The Value Recommender system is the first of a planned set of intelligent authoring components in... more The Value Recommender system is the first of a planned set of intelligent authoring components in the CEDAR system. Future efforts will concentrate on deeper analyses of metadata to discover more interesting relationships between metadata fields, which will then drive new tools to assist biomedical investigators when annotating their data. The Value Recommender supports both freetext values and controlled terms. In this particular example, the system suggests terms from the Human Disease Ontology (DOID).
We present WebProt ég é 2, a Web-based tool for the collaborative editing of OWL ontologies. WebP... more We present WebProt ég é 2, a Web-based tool for the collaborative editing of OWL ontologies. WebProt ég é 2 is "Google docs" environment for ontologies which allows users to create and upload ontologies. It contains various tools that are designed to support collaborative ontology editing such as ontology change tracking, watches, notifications and issue tracking. Users can download a snapshot of an ontology at any point. In addition to this WebProt ég é 2 also features a simple user interface that offers quick and easy editing of commonly used OWL 2 axiom and class constructors. This interface works particularly well for biomedical ontologies which typically fall into the lightweight OWL2EL profile. WebProt ég é 2 is available to use at .
National Conference on Artificial Intelligence, Jul 1, 1992
The effectiveness of tools that provide support for software development is highly dependent on t... more The effectiveness of tools that provide support for software development is highly dependent on the match between the tools and their task. Knowledge-acquisition (KA) tools constitute a class of development tools targeted at knowledge-based systems. Generally, KA tools that are custom-tailored for particular application domains are more effective than are general KA tools that cover a large class of domains. The high cost of custom-tailoring KA tools manually has encouraged researchers to develop recta-tools for KA tools. Current research issues in meta-tooZs for knowledge acquisition are the specification styles, or me,a-views, for target KA tools used, and the relationships between the specification entered in the metatool and other specifications for the target program under development. We examine different types of meta-views and meta-tools. Our current project is to provide meta-too!s that produce KA tools from multiple specification sources--for instance, from a task analysis of the target application. = :. _
Property restrictions play an important definitional role in an ontology. The correct introductio... more Property restrictions play an important definitional role in an ontology. The correct introduction and inheritance of restrictions is important for ensuring the correct modeling of a domain. Many ontologies have large, complex class hierarchies, and many classes are defined with restrictions. When editing such an ontology, it is often difficult to determine the global impact of a local change. For example, removing a subclass link (axiom) can result in the unintentional loss of inherited restrictions over many levels. In this paper, we introduce a dynamic summarization and visualization methodology, called a Live Difference Taxonomy (LDT), to succinctly display a summary of the effects of changes to the ontology. LDTs are created on-the-fly as the ontology is edited, allowing an ontology developer to view the overall impact of their changes in a compact, visual display. We introduce an open-source plugin for the Protégé ontology editor that implements LDTs. It lets the users choose from several kinds of LDT summaries and lets them control the degree of summarization. The LDT Plugin supports heuristics-based alerts that inform the user of changes to sets of classes that are modeled with the same types of restrictions.
Interactive knowledge-acquisition (KA) programs allow users to enter relevant domain knowledge ac... more Interactive knowledge-acquisition (KA) programs allow users to enter relevant domain knowledge according to a model predefined by the tool developers. KA tools are designed to provide conceptual models of the knowledge to their users. Many different classes of models are possible, resulting in different categories of tools. Whenever it is possible to describe KA tools according to explicit conceptual models, it is also possible to edit the models and to instantiate new KA tools automatically for specialized purposes. Several meta-tools that address this task have been implemented. Meta-tools provide developers of domain-specific KA tools with generic design models, or meta-views, of the emerging KA tools. The same KA tool can be specified according to several alternative meta-views.
