Matthew Horridge

Matthew Horridge
Stanford University | SU · Stanford Center for Biomedical Informatics Research

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76
Publications
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4,345
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Publications

Publications (76)
Preprint
Full-text available
Knowledge graphs are developed and used in academia and industry to tackle complex challenges in healthcare and biomedical research. Elsevier's Healthcare Knowledge Graph (HG) is developed by extracting and integrating medical knowledge from several heterogeneous sources such as clinical guidelines, medical textbooks, and legacy databases. The HG p...
Article
With the growth of ontologies used in diverse application areas, the need for module extraction and modularisation techniques has risen. The notion of the modular structure of an ontology, which comprises a suitable set of base modules together with their logical dependencies, has the potential to help users and developers in comprehending, sharing...
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...
Conference Paper
We present Snap-SPARQL, which is a Java framework for working with SPARQL and OWL. The framework includes a parser, axiom template API, SPARQL algebra implementation, and graphical user interface components for reading, processing and executing SPARQL queries under the SPARQL 1.1 OWL Entailment Regime. While the framework was originally designed to...
Conference Paper
An ontology is a machine processable artifact that captures knowledge about some domain of interest. Ontologies are used in various domains including healthcare, science, and commerce. In this paper we examine the ontology bootstrapping problem. Specifically, we look at an approach that uses both competency questions and knowledge source reuse via...
Article
The World Health Organisation is using OWL as a key technology to develop ICD-11 - the next version of the well-known International Classification of Diseases. Besides providing better opportunities for data integration and linkages to other well-known ontologies such as SNOMED-CT, one of the main promises of using OWL is that it will enable variou...
Conference Paper
The Atomic Decomposition of an ontology is a succinct representation of the logic-based modules in that ontology. Ultimately, it reveals the modular structure of the ontology. Atomic Decompositions appear to be useful for both user and non-user facing services. For example, they can be used for ontology comprehension and to facilitate reasoner opti...
Conference Paper
We present a domain specific ontology editor for viewing, updating and managing a clinical documentation knowledge base. The editor is designed to allow clinical content specialists, who do not have a working knowledge of OWL, Semantic Web technologies or knowledge engineering, to quickly generate ontologies that describe clinical documentation tem...
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...
Article
Justifications are the dominant form of explanation for entailments of OWL ontologies, with popular OWL ontology editors, such as Protege 4, providing justification-based explanation facilities. A justification is a minimal subset of an ontology which is sufficient for an entailment to hold; they correspond to the premises of a proof. Unlike proofs...
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
The increase in volume and complexity of biological data has led to increased requirements to reuse that data. Consistent and accurate metadata is essential for this task, creating new challenges in semantic data annotation and in the constriction of terminologies and ontologies used for annotation. The BioSharing community are developing standards...
Article
This paper presents a binary format for both storing OWL ontologies and describing changes in OWL ontologies. The format is designed to be a fast to parse and serialise format. It is intended as a low level storage and transmission mechanism rather than an end user exchange syntax. Software to parse and serialise binary OWL has been implemented in...
Conference Paper
This paper presents an evaluation of state of the art black box justification finding algorithms on the NCBO BioPortal ontology corpus. This corpus represents a set of naturally occurring ontologies that vary greatly in size and expressivity. The results paint a picture of the performance that can be expected when finding all justifications for ent...
Conference Paper
Full-text available
BioPortal is a repository of biomedical ontologies—the largest such repository, with more than 300 ontologies to date. This set includes ontologies that were developed in OWL, OBO and other languages, as well as a large number of medical terminologies that the US National Library of Medicine distributes in its own proprietary format. We have publis...
Article
Full-text available
Ontology design patterns (ODPs) are a proposed solution to facilitate ontology development, and to help users avoid some of the most frequent modeling mistakes. ODPs originate from similar approaches in software engineering, where software design patterns have become a critical aspect of software development. There is little empirical evidence for...
Conference Paper
RightField is a Java application that provides a mechanism for embedding ontology annotation support for scientific data in Microsoft Excel or Open Office spreadsheets. The result is semantic annotation by stealth, with an annotation process that is less error-prone, more efficient, and more consistent with community standards. By automatically gen...
Article
Full-text available
This paper presents use cases for modular development of ontologies using the OWL imports mechanism. Many of the methods are inspired by work in modular development in software engineering. The approach is aimed at developers of large ontologies covering multiple subdomains that make use of OWL reasoners for inference. Such ontologies are common in...
Article
Full-text available
Background Ontologies are being developed for the life sciences to standardise the way we describe and interpret the wealth of data currently being generated. As more ontology based applications begin to emerge, tools are required that enable domain experts to contribute their knowledge to the growing pool of ontologies. There are many barriers tha...
Article
This paper presents a characterisation of and definitions for the phenomenon of masking in the context of justifications for entailments in ontologies. In essence masking is present within a justification, over a set of justifications, or over a complete ontology when the number of justifications for an entailment does not reflect the number of rea...
