MScanner: a classifier for retrieving Medline citations (2008)
Poulter, Graham L, Rubin, Daniel L, Altman, Russ B, Seoighe, Cathal
Abstract Background Keyword searching through PubMed and other systems is the standard means of retrieving information from Medline. However, ad-hoc retrieval systems do not meet all of the needs of...
Annotation and query of tissue microarray data using the NCI Thesaurus (2007)
Shah, Nigam H, Rubin, Daniel L, Espinosa, Inigo, Montgomery, Kelli, Musen, Mark A
Abstract Background The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated...
Rubin, Daniel L., Lewis, Suzanna E., Mungall, Chris J., Misra, Sima, Westerfield, Monte, Ashburner, Michael, ...
The National Center for Biomedical Ontology (http://bioontology.org) is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists funded by the NIH Roadmap to...
Indexing pharmacogenetic knowledge on the World Wide (2004)
Russ B. Altman, David A. Flockhart, Stephen T. Sherry, Diane E. Oliver, Daniel L. Rubin, Teri E. Klein
this article is prohibited
Daniel L. Rubin, Farhad Shafa, Diane E. Oliver, Micheal Hewett, Russ B. Altman
Motivation: The information model chosen to store biological data affects the types of queries possible, database performance, and difficulty in updating that information model. Genetic sequence data...
Ontology Development For A Pharmacogenetics Knowledge Base (2002)
Diane E. Oliver, Daniel L. Rubin, Joshua M. Stuart, Micheal Hewett, Teri E. Klein, B. Altman
this paper is limited to the problem of modeling biological, pharmacological, and clinical data to support the goal of linking genotype to phenotype
Automating Data Acquisition Into Ontologies From (2002)
Daniel L. Rubin, Micheal Hewett, Diane E. Oliver, Teri E. Klein, B. Altman
armacogenetics data amenable to computational analysis. 1 Introduction 1.1 Pharmacogenetics and the need to connect diverse data Connecting genotype and phenotype data is the quest of...
Daniel L. Rubin, Micheal Hewett, Diane E. Oliver, Teri E. Klein, B. Altman
eous information sources in order make the diversity of pharmacogenetics data amenable to computational analysis. 1 Introduction 1.1 Pharmacogenetics and the need to connect diverse data Connecting...
PharmGKB: the Pharmacogenetics Knowledge Base (2002)
Micheal Hewett, Diane E. Oliver, Daniel L. Rubin, Katrina L. Easton, Joshua M. Stuart, Russ B. Altman, ...
The Pharmacogenetics Knowledge Base (PharmGKB; http://www.pharmgkb.org/) contains genomic, phenotype and clinical information collected from ongoing pharmacogenetic studies. Tools to browse, query,...
Ontology Development for a Pharmacogenetics Knowledge Base (2001)
Diane E. Oliver, Daniel L. Rubin, Joshua M. Stuart, Micheal Hewett, Teri E. Klein, B. Altman
this paper is limited to the problem of modeling biological, pharmacological, and clinical data to support the ultimate goals of linking genotype to phenotype
Knowledge Representation and Tool Support for Critiquing (2000)
Daniel L. Rubin, John Gennari, Mark A. Musen
The increasing complexities of clinical trials have led to increasing costs for investigators and organizations that author and administer those trials. The process of authoring a clinical trial...
Tool Support for Authoring Eligibility Criteria for Cancer Trials (1999)
Daniel L. Rubin, John H. Gennari, Sandra Srinivas, Allen Yuen, Herbert Kaizer, Mark A. Musen, ...
A critical component of authoring new clinical trial protocols is assembling a set of eligibility criteria for patient enrollment. We found that clinical protocols in three different cancer domains...
PharmGKB: the Pharmacogenetics Knowledge Base
Hewett, Micheal, Oliver, Diane E., Rubin, Daniel L., Easton, Katrina L., Stuart, Joshua M., Altman, Russ B., ...
The Pharmacogenetics Knowledge Base (PharmGKB; http://www.pharmgkb.org/) contains genomic, phenotype and clinical information collected from ongoing pharmacogenetic studies. Tools to browse, query,...
A Statistical Approach to Scanning the Biomedical Literature for Pharmacogenetics Knowledge
Rubin, Daniel L., Thorn, Caroline F., Klein, Teri E., Altman, Russ B.
Objective: Biomedical databases summarize current scientific knowledge, but they generally require years of laborious curation effort to build, focusing on identifying pertinent literature and data...
PharmGKB: the Pharmacogenetics Knowledge Base
Hewett, Micheal, Oliver, Diane E., Rubin, Daniel L., Easton, Katrina L., Stuart, Joshua M., Altman, Russ B., ...
The Pharmacogenetics Knowledge Base (PharmGKB; http://www.pharmgkb.org/) contains genomic, phenotype and clinical information collected from ongoing pharmacogenetic studies. Tools to browse, query,...
A Statistical Approach to Scanning the Biomedical Literature for Pharmacogenetics Knowledge
Rubin, Daniel L., Thorn, Caroline F., Klein, Teri E., Altman, Russ B.
Objective: Biomedical databases summarize current scientific knowledge, but they generally require years of laborious curation effort to build, focusing on identifying pertinent literature and data...
Ontology-based Annotation and Query of Tissue Microarray Data
Shah, Nigam H., Rubin, Daniel L., Supekar, Kaustubh S., Musen, Mark A.
The Stanford Tissue Microarray Database (TMAD) is a repository of data amassed by a consortium of pathologists and biomedical researchers. The TMAD data are annotated with multiple free-text fields,...
Ontology-Based Representation of Simulation Models of Physiology
Rubin, Daniel L., Grossman, David, Neal, Maxwell, Cook, Daniel L., Bassingthwaighte, James B., Musen, Mark A.
Dynamic simulation models of physiology are often represented as a set of mathematical equations. Such models are very useful for studying and understanding the dynamic behavior of physiological...
Protégé-OWL: Creating Ontology-Driven Reasoning Applications with the Web Ontology Language
Rubin, Daniel L., Knublauch, Holger, Fergerson, Ray W., Dameron, Olivier, Musen, Mark A.
Protégé OWL1 is an open source tool created to support ontology development for the Semantic Web. It is a plug-in extension to the Protégé ontology development platform. Protégé OWL allows...
Use of Description Logic Classification to Reason about Consequences of Penetrating Injuries
Rubin, Daniel L., Dameron, Olivier, Musen, Mark A.
The consequences of penetrating injuries can be complex, including abnormal blood flow through the injury channel and functional impairment of organs if arteries supplying them have been severed....
Challenges in Converting Frame-Based Ontology into OWL: the Foundational Model of Anatomy Case-Study
Dameron, Olivier, Rubin, Daniel L., Musen, Mark A.
A description logics representation of the Foundational Model of Anatomy (FMA) in the Web Ontology Language (OWL-DL) would allow developers to combine it with other OWL ontologies, and would provide...
Annotation and query of tissue microarray data using the NCI Thesaurus
Shah, Nigam H, Rubin, Daniel L, Espinosa, Inigo, Montgomery, Kelli, Musen, Mark A
Protégé: A Tool for Managing and Using Terminology in Radiology Applications
Rubin, Daniel L., Noy, Natalya F., Musen, Mark A.
The development of standard terminologies such as RadLex is becoming important in radiology applications, such as structured reporting, teaching file authoring, report indexing, and text mining. The...