Marcos Martinez-Romero, PhD (Research Software Developer)
Martin J. O’Connor, M.S. (Senior Software Developer)
The CEDAR system: a suite of tools to simplify the authoring of high-quality metadata in biomedicine
Abstract:
The ability to find and to access biomedical data that are stored in online repositories depends on the quality of the associated metadata. There is a growing set of community-developed guidelines and standards for defining such metadata, but the barriers to creating metadata using those standards are tremendously high. Producing well-defined metadata takes time and effort, and many investigators view the metadata authoring task as a burden. The Center for Expanded Data Annotation and Retrieval (CEDAR) is a Center of Excellence supported by the NIH Big Data to Knowledge (BD2K) initiative that is developing technologies to assist the process of managing biomedical metadata. We take advantage of emerging community-based standard templates for describing different kinds of biomedical datasets, and we investigate the use of computational techniques to help investigators to assemble templates and to fill in their values. Our goal is to develop an end-to-end system to support the creation of comprehensive and expressive metadata to facilitate data discovery, interoperability, and reuse. In this talk, we will provide an overview of the tools that we are developing and outline our future plans for simplifying the process by which biomedical investigators annotate their experimental data with high-quality metadata.
Peter Hendler, MD
Kaiser Permanente
Abstract:
Oxford University Department of Computer Science has developed an RDF triple store optimized for large scale data analysis. It uses a profile of OWL called OWL2 RL. It uses Datalog language and can materialize data on multiple threads. We will explain how this was used to calculate HEDIS diabetes quality measures in one region of Kaiser Permanente.
Maulik Kamdar, Graduate Student
Musen Lab, Stanford University
Abstract:
Biomedical informatics research relies on the ability to integrate and analyze data and knowledge from several heterogeneous sources simultaneously. However, biomedical data and knowledge exist in isolated databases and knowledgebases, with varying schemas, notations and formats. This necessitates biomedical researchers to jump across these sources, or require increased skills and knowledge to query them in unison, and to integrate the retrieved results. To address the challenges of integrative bioinformatics, data publishers have started using Semantic Web technologies, such as the Resource Description Framework (RDF) and the SPARQL structured query language. Semantic Web technologies generate a linked and heterogeneous data space, termed Life Sciences Linked Open Data Cloud (LSLOD), which extends over the traditional Web. However, the current state of the LSLOD cloud is still unusable for most biomedical researchers due to architectural issues and learning requirements.
In this talk, I will discuss current methods in query federation over the LSLOD cloud. I will also present our research and ideas for a rule-based query federation method. Finally, I will discuss application of this method towards biomedical question-answering and systems pharmacology.
Marcos Martínez-Romero, PhD
Research Software Developer
BMIR, Stanford University
Abstract:
The ability to find and to access biomedical data that are stored in online repositories depends on the quality of the associated metadata. Despite the growing number of community-developed standards for describing biomedical experiments, the practical difficulties to creating accurate, complete, and consistent metadata are still considerable.
The Center for Expanded Data Annotation and Retrieval (CEDAR) is developing novel methods and tools to simplify the process by which investigators annotate their experimental data with metadata. The CEDAR Workbench is a suite of Web-based tools that together form a pipeline for authoring metadata. As a step towards decreasing authoring time and effort while increasing metadata quality, we have enhanced the CEDAR Workbench with predictive data entry capabilities. Our system identifies common patterns in the CEDAR metadata repository, and generates real-time suggestions for filling out metadata acquisition forms. These suggestions are context-sensitive, meaning that the values predicted for a particular field are generated and ranked based on previously entered values.
In this talk, I will discuss some of the challenges that have arisen while implementing our approach, and our strategies for making this capability useful to the end users of CEDAR. I will demonstrate CEDAR’s intelligent authoring capabilities, and show how the technology that we are developing leverages existing metadata to make the authoring of high-quality metadata a manageable task.