In this demonstration, we present the main features of WebProtégé, a free, opensource, cloud-base... more In this demonstration, we present the main features of WebProtégé, a free, opensource, cloud-based OWL ontology editor that supports simultaneous collaborative editing for geographically distributed users. WebProtégé is available for general purpose use at , where it hosts over 55,000 OWL ontology projects and over 42,500 user accounts. The software is open-source and all source code is available on GitHub 1 . WebProtégé 3.0 builds on the success of previous versions but features a new modern interface and new features for collaboration and review. This demonstration, at the ISWC2018 posters and demos session will enable attendees to see the latest features as well as providing them with an opportunity to interact with, and provide feedback to, the WebProtégé developers. We discuss the main features here. WebProtégé is essentially a "Google docs" for editing ontologies. Users access "projects" that are collections of OWL ontologies augmented with a change history, and issues/comments. WebProtégé provides a default user-interface that supports lightweight ontology editing, for ontologies that more or less fit within the OWL2EL profile. However, it can also be configured for editing ontologies that require full-blown OWL 2 axioms and class expressions. Ontology Editing Figure shows the main editing interface, which provides the familiar tabbed look and feel that is common to all desktop versions of Protégé. The classes tab is shown here, which comprises four resizable views: (Class Hierarchy, Class Description, Comments and Project Feed). Users can add, remove and customize the layout of views on a tab and the state of the user-interface is automatically persisted for each user in the context of a project. In contrast to previous versions, WebProtégé 3.0 uses proper URL routing, meaning that entities, such as classes, properties and individuals, and the tabs
Metadata that are structured using principled schemas and that use terms from ontologies are esse... more Metadata that are structured using principled schemas and that use terms from ontologies are essential to making biomedical data findable and reusable for downstream analyses. The largest source of metadata that describes the experimental protocol, funding, and scientific leadership of clinical studies is ClinicalTrials.gov. We evaluated whether values in 302,091 trial records adhere to expected data types and use terms from biomedical ontologies, whether records contain fields required by government regulations, and whether structured elements could replace free-text elements. Contact information, outcome measures, and study design are frequently missing or underspecified. Important fields for search, such as condition and intervention, are not restricted to ontologies, and almost half of the conditions are not denoted by MeSH terms, as recommended. Eligibility criteria are stored as semi-structured free text. Enforcing the presence of all required elements, requiring values for certain fields to be drawn from ontologies, and creating a structured eligibility criteria element would improve the reusability of data from ClinicalTrials.gov in systematic reviews, metanalyses, and matching of eligible patients to trials. .
Data Processing.- Database Management.- Telecommunication, Networking, and Integration.- Coding a... more Data Processing.- Database Management.- Telecommunication, Networking, and Integration.- Coding and Classification.- The Patient Record.- Biosignal Analysis.- Medical Imaging.- Image Processing and Analysis.- Primary Care.- Clinical Departmental Systems.- Clinical Support Systems.- Nursing Information Systems.- Methods for Decision Support.- Clinical Decision-Support Systems.- Strategies for Medical Knowledge Acquisition.- Predictive Tools for Clinical Decision Support.- Health Care Modeling.- Hospital Information Systems: Clinical Use and Technical Choices.- Health Information Resources Logical Operations.- Biostatistical Methods.- Biosignal Processing Methods.- Advances in Image Processing.- Pattern Recognition.- Modeling for Decision Support.- Structuring the CPR.- Evaluation of Information Systems.- Human-Computer Interaction in Health Care.- Costs and Benefits of Information Systems.- Security in Medical Information Systems.- Standards in Health Care.- Project Management.- Education and Training.- International Developments.
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Oct 11, 2017
Learning why similar experiments gave different results required over two years, countless confer... more Learning why similar experiments gave different results required over two years, countless conference calls, an obsessive attention to detail, and a new understanding of biology, explain
The outcome of clinical trials for cancer is typically summarized in terms of survival. However, ... more The outcome of clinical trials for cancer is typically summarized in terms of survival. However, different trials for the same disease may use different measures of survival, or use differing vocabulary to refer to the same outcome measure. This makes it harder to automate an objective comparison of treatments. We propose a temporal ontology of survival outcome measures that a) helps to standardize the vocabulary for reporting survival outcomes and b) makes it possible to automatically rank the relative efficacy of different treatments. The approach has been illustrated by examples from the oncology literature. The temporal ontology and the accompanying reasoner are freely available on Github ().