Article
Ontology Design Patterns (ODPs) provide a means to capture best practice, to prevent modeling errors, and to encode formally common modeling situations for use during ontology development. Despite the popularity of ODPs and supposed positive effects from their use, there is scant empirical evidence of their level of adoption in real world ontologie...
Article
Full-text available
Motivation: In the Life Sciences, guidelines, checklists and ontologies describing what metadata is required for the interpretation and reuse of experimental data are emerging. Data producers, however, may have little experience in the use of such standards and require tools to support this form of data annotation. Results: RightField is an open...
Article
We present the OWL API, a high level Application Programming Interface (API) for working with OWL ontologies. The OWL API is closely aligned with the OWL 2 structural specification. It supports parsing and rendering in the syntaxes defined in the W3C specification (Functional Syntax, RDF/XML, OWL/XML and the Manchester OWL Syntax); manipulation of...
Conference Paper
Current ontology development tools offer debugging support by presenting justifications for entailments of OWL ontologies. While these minimal subsets have been shown to support debugging and understanding tasks, the occurrence of multiple justifications presents a significant cognitive challenge to users. In many cases even a single entailment may...
Conference Paper
In this paper, we present an approach to determining the cognitive complexity of justifications for entailments of OWL ontologies. We introduce a simple cognitive complexity model and present the results of validating that model via experiments involving OWL users. The validation is based on test data derived from a large and diverse corpus of natu...
Article
Full-text available
We present Populous, a tool for gathering content with which to populate an ontology. Domain experts need to add content, that is often repetitive in its form, but without having to tackle the underlying ontological representation. Populous presents users with a table based form in which columns are constrained to take values from particular ontolo...
Conference Paper
Justifications — that is, minimal entailing subsets of an ontology — are currently the dominant form of explanation provided by ontology engineering environments, especially those focused on the Web Ontology Language (OWL). Despite this, there are naturally occurring justifications that can be very difficult to understand. In essence, justification...
Conference Paper
This paper presents a discussion on the phenomena of mask- ing in the context of justifications for entailments. Various types of mask- ing are introduced and a definition for each type is given.
Article
Full-text available
OWL: Experiences and Directions, 7th International Workshop. 21-22 June 2010, San Francisco, California, USA Objects can be said to be structured when their representation also contains their parts. While OWL in general can describe structured objects, description graphs are a recent, decidable extension to OWL which support the description of clas...
Technical Report
OWL 2 extends the W3C OWL Web Ontology Language with a small but useful set of features that have been requested by users, for which effective reasoning algorithms are now available, and that OWL tool developers are willing to support. The new features include extra syntactic sugar, additional property and qualified cardinality constructors, extend...
Conference Paper
Justifications play a central role as the basis for explaining entailments in OWL ontologies. While techniques for computing justifications for entailments in consistent ontologies are theoretically and practically well-understood, little is known about the practicalities of computing justifications for inconsistent ontologies. This is despite the...
Conference Paper
Being able to extend an OWL ontology with some form of rules is a feature that many ontology developers consider as very impor- tant. Nevertheless, working with rules in practice can be difficult since the tool support is not as good as for handling standard ontologies. Fur- thermore, the existing rule syntaxes are not very well aligned with the ne...
Conference Paper
This paper presents the OWL API a high level Application Programming Interface (API) for working with OWL 2 ontologies. The API is closely aligned with the OWL 2 structural specification. It sup- ports parsing and rendering in the syntaxes defined in the W3C specifi- cation, namely, the Functional Syntax, RDF/XML, OWL/XML and the Manchester OWL Syn...
Conference Paper
A justification for an entailment in an OWL ontology is a minimal subset of the ontology that is sufficient for that entailment to hold. Since justifications respect the syntactic form of axioms in an ontology, they are usually neither syntactically nor semantically minimal. This paper presents two new subclasses of justifications—laconic justifica...
Conference Paper
This paper describes the explanation in OWL landscape. In recent years there has been huge progress, both in theory and imple- mentation, in the area of explaining the causes of entailments in OWL ontologies. This paper charts the course of explanation in OWL and then looks at ways in which user understanding of ontologies might be further improved...
Conference Paper
Full-text available
The OWLlink interface provides an implementation-neutral mechanism for accessing OWL reasoner functionality. In contrast to its DL-oriented predecessor DIG, OWLlink relies on OWL 2 for the prim- itives of the modelling language, and is thus fully compatible with the forthcoming incarnation of OWL. The OWLlink core introduced in this document covers...
Conference Paper
The notion of an Application Programming Interface (API) proved a breakthrough in software modularization and re- use by allowing developers to separate applications' public interfaces from their detailed internal structure. No comparable notion exists currently for ontologies, although there is considerable other work on issues related to modulari...
Conference Paper
ABSTRACT This poster and demo,presents new,OWL ontology expla- nation tools and facilities that are available in Prot,eg,e 4. These explanations take the form of justications . A jus- tication,is a minimal set of axioms that is sucient,for a given entailment to hold. Justication,nding services for Prot eg e 4 are presented, including what have beco...
