Csongor Nyulas

Csongor Nyulas

About

61
Publications
23,340
Reads
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1,700
Citations
Citations since 2016
17 Research Items
920 Citations
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
Additional affiliations
September 2006 - present
Stanford University
Position
  • Senior Research Software Engineer
September 2006 - present
Stanford Medicine
Position
  • Senior Research Software Engineer

Publications

Publications (61)
Conference Paper
Full-text available
An overarching WHO-FIC Content Model will allow uniform modeling of classifications in the WHO Family of International Classifications (WHO-FIC). It will facilitate the development of a unified Foundation to generate variants of ICD, ICF, and ICHI as linearizations and will promote their joint use. We describe a conceptualization and formalization...
Article
Full-text available
An overarching WHO-FIC Content Model will allow uniform modeling of classifications in the WHO Family of International Classifications (WHO-FIC) and promote their joint use. We provide an initial conceptualization of such a model.
Chapter
Full-text available
Pinterest is a popular Web application that has over 250 million active users. It is a visual discovery engine for finding ideas for recipes, fashion, weddings, home decoration, and much more. In the last year, the company adopted Semantic Web technologies to create a knowledge graph that aims to represent the vast amount of content and users on Pi...
Preprint
Full-text available
Pinterest is a popular Web application that has over 250 million active users. It is a visual discovery engine for finding ideas for recipes, fashion, weddings, home decoration, and much more. In the last year, the company adopted Semantic Web technologies to create a knowledge graph that aims to represent the vast amount of content and users on Pi...
Conference Paper
Full-text available
We present WebProtégé, a tool to develop ontologies represented in the Web Ontology Language (OWL). WebProtégé is a cloud-based application that allows users to collaboratively edit OWL ontologies, and it is available for use at https://webprotege.stanford.edu. WebProtégé currently hosts more than 68,000 OWL ontology projects and has over 50,000 us...
Preprint
Full-text available
We present the WebProtégé application to develop ontologies represented in the Web Ontology Language (OWL). WebProtégé is a cloud-based application that allows users to collaboratively edit OWL ontologies, and it is available for use at https://webprotege.stanford.edu. WebProtégé currently hosts more than 66,000 OWL ontology projects and has over 5...
Article
Full-text available
Background Structured data acquisition is a common task that is widely performed in biomedicine. However, current solutions for this task are far from providing a means to structure data in such a way that it can be automatically employed in decision making (e.g., in our example application domain of clinical functional assessment, for determining...
Article
The International Classification of Diseases (ICD) is the de facto standard international classification for mortality reporting and for many epidemiological, clinical, and financial use cases. The next version of ICD, ICD-11, will be submitted for approval by the World Health Assembly in 2018. Unlike previous versions of ICD, where coders mostly s...
Article
Full-text available
Online biomedical repositories contain a wealth of freely available data submitted by the research community, but to reuse this data in further studies requires well-annotated associated metadata. There is a growing set of community-developed standards for creating this metadata, often in the form of templates; still, the difficulties of working wi...
Article
Full-text available
Online biomedical repositories contain a wealth of freely available data submitted by the research community, but to reuse this data in further studies requires well-annotated associated metadata. There is a growing set of community-developed standards for creating this metadata, often in the form of templates; still, the difficulties of working wi...
Article
Full-text available
Online biomedical repositories contain a wealth of freely available data submitted by the research community, but to reuse this data in further studies requires well-annotated associated metadata. There is a growing set of community-developed standards for creating this metadata, often in the form of templates; still, the difficulties of working wi...
Article
Full-text available
Online biomedical repositories contain a wealth of freely available data submitted by the research community, but to reuse this data in further studies requires well-annotated associated metadata. There is a growing set of community-developed standards for creating this metadata, often in the form of templates; still, the difficulties of working wi...
Article
Full-text available
Online biomedical repositories contain a wealth of freely available data submitted by the research community, but to reuse this data in further studies requires well-annotated associated metadata. There is a growing set of community-developed standards for creating this metadata, often in the form of templates; still, the difficulties of working wi...
Article
Full-text available
Online biomedical repositories contain a wealth of freely available data submitted by the research community, but to reuse this data in further studies requires well-annotated associated metadata. There is a growing set of community-developed standards for creating this metadata, often in the form of templates; still, the difficulties of working wi...
Article
Full-text available
Online biomedical repositories contain a wealth of freely available data submitted by the research community, but to reuse this data in further studies requires well-annotated associated metadata. There is a growing set of community-developed standards for creating this metadata, often in the form of templates; still, the difficulties of working wi...
Article
Full-text available
The Library of Integrated Network-based Signatures (LINCS) program generates a wide variety of cell-based perturbation-response signatures using diverse assay technologies. For example, LINCS includes large-scale transcriptional profiling of genetic and small molecule perturbations, and various proteomics and imaging datasets. We have developed dat...