The Value Recommender system is the first of a planned set of intelligent authoring components in... more The Value Recommender system is the first of a planned set of intelligent authoring components in the CEDAR system. Future efforts will concentrate on deeper analyses of metadata to discover more interesting relationships between metadata fields, which will then drive new tools to assist biomedical investigators when annotating their data. The Value Recommender supports both freetext values and controlled terms. In this particular example, the system suggests terms from the Human Disease Ontology (DOID).
We present WebProt ég é 2, a Web-based tool for the collaborative editing of OWL ontologies. WebP... more We present WebProt ég é 2, a Web-based tool for the collaborative editing of OWL ontologies. WebProt ég é 2 is "Google docs" environment for ontologies which allows users to create and upload ontologies. It contains various tools that are designed to support collaborative ontology editing such as ontology change tracking, watches, notifications and issue tracking. Users can download a snapshot of an ontology at any point. In addition to this WebProt ég é 2 also features a simple user interface that offers quick and easy editing of commonly used OWL 2 axiom and class constructors. This interface works particularly well for biomedical ontologies which typically fall into the lightweight OWL2EL profile. WebProt ég é 2 is available to use at .
National Conference on Artificial Intelligence, Jul 1, 1992
The effectiveness of tools that provide support for software development is highly dependent on t... more The effectiveness of tools that provide support for software development is highly dependent on the match between the tools and their task. Knowledge-acquisition (KA) tools constitute a class of development tools targeted at knowledge-based systems. Generally, KA tools that are custom-tailored for particular application domains are more effective than are general KA tools that cover a large class of domains. The high cost of custom-tailoring KA tools manually has encouraged researchers to develop recta-tools for KA tools. Current research issues in meta-tooZs for knowledge acquisition are the specification styles, or me,a-views, for target KA tools used, and the relationships between the specification entered in the metatool and other specifications for the target program under development. We examine different types of meta-views and meta-tools. Our current project is to provide meta-too!s that produce KA tools from multiple specification sources--for instance, from a task analysis of the target application. = :. _
Property restrictions play an important definitional role in an ontology. The correct introductio... more Property restrictions play an important definitional role in an ontology. The correct introduction and inheritance of restrictions is important for ensuring the correct modeling of a domain. Many ontologies have large, complex class hierarchies, and many classes are defined with restrictions. When editing such an ontology, it is often difficult to determine the global impact of a local change. For example, removing a subclass link (axiom) can result in the unintentional loss of inherited restrictions over many levels. In this paper, we introduce a dynamic summarization and visualization methodology, called a Live Difference Taxonomy (LDT), to succinctly display a summary of the effects of changes to the ontology. LDTs are created on-the-fly as the ontology is edited, allowing an ontology developer to view the overall impact of their changes in a compact, visual display. We introduce an open-source plugin for the Protégé ontology editor that implements LDTs. It lets the users choose from several kinds of LDT summaries and lets them control the degree of summarization. The LDT Plugin supports heuristics-based alerts that inform the user of changes to sets of classes that are modeled with the same types of restrictions.
Interactive knowledge-acquisition (KA) programs allow users to enter relevant domain knowledge ac... more Interactive knowledge-acquisition (KA) programs allow users to enter relevant domain knowledge according to a model predefined by the tool developers. KA tools are designed to provide conceptual models of the knowledge to their users. Many different classes of models are possible, resulting in different categories of tools. Whenever it is possible to describe KA tools according to explicit conceptual models, it is also possible to edit the models and to instantiate new KA tools automatically for specialized purposes. Several meta-tools that address this task have been implemented. Meta-tools provide developers of domain-specific KA tools with generic design models, or meta-views, of the emerging KA tools. The same KA tool can be specified according to several alternative meta-views.
