planning. From this initial tool, the Protege system has evolved into a durable, extensible platform for knowledge-based systems development and research. The current version, Protege-2000, can be run on a variety of platforms, supports customized user-interface extensions, incorporates the Open Knowledge-Base Connectivity (OKBC) knowledge model, interacts with standard storage formats such as relational databases, XML, and RDF, and has been used by hundreds of individuals and research groups. In this paper, we follow the evolution of the Protege project through three distinct re-implementations. We describe our overall methodology, our design decisions, and the lessons we have learned over the duration of the project. We believe that our success is one of infrastructure: Protege is a flexible, well-supported, and robust development environment. Using Protege, developers and domain experts can easily build effective knowledge-based systems, and researchers can explore ideas in a variety of knowledge-based domains.

Semantic integration: a survey of ontology-based approaches

Abstract: Semantic integration is an active area of research in several disciplines, such as databases, information-integration, and ontologies. This paper provides a brief survey of the approaches to semantic integration developed by researchers in the ontology community. We focus on the approaches that differentiate the ontology research from other related areas. The goal of the paper is to provide a reader who may not be very familiar with ontology research with introduction to major themes in this research and with pointers to different research projects. We discuss techniques for finding correspondences between ontologies, declarative ways of representing these correspondences, and use of these correspondences in various semantic-integration tasks

Algorithm and Tool for Automated Ontology Merging and Alignment

Abstract: Researchers in the ontology-design field have developed the content for ontologies in many domain areas. Recently, ontologies have become increasingly common on the WorldWide Web where they provide semantics for annotations in Web pages. This distributed nature of ontology development has led to a large number of ontologies covering overlapping domains. In order for these ontologies to be reused, they first need to be merged or aligned to one another. The processes of ontology alignment and merging are usually handled manually and often constitute a large and tedious portion of the sharing process. We have developed and implemented PROMPT, an algorithm that provides a semi-automatic approach to ontology merging and alignment. PROMPT performs some tasks automatically and guides the user in performing other tasks for which his intervention is required. PROMPT also determines possible inconsistencies in the state of the ontology, which result from the user’s actions, and suggests ways to remedy these inconsistencies. PROMPT is based on an extremely general knowledge model and therefore can be applied across various platforms. Our formative evaluation showed that a human expert followed 90% of the suggestions that PROMPT generated and that 74% of the total knowledge-base operations invoked by the user were suggested by PROMPT.

Creating Semantic Web contents with Protege-2000

Abstract: As researchers continue to create new languages in the hope of developing a Semantic Web, they still lack consensus on a standard. The authors describe how Protege-2000, a tool for ontology development and knowledge acquisition, can be adapted for editing models in different Semantic Web languages.

Visual Genome: Connecting Language and Vision Using Crowdsourced Dense Image Annotations

Abstract: Despite progress in perceptual tasks such as image classification, computers still perform poorly on cognitive tasks such as image description and question answering. Cognition is core to tasks that involve not just recognizing, but reasoning about our visual world. However, models used to tackle the rich content in images for cognitive tasks are still being trained using the same datasets designed for perceptual tasks. To achieve success at cognitive tasks, models need to understand the interactions and relationships between objects in an image. When asked "What vehicle is the person riding?", computers will need to identify the objects in an image as well as the relationships riding(man, carriage) and pulling(horse, carriage) to answer correctly that "the person is riding a horse-drawn carriage." In this paper, we present the Visual Genome dataset to enable the modeling of such relationships. We collect dense annotations of objects, attributes, and relationships within each image to learn these models. Specifically, our dataset contains over 108K images where each image has an average of $$35$$35 objects, $$26$$26 attributes, and $$21$$21 pairwise relationships between objects. We canonicalize the objects, attributes, relationships, and noun phrases in region descriptions and questions answer pairs to WordNet synsets. Together, these annotations represent the densest and largest dataset of image descriptions, objects, attributes, relationships, and question answer pairs.

Yago: a core of semantic knowledge

Abstract: We present YAGO, a light-weight and extensible ontology with high coverage and quality. YAGO builds on entities and relations and currently contains more than 1 million entities and 5 million facts. This includes the Is-A hierarchy as well as non-taxonomic relations between entities (such as HASONEPRIZE). The facts have been automatically extracted from Wikipedia and unified with WordNet, using a carefully designed combination of rule-based and heuristic methods described in this paper. The resulting knowledge base is a major step beyond WordNet: in quality by adding knowledge about individuals like persons, organizations, products, etc. with their semantic relationships - and in quantity by increasing the number of facts by more than an order of magnitude. Our empirical evaluation of fact correctness shows an accuracy of about 95%. YAGO is based on a logically clean model, which is decidable, extensible, and compatible with RDFS. Finally, we show how YAGO can be further extended by state-of-the-art information extraction techniques.

Knowledge engineering: principles and methods

Abstract: This paper gives an overview of the development of the field of Knowledge Engineering over the last 15 years. We discuss the paradigm shift from a transfer view to a modeling view and describe two approaches which considerably shaped research in Knowledge Engineering: Role-limiting Methods and Generic Tasks. To illustrate various concepts and methods which evolved in recent years we describe three modeling frameworks: CommonKADS, MIKE and PROTEGE-II. This description is supplemented by discussing some important methodological developments in more detail: specification languages for knowledge-based systems, problem-solving methods and ontologies. We conclude by outlining the relationship of Knowledge Engineering to Software Engineering, Information Integration and Knowledge Management.

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

Abstract: The National Human Genome Research Institute (NHGRI) Catalog of Published Genome-Wide Association Studies (GWAS) Catalog provides a publicly available manually curated collection of published GWAS assaying at least 100000 singlenucleotide polymorphisms (SNPs) and all SNP-trait associations with P <110 5 . The Catalog includes 1751 curated publications of 11912 SNPs. In addition to the SNP-trait association data, the Catalog also publishes a quarterly diagram of all SNP-trait associations mapped to the SNPs’ chromosomal locations. The Catalog can be accessed via a tabular web interface, via a dynamic visualization on the human karyotype, as a downloadable tab-delimited file and as an OWL knowledge base. This article presents a number of recent improvements to the Catalog, including novel ways for users to interact with the Catalog and changes to the curation infrastructure.