Presenter: Dr. Manali I. Patel, MD
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The mission of the Stanford Center for Clinical Research (SCCR) includes offering educational resources, training, and support for investigators and research staff. We have invited the Assistant Professor of Medicine in Oncology, Dr. Manali I. Patel, MD, to provide you with the principles of oncology and treatments. The speaker will review etiologies and determinants for disparities. She will also review research areas including delivery science and its application to care delivery for patients with oncologic diseases.
At the conclusion of this class, you will be able to:
- Apply principles of Cancer Epidemiology
- Examine Screening Policies and Implications for Cancer
- Explain principles of ZNA as etiologies for disparities in cancer development and outcomes
- Analyze barriers that lead to disparities across the cancer continuum
- Apply strategies to overcome barriers in current cancer care delivery
Attendance is open to all research staff.
About the Instructors:
Dr. Manali I. Patel, MD, is a medical thoracic oncologist and health services researcher at the Stanford University School of Medicine and the Veterans Affairs Palo Alto Health Care System. She obtained her MD and Masters in Public Health at UNC-Chapel Hill and completed her Internal Medicine residency, fellowship in Hematology and Oncology, and Masters in Science in Health Services Research at Stanford University. Dr. Patel’s research involves evaluating systems-level and social factors that influence disparities in cancer and value-based care delivery. Her expertise lies in designing, implementing, and evaluating new models of cancer care delivery with academic, community, and VA oncology practices aimed to improve patient experiences with care, clinical outcomes, and reduce unwanted healthcare utilization and health disparities. Dr. Patel also has expertise in linking large cancer registries to investigate modifiable etiologies for disparate care receipt among populations.
BRN OPTIONAL
Spectrum is an approved provider by the California Board of Registered Nursing, Provider Number CEP15435 for 2 contact hour(s).
To receive your certificate with BRN credit, you are required to complete an evaluation at the conclusion of this class.
BRN Cancellation Policy: If you wish to cancel your registration, please contact the course coordinators, Susan Saba, ssaba@stanford.edu.
Speakers: Corinna Louise Delucia, MSN, PNP, RN, CPHON, & Christina Baggott, PhD, PPCNP, RN, CPON
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The mission of the Stanford Center for Clinical Research (SCCR) includes offering educational resources, training, and support for investigators and research staff. We have invited two clinical research Nurse Practitioners from Cancer Clinical Trial Office, Corinna Louise Delucia, MSN, PNP, RN, CPHON, and Christina Baggott, PhD, PPCNP, RN, CPON, to provide you with a brief overview of the main and common pediatric leukemia, for the 1st hour of the class; then summarize the development and implementation of a novel Phase I trial using Chimeric Antigen Receptor T-cell Therapy for patients with Diffuse Midline Gliomas, during the 2nd hour of the class.
At the conclusion of this class, you will be able to:
- Discuss the classification, incidence, and risk factors of the main pediatric leukemias
- Discuss in detail Acute Lymphoblastic Leukemia (ALL) including presentation, diagnostic workup, risk evaluation, and treatment
- Review the frontline study for ALL open at Stanford
- Review the rationale for using GD2 CAR-T for patients with DIPG and other midline gliomas.
- Describe methods to administer GD2 CAR-T therapy.
- Identify common toxicities experienced by patients who receive GD2 CAR-T therapy.
- Review methods to ameliorate toxicities experienced by patients who receive GD2 CAR-T therapy.
Attendance is open to all research staff.
About the Instructors:
Corinna Louise DeLucia, MSN, PNP, RN, CPHON, is a Pediatric Nurse Practitioner with almost 10 years of experience in pediatric hematology and oncology. She completed her first undergraduate degree at Cornell University where she majored in Biological Sciences and minored in Business. She then went to The University of Rochester where she obtained her bachelor’s and master’s degrees in nursing. She has worked in a variety of roles within pediatric oncology which has provided her a diverse understanding of the many facets of health care. She has worked as a bedside nurse, travel nurse, nurse manager, inpatient nurse practitioner, outpatient nurse practitioner, and currently as a research nurse practitioner. Most of her more recent experience has focused specifically on patients with liquid tumors. She currently supports 3 studies opened at Stanford which focus on patients with leukemia (ALL and AML) as well as Classical Hodgkin’s Lymphoma. She has been helping to teach the newest pediatric oncology nurses about pediatric oncology and chemotherapy for the past 3.5 years as an instructor for the APHON chemotherapy provider course.