Article
Full-text available
We developed a method to evaluate the extent to which the International Classification of Function, Disability, and Health (ICF) and SNOMED CT cover concepts used in the disability listing criteria of the U.S. Social Security Administration's "Blue Book." First we decomposed the criteria into their constituent concepts and relationships. We defined...
Article
Full-text available
The need to examine the behavior of different user groups is a fundamental requirement when building information systems. In this paper, we present Ontology-based Decentralized Search (OBDS), a novel method to model the navigation behavior of users equipped with different types of background knowledge. Ontology-based Decentralized Search combines o...
Article
Full-text available
WebProtégé is an open-source Web application for editing OWL 2 ontologies. It contains several features to aid collaboration, including support for the discussion of issues, change notification, and revision based change tracking. WebProtégé also features a simple user interface which is geared towards editing the kinds of class descriptions and an...
Article
We present the latest version of WebProtégé: a free, opensource Web-based tool for editing OWL ontologies. WebProtégé allows users to create, upload, share and collaboratively edit OWL ontologies. It contains various tools that are designed to support collaborative editing processes, including issue discussion, complete change tracking support and...
Conference Paper
The World Health Organization is using Semantic Web technologies in the development of the 11th revision of the International Classification of Diseases (ICD-11). Health officials use ICD in all United Nations member countries to compile basic health statistics, to monitor health-related spending, and to inform policy makers. In 2010, we published...
Conference Paper
Ontology engineering is a task that is notorious for its difficulty. As the group that developed Protégé, the most widely used ontology editor, we are keenly aware of how difficult the users perceive this task to be. In this paper, we present the new version of WebProtégé that we designed with two main goals in mind: (1) create a tool that will be...
Article
Full-text available
In this paper, we present WebProtégé-a lightweight ontology editor and knowledge acquisition tool for the Web. With the wide adoption of Web 2.0 platforms and the gradual adoption of ontologies and Semantic Web technologies in the real world, we need ontology-development tools that are better suited for the novel ways of interacting, constructing a...
Article
Traditionally, evaluation methods in the field of semantic technologies have focused on the end result of ontology engineering efforts, mainly, on evaluating ontologies and their corresponding qualities and characteristics. This focus has led to the development of a whole arsenal of ontology-evaluation techniques that investigate the quality of ont...
Article
Full-text available
With the emergence of tools for collaborative ontology engineering, more and more data about the creation process behind collaborative construction of ontologies is becoming available. Today, collaborative ontology engineering tools such as Collaborative Protégé offer rich and structured logs of changes, thereby opening up new challenges and opport...
Conference Paper
Full-text available
Biomedical ontologies such as the 11th revision of the International Classification of Diseases and others are increasingly produced with the help of collaborative ontology engineering platforms that facilitate cooperation and coordination among a large number of users and contributors. While collaborative approaches to engineering biomedical ontol...
Conference Paper
Full-text available
In many scientific disciplines, and in biomedicine in particular, researchers rely on ontologies to enable them to annotate and integrate their data. These ontologies are living and constantly evolving artifacts and the ontology authors must rely on their user community to ensure that the coverage of the ontologies is sufficient for annotations and...
Article
Full-text available
The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontolo...
Article
The biomedical research community relies on a diverse set of resources, both within their own institutions and at other research centers. In addition, an increasing number of shared electronic resources have been developed. Without effective means to locate and query these resources, it is challenging, if not impossible, for investigators to be awa...
Article
Full-text available
Ontologies have become a critical component of many applications in biomedical informatics. However, the landscape of the ontology tools today is largely fragmented, with independent tools for ontology editing, publishing, and peer review: users develop an ontology in an ontology editor, such as Protégé; and publish it on a Web server or in an onto...
Article
Full-text available
The World Health Organization (WHO) is well under way with the new revision of the International Classification of Diseases (ICD-11). The current revision process is significantly different from past ones: the ICD-11 authoring is now open to a large international community of medical experts, who perform the authoring in a web-based collaborative p...
Conference Paper
Full-text available
The World Health Organization is beginning to use Semantic Web technologies in the development of the 11th revision of the International Classification of Diseases (ICD-11). Health officials use ICD in all United Nations member countries to compile basic health statistics, to monitor health-related spending, and to inform policy makers. While previ...
Conference Paper
Full-text available
The World Health Organization is currently developing the 11th revision of the International Classification of Diseases (ICD-11). ICD is the standard diagnostic classification used in health care all over the world. In contrast to previous ICD revisions that did not have a formal representation and were mainly available as printed books, ICD-11 use...
Article
Full-text available