In this demonstration, we present the main features of WebProtégé, a free, opensource, cloud-base... more In this demonstration, we present the main features of WebProtégé, a free, opensource, cloud-based OWL ontology editor that supports simultaneous collaborative editing for geographically distributed users. WebProtégé is available for general purpose use at , where it hosts over 55,000 OWL ontology projects and over 42,500 user accounts. The software is open-source and all source code is available on GitHub 1 . WebProtégé 3.0 builds on the success of previous versions but features a new modern interface and new features for collaboration and review. This demonstration, at the ISWC2018 posters and demos session will enable attendees to see the latest features as well as providing them with an opportunity to interact with, and provide feedback to, the WebProtégé developers. We discuss the main features here. WebProtégé is essentially a "Google docs" for editing ontologies. Users access "projects" that are collections of OWL ontologies augmented with a change history, and issues/comments. WebProtégé provides a default user-interface that supports lightweight ontology editing, for ontologies that more or less fit within the OWL2EL profile. However, it can also be configured for editing ontologies that require full-blown OWL 2 axioms and class expressions. Ontology Editing Figure shows the main editing interface, which provides the familiar tabbed look and feel that is common to all desktop versions of Protégé. The classes tab is shown here, which comprises four resizable views: (Class Hierarchy, Class Description, Comments and Project Feed). Users can add, remove and customize the layout of views on a tab and the state of the user-interface is automatically persisted for each user in the context of a project. In contrast to previous versions, WebProtégé 3.0 uses proper URL routing, meaning that entities, such as classes, properties and individuals, and the tabs
Metadata that are structured using principled schemas and that use terms from ontologies are esse... more Metadata that are structured using principled schemas and that use terms from ontologies are essential to making biomedical data findable and reusable for downstream analyses. The largest source of metadata that describes the experimental protocol, funding, and scientific leadership of clinical studies is ClinicalTrials.gov. We evaluated whether values in 302,091 trial records adhere to expected data types and use terms from biomedical ontologies, whether records contain fields required by government regulations, and whether structured elements could replace free-text elements. Contact information, outcome measures, and study design are frequently missing or underspecified. Important fields for search, such as condition and intervention, are not restricted to ontologies, and almost half of the conditions are not denoted by MeSH terms, as recommended. Eligibility criteria are stored as semi-structured free text. Enforcing the presence of all required elements, requiring values for certain fields to be drawn from ontologies, and creating a structured eligibility criteria element would improve the reusability of data from ClinicalTrials.gov in systematic reviews, metanalyses, and matching of eligible patients to trials. .
Data Processing.- Database Management.- Telecommunication, Networking, and Integration.- Coding a... more Data Processing.- Database Management.- Telecommunication, Networking, and Integration.- Coding and Classification.- The Patient Record.- Biosignal Analysis.- Medical Imaging.- Image Processing and Analysis.- Primary Care.- Clinical Departmental Systems.- Clinical Support Systems.- Nursing Information Systems.- Methods for Decision Support.- Clinical Decision-Support Systems.- Strategies for Medical Knowledge Acquisition.- Predictive Tools for Clinical Decision Support.- Health Care Modeling.- Hospital Information Systems: Clinical Use and Technical Choices.- Health Information Resources Logical Operations.- Biostatistical Methods.- Biosignal Processing Methods.- Advances in Image Processing.- Pattern Recognition.- Modeling for Decision Support.- Structuring the CPR.- Evaluation of Information Systems.- Human-Computer Interaction in Health Care.- Costs and Benefits of Information Systems.- Security in Medical Information Systems.- Standards in Health Care.- Project Management.- Education and Training.- International Developments.
Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature, Oct 11, 2017
Learning why similar experiments gave different results required over two years, countless confer... more Learning why similar experiments gave different results required over two years, countless conference calls, an obsessive attention to detail, and a new understanding of biology, explain
The outcome of clinical trials for cancer is typically summarized in terms of survival. However, ... more The outcome of clinical trials for cancer is typically summarized in terms of survival. However, different trials for the same disease may use different measures of survival, or use differing vocabulary to refer to the same outcome measure. This makes it harder to automate an objective comparison of treatments. We propose a temporal ontology of survival outcome measures that a) helps to standardize the vocabulary for reporting survival outcomes and b) makes it possible to automatically rank the relative efficacy of different treatments. The approach has been illustrated by examples from the oncology literature. The temporal ontology and the accompanying reasoner are freely available on Github ().
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Papers by Mark Musen