Christina Baggott (Tina), PhD, PPCNP, RN, CPON, is a Clinical Research Nurse Practitioner in the Cancer Clinical Trials Office at Stanford University. She received her Undergraduate Degree from the University of Alabama; her Master’s Degree from Emory University; and her Doctoral degree from the University of California, San Francisco. Currently Dr. Baggott helps manage clinical trials for patients who are receiving Chimeric Antigen Receptor T-cell (CART) therapy. Her program of research is focused on an evaluation of the symptom experience of children receiving treatment for cancer. Aspects of this program of research include the assessment of changes in symptom occurrence, severity, and distress across the child’s treatment trajectory, potential genetic influences on symptom severity, the impact of symptoms on patient outcomes (e.g., functional status, quality of life), and parents’ perceptions of children’s symptoms. An additional focus of her research is the use of technology to develop and evaluate tools on mobile platforms to assess and manage cancer-related symptoms (mHealth).
BRN OPTIONAL
Spectrum is an approved provider by the California Board of Registered Nursing, Provider Number CEP15435 for 2 contact hour(s).
To receive your certificate with BRN credit, you are required to complete an evaluation at the conclusion of this class.
BRN Cancellation Policy: If you wish to cancel your registration, please contact the course coordinators, Susan Saba, ssaba@stanford.edu.
Speakers: Dr. Everett Meyer, MD, PhD, and Dr. Stephan Busque, MD
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The mission of the Stanford Center for Clinical Research (SCCR) includes offering educational resources, training, and support for investigators and research staff. We have invited the Associate Professor of Medicine, BMT and Cell Therapy, Dr. Everett Meyer, MD, PhD, and the Professor of Surgery and Abdominal Transplantation, Dr. Stephan Busque, MD, to provide you with the Stanford Experience on the Cell Immune Therapy Tolerance, and discuss a patient experience as CIT trial participant. The speakers will review the genesis and development of the “Strober Protocol” where kidney transplant patients also get a minimally intensive allogeneic hematopoietic transplant from their patient. They will review how clinical trial conduct has been implemented and developed.
At the conclusion of this class, you will be able to:
- Explain the biology and science of how mixed hematopoietic chimerism induces immune tolerance.
- Review two decades of clinical trial results testing kidney and hematopoietic stem cell transplantation at Stanford.
- Understand clinical trial conduct and successes and challenges of these trial.
- Discuss patient experience being a trial participant.
Attendance is open to all research staff.
About the Presenters:
Dr. Everett Meyer, MD, PhD, MS, is an Associate Professor in the division of Blood and Marrow Transplantation and Cellular Therapy, with courtesy appointments in Surgery and Pediatrics. He has a focus on the pre-clinical and clinical study of immune tolerance. He serves as director of the Cellular Immune Tolerance program supported by DOM and Surgery and which receives critical clinical trial support from SCCR. His scientific focus is the study of hematopoietic chimerism and T regulatory cell therapy.
Dr. Stephan Busque, MD, is a Professor in the division of Abdominal Transplantation Surgery. He serves as Director Adult Kidney and Pancreas Transplant Program and Surgical Director of the Cellular Immune Tolerance Program and is widely regarded as a leading expert in the clinical implementation of immune tolerance in kidney transplantation. His research interest is focused on the improvement of clinical immunosuppression. He is involved in the evaluation of new immunosuppressive drugs, potentially more efficacious or less toxic, with the ultimate goal to achieve tolerance.
BRN OPTIONAL
Spectrum is an approved provider by the California Board of Registered Nursing, Provider Number CEP15435 for 2 contact hour(s).
To receive your certificate with BRN credit, you are required to complete an evaluation at the conclusion of this class.
BRN Cancellation Policy: If you wish to cancel your registration, please contact the course coordinators, Susan Saba, ssaba@stanford.edu.