Article
The Manchester OWL syntax is a user-friendly syntax for OWL DL, fundamentally based on collecting all information about a particular class, property, or individual into a single construct, called a frame. The Manchester OWL syntax has been revised to be a syntax for OWL 1.1, involving adding the new OWL 1.1 description constructs and the new axioms...
Article
Full-text available
The notion of an Application Programming Interface (API) was a breakthrough in re-usable software development. OWL's import mechanism makes it possible to define analogous strategies for modular ontology development. This paper explores five use cases for such development: normalization, pluggable ontologies, extensions, localization, and ontology...
Article
Much has been written of the facilities for ontology building and reasoning offered for ontologies expressed in the Web Ontology Language (OWL). Less has been written about how the modelling requirements of different areas of interest are met by OWL-DL's underlying model of the world. In this paper we use the disciplines of biology and bioinformati...
Chapter
Full-text available
OBO is an ontology language that has often been used for modeling ontologies in the life sciences. Its definition is relatively infor- mal, so, in this paper, we provide a clear specification for OBO syntax and semantics via a mapping to OWL. This mapping also allows us to apply existing Semantic Web tools and techniques to OBO. We show that Semant...
Article
Full-text available
Much has been written of the facilities for ontology building and reasoning offered for ontologies expressed in the Web Ontology Language (OWL). Less has been written about how the modelling requirements of different areas of interest are met by OWL-DL's underlying model of the world. In this paper we use the disciplines of biology and bioinformati...
Conference Paper
This paper describes the design and implementation of an OWL 1.1 API, herein referred to as the OWL API . The API is designed to facilitate the manipulation of OWL 1.1 ontologies at a high level of abstraction for use by editors, reasoners and other tools. The API is based on the OWL 1.1 specification and influenced by the experience of designing a...
Conference Paper
Finding the justifications of an entailment (that is, all the minimal set of axioms sufficient to produce an entailment) has emerged as a key inference service for the Web Ontology Language (OWL). Justifica- tions are essential for debugging unsatisfiable classes and contradictions. The availability of justifications as explanations of entailments...
Conference Paper
Full-text available
This paper describes a new syntax that can be used to write OWL ontologies, and fragments of OWL ontologies for presentation and editing purposes. The syntax, which is known as the Manchester OWL Syntax, was developed in response to a demand from a wide range of users, who do not have a Description Logic background, for a"less logician like" syntax...
Conference Paper
Full-text available
Sequences are a natural part of the world to be modelled in ontologies. Yet the Web Ontology Language, OWL, contains no specific support for ordering. It does, however, have constructs that can be used to model many aspects of sequences, albeit imperfectly. This paper demonstrates a design pattern for modeling order within OWL-DL. This allows us to...
Conference Paper
Full-text available
This paper describes integrated tools support for OWL 1.1 in the form of the FaCT++ Description Logic reasoner and the Protege- OWL ontology editor. Challenges of designing and implementing OWL 1.1 reasoning algorithms are highlighted, and an outline of an OWL 1.1 API and editing environment is provided.
Conference Paper
Full-text available
After becoming a W3C Recommendation, OWL is becoming increas- ingly widely accepted and used. However most people still find it difficult to cre- ate and use OWL ontologies. On major difficulty is "debugging" the ontologies - discovering why a reasoners has inferred that a class is "unsatisfiable" (inconsis- tent). Even for people who do understand...
Conference Paper
Full-text available
Protégé is one of the most widely used development platforms for ontology-based systems. We report on our experiences with the development of OWL support for Protégé, and on the experiences of our user community with OWL. While the overall feedback from the community has been positive, our experience suggests that there are considerable gaps betwee...
Conference Paper
Full-text available
Understanding the logical meaning of any description logic or sim- ilar formalism is difficult for most people, and OWL-DL is no exception. This paper presents the most common difficulties encountered by newcomers to the language, that have been observed during the course of more than a dozen work- shops, tutorials and modules about OWL-DL and it's...
Article
Full-text available
The Protégé-OWL environment including visualization, debugging, and wizard tools from the CO-ODE programme provides a user oriented environment for developing OWL ontologies. The long-term goal is to help subject matter experts to build and manage their own ontologies. The environment has been designed based on experience in teaching OWL and its pr...
Article
Full-text available
Understanding and using OWL can be difficult. Until recently, the difficulty was made, if anything, greater by user interfaces which were designed more to demonstrate OWL than to fit users requirements. The new interfaces being developed in the Protégé-OWL/CO-ODE/HyOntUse projects are based, to a large extent, on experience in tutorials, workshops,...
Article
Recent work in explanation of entailments in ontologies has focused on justications and their variants. While in many cases, just presenting the justication is sucient for user understanding, and in all cases justications are much bet- ter than nothing, we have empirically identied cases where understanding how a justication supports an entailment...