Nigam H Shah
Affiliation: Stanford University
- Translational bioinformatics embraces big dataN H Shah
Stanford University School of Medicine, 1265 Welch Road, Room X 229, Stanford, CA 94305, USA E mail
Yearb Med Inform 7:130-4. 2012..Research that bridges the latest multimodal measurement technologies with large amounts of electronic healthcare data is increasing; and is where new breakthroughs will occur...
- Selected papers from the 15th Annual Bio-Ontologies Special Interest Group MeetingLarisa N Soldatova
Brunel University, London, UK
J Biomed Semantics 4:I1. 2013....
- STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentationTobias Wittkop
Buck Institute for Research on Aging, Novato, CA, USA
BMC Bioinformatics 14:53. 2013..Here, we developed and evaluated a tool for hypothesis generation from gene or protein lists using ontological concepts present in manually curated text that describes those genes and proteins...
- Chapter 9: Analyses using disease ontologiesNigam H Shah
Center for Biomedical Informatics Research, Stanford University, Stanford, California, United States of America
PLoS Comput Biol 8:e1002827. 2012....
- Selected papers from the 14th Annual Bio-Ontologies Special Interest Group MeetingLarisa N Soldatova
Aberystwyth University, Wales, UK
J Biomed Semantics 3:I1. 2012....
- Mapping between the OBO and OWL ontology languagesSyed Hamid Tirmizi
Department of Computer Science, The University of Texas at Austin, Austin, Texas 78701, USA
J Biomed Semantics 2:S3. 2011..In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner...
- HyQue: evaluating hypotheses using Semantic Web technologiesAlison Callahan
Department of Biology, Carleton University, Ottawa, Ontario, Canada
J Biomed Semantics 2:S3. 2011..Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks...
- Integration and publication of heterogeneous text-mined relationships on the Semantic WebAdrien Coulet
LORIA INRIA Nancy Grand Est, Campus Scientifique BP 239 54506 Vandoeuvre lès Nancy Cedex, France
J Biomed Semantics 2:S10. 2011....
- Selected papers from the 13th Annual Bio-Ontologies Special Interest Group MeetingLarisa N Soldatova
Aberystwyth University, Wales, UK
J Biomed Semantics 2:I1. 2011....
- Ontology-driven indexing of public datasets for translational bioinformaticsNigam H Shah
Centre for Biomedical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA
BMC Bioinformatics 10:S1. 2009..The key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts...
- Comparison of concept recognizers for building the Open Biomedical AnnotatorNigam H Shah
Centre for Biomedical Informatics, Stanford University, Stanford, CA 94305, USA
BMC Bioinformatics 10:S14. 2009..The Annotator service is available to the community as a REST Web service for creating ontology-based annotations of their data...
- Annotation and query of tissue microarray data using the NCI ThesaurusNigam H Shah
Stanford Medical Informatics, School of Medicine, Stanford University, Stanford, CA 94305, USA
BMC Bioinformatics 8:296. 2007..These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult...
- Biomedical ontologies: a functional perspectiveDaniel L Rubin
Stanford Center for Biomedical Informatics Research, Stanford, CA, USA
Brief Bioinform 9:75-90. 2008....
- The National Center for Biomedical OntologyMark A Musen
Center for Biomedical Informatics Research, Stanford University, Stanford, California 94305 5479, USA
J Am Med Inform Assoc 19:190-5. 2012....
- Identifying phenotypic signatures of neuropsychiatric disorders from electronic medical recordsSvetlana Lyalina
Department of Bioengineering, Stanford University, Stanford, California, USA
J Am Med Inform Assoc 20:e297-305. 2013..We investigated how EMR-based text mining and statistical analysis could elucidate the phenotypic boundaries of three important neuropsychiatric illnesses-autism, bipolar disorder, and schizophrenia...
- Using ontology-based annotation to profile disease researchYi Liu
Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California 94305, USA
J Am Med Inform Assoc 19:e177-86. 2012..Analyzing over a decade of funding data and publication data, the trends of disease research are profiled across topics, across institutions, and over time...
- Enabling enrichment analysis with the Human Disease OntologyPaea Lependu
Stanford Center for Biomedical Informatics Research, 251 Campus Drive, Medical School Office Building, Mail Code 5479, Stanford University, Stanford, CA 94305 5479, USA
J Biomed Inform 44:S31-8. 2011....
- Current progress in network research: toward reference networks for key model organismsBalaji S Srinivasan
318 Campus Drive, Clark Center S251, Stanford, CA 94305, USA
Brief Bioinform 8:318-32. 2007....
- BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applicationsPatricia L Whetzel
Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA
Nucleic Acids Res 39:W541-5. 2011..Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection...
- Mining clinical text for signals of adverse drug-drug interactionsSrinivasan V Iyer
Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
J Am Med Inform Assoc 21:353-62. 2014..We present an approach for identifying DDI signals directly from the textual portion of EHRs...
- Analyzing patterns of drug use in clinical notes for patient safetyPaea Lependu
Stanford University, Stanford, CA
AMIA Summits Transl Sci Proc 2012:63-70. 2012..Given our ability to quantify adverse event risks using the clinical notes, this will enable us to address patient safety because we can now rank-order off-label drug use and prioritize the search for their adverse event profiles...
- Automated detection of off-label drug useKenneth Jung
Program in Biomedical Informatics, Stanford University, Stanford, California, United States of America
PLoS ONE 9:e89324. 2014..We validated 403 predicted uses across independent data sources. Finally, we prioritize well-supported novel usages for further investigation on the basis of drug safety and cost. ..
- Practice-based evidence: profiling the safety of cilostazol by text-mining of clinical notesNicholas J Leeper
Division of Vascular Surgery and Cardiovascular Medicine, Stanford University, Stanford, California, United States of America
PLoS ONE 8:e63499. 2013..To assess the validity of this black box warning, we employed a novel text-analytics pipeline to quantify the adverse events associated with Cilostazol use in a clinical setting, including patients with congestive heart failure (CHF)...
- The Stanford Tissue Microarray DatabaseRobert J Marinelli
Department of Biochemistry, Stanford University School of Medicine, Howard Hughes Medical Institute, Stanford, CA, USA
Nucleic Acids Res 36:D871-7. 2008..The production server uses the Apache HTTP Server, Oracle Database and Perl application code. Source code is available to interested researchers under a no-cost license...
- The open biomedical annotatorClement Jonquet
Stanford Center for Biomedical Informatics Research and the National Center for Biomedical Ontology, Stanford University, Stanford, CA
Summit on Translat Bioinforma 2009:56-60. 2009..The biomedical community can use the annotator service to tag datasets automatically with ontology terms (from UMLS and NCBO BioPortal ontologies). Such annotations facilitate translational discoveries by integrating annotated data....
- Building a biomedical ontology recommender web serviceClement Jonquet
Center for Biomedical Informatics Research, Stanford University, CA 94305, USA
J Biomed Semantics 1:S1. 2010..The Recommender service (alpha version) is available to the community and is embedded into BioPortal...
- Unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginineYohannes T Ghebremariam
Department of Cardiovascular Sciences, Texas Methodist Hospital Research Institute, Houston, TX 77030, USA
Circulation 128:845-53. 2013..The mechanism of this possible adverse effect is not known. Whether the general population might also be at risk has not been addressed...
- Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical NotesPaea Lependu
Stanford Center for Biomedical Informatics Research, Stanford University, USA
J Biomed Semantics 3:S5. 2012..With the increasing access to large volumes of electronic medical data-in particular the clinical notes-it may be possible to computationally encode and to test drug safety signals in an active manner...
- Using temporal patterns in medical records to discern adverse drug events from indicationsYi Liu
Stanford University, Stanford, CA
AMIA Summits Transl Sci Proc 2012:47-56. 2012....
- Using text to build semantic networks for pharmacogenomicsAdrien Coulet
Department of Medicine, 300 Pasteur Drive, Room S101, Mail Code 5110, Stanford University, Stanford, CA 94305, USA
J Biomed Inform 43:1009-19. 2010..This network is used to guide the curation of PGx knowledge and provide a computable resource for knowledge discovery...
- An ontology-neutral framework for enrichment analysisRob Tirrell
Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305
AMIA Annu Symp Proc 2010:797-801. 2010..We outline the methodology of enrichment analysis, the associated challenges, and discuss novel analyses enabled by RANSUM...
- A Comprehensive Analysis of Five Million UMLS Metathesaurus Terms Using Eighteen Million MEDLINE CitationsRong Xu
Center for Biomedical Informatics Research, Stanford University School of Medicine Stanford, CA 94305, USA
AMIA Annu Symp Proc 2010:907-11. 2010..This filtered and augmented UMLS Metathesaurus can potentially be used to improve efficiency and precision of UMLS-based information retrieval and NLP tasks...
- A case study in pathway knowledgebase verificationStephen A Racunas
Computational Learning Laboratory, Stanford University, CA, USA
BMC Bioinformatics 7:196. 2006..But before we can reliably use a pathway knowledge-base as a data source, we need to proofread it to ensure that it can fully support computer-aided information integration and inference...