We present DataMaster, a Protégé plug-in that supports the importing of schema structure and data from relational databases into Protégé. The plug-in supports both OWL and frames-based ontologies and can be used with any relational database with JDBC/ODBC drivers.
Conference Paper
Full-text available
Cloud-based systems have proven to be a powerful technology for building data-intensive applications. However, the process of designing and deploying such applications is still primarily a manual one. There is a need for mechanisms and tools to help automate the required development steps. Using the Semantic Web ontology language OWL and the Hadoop...
Conference Paper
Full-text available
This paper describes an approach to how ontologies can be used for modeling of real-time monitoring systems that provide both efficiency and intelligence. An ontology-based framework is described that allows for fusion of various data-processing and reasoning techniques. This solution supports the construction of detailed models of data dependencie...
Article
Full-text available
Ontology repositories provide the crucial infrastructure for publish-ing and sharing ontologies in an increasing number of domains. Some of these ontology repositories expose the metadata and the ontology content using APIs or Web services that enable the mashing up of applications in a straightforward way. In this paper, we describe two use cases...
Article
Full-text available
Worldwide developments concerning infectious diseases and bioterrorism are driving forces for improving aberrancy detection in public health surveillance. The performance of an aberrancy detection algorithm can be measured in terms of sensitivity, specificity and timeliness. However, these metrics are probabilistically dependent variables and there...
Article
Full-text available
Problem solving methods (PSMs) are software components that represent and encode reusable algorithms. They can be combined with representations of domain knowledge to produce intelligent application systems. A goal of research on PSMs is to provide principled methods and tools for composing and reusing algorithms in knowledge-based systems. The ult...
Conference Paper
Full-text available
As we are witnessing a steady increase of semantic content on the Web, there is a (maybe not so obvious) increase in the number of web-applications that are used to produce or consume that content. Protégé offers a great toolset to deal with almost every aspect of authoring and handling ontology based semantic content. Creating easy to use applicat...
Article
Full-text available
Using ontologies to represent and drive knowledge infrastructure of software projects is the Semantic Web answer to the paradigm of Model-Driven Architecture. Advocates of this approach argue that using ontologies in this ca- pacity provides separation of the declarative and procedural knowledge and en- ables easier evolution of the declarative kno...
Conference Paper
Full-text available
Multi-agent systems have proven to be a powerful technology for building distributed applications. However, the process of designing, configuring and deploying agent-based applications is still primarily a manual one. There is a need for mechanisms and tools to help automate the many development steps required when building these applications. Usin...
Article
Statistical aberrancy-detection algorithms play a central role in automated public health systems, analyzing large volumes of clinical and administrative data in real-time with the goal of detecting disease outbreaks rapidly and accurately. Not all algorithms perform equally well in terms of sensitivity, specificity, and timeliness in detecting dis...
Article
Full-text available
Public health surveillance is critical for accurate and timely outbreak detection and effective epidemic control. A wide range of statistical algorithms is used for surveillance, and important differences have been noted in the ability of these algorithms to detect outbreaks. The evidence about the relative performance of these algorithms, however,...
Conference Paper
Full-text available
SWRL is an expressive OWL-based rule language that can be used to increase the amount of knowledge encoded in OWL ontologies. While semantically a SWRL rule can be considered as an additional type of OWL axiom, the authoring and management of SWRL rule bases requires specialized tools that are not typically present in standard OWL development envir...
Conference Paper
Full-text available
Data integration is central in Web application development because these applications typically deal with a variety of information formats. Ontology-driven applications face the additional challenge of integrating these multiple formats with the information stored in ontologies. A number of mappings are required to reconcile the variety of formats...
Conference Paper
Full-text available
The SWRLTab is a development environment for working with SWRL rules in Protégé-OWL. It supports the editing and execution of SWRL rules. It also provides mechanisms to allow interoperation with a variety of rule engines and the incorporation of user-defined libraries of methods that can be used in rules. Several built-in libraries are provided, in...
Conference Paper
Full-text available
Software applications that work with biomedical data have significant knowledge-management requirements. Formal knowledge models and knowledge-based methods can be very useful in meeting these requirements. However, most biomedical data are stored in relational databases, a practice that will continue for the foreseeable future. Using these data in...
Conference Paper
Full-text available
For the foreseeable future, most data will continue to be stored in relational databases. To work with these data in ontology-based applications, tools and techniques that bridge the two models are required. Mapping all relational data to ontology instances is often not practical so dynamic data access approaches are typically employed, though thes...
Article
Full-text available
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language process-ing, and decision support. The National Center for Biomedical Ontology is devel-oping BioPortal, a web-based library of biomedical ontologies. As the biomedical community develops the ever growing set...