BMIR News

The Shah Lab Green Button Team Awarded The 2019 ISP Star Award

The Shah Lab Green Button team (center, from left to right: Ken Jung, Vladimir Polony, Alison Callahan, Saurabh Gombar) received a 2019 ISP Star Award, which recognizes individuals from the Stanford Medicine community who, through their extraordinary efforts, embody the strategic priorities of our Integrated Strategic Plan (ISP): Value Focused, Digitally Driven, and Uniquely Stanford. By developing a technology that amplifies the clinical impact of our world-class faculty and creates outcome-driven recommendations at the point care, the Green Button exemplifies the transformative power of collaboration at Stanford Medicine. They were presented the award by David Entwistle (President and CEO of Stanford Health Care; left), Lloyd Minor (Dean of the School of Medicine; second from right) and Paul A. King (President and CEO of Stanford Children's Health; right).

 

 

Hernandez-Boussard and Colleagues Find that SSRIs Reduce the Effectiveness of Hydrocodone and Codeine

Research led by BMIR's Tina Hernandez-Boussard, colleague Ian Carroll and grad student Arjun Parthipan found that patients on SSRIs such as Zoloft, Paxil and Prozac who were prescribed prodrug opoids such as hydrocodone or codeine experienced more post-surgery pain than patients not on SSRIs. Hernandez-Boussard's team built a machine-learning algorithm that predicts how a patient will respond to different types of opoids. 

Read the NPR article

Read the Scope article

 

Gevaert and Lucence Dx Team Up to Apply AI to Liver Cancer Diagnosis and Treatment

BMIR’s Olivier Gevaert and Lucence Diagnostics have teamed up to develop artificial intelligence algorithms for improving diagnosis and treatment of liver cancer with the goal of combining imaging and molecular data from liver cancer patients into smarter software tools that help physicians make better treatment decisions.

GO FAIR

The CEDAR project has been chosen as a key participant in the GO FAIR Metadata for Machines (M4M) workshops and the FAIR Funder pilot program. The GO FAIR initiative, an international program to advance FAIR (findable, accessible, interoperable, reusable) data and services, launched the M4M workshop series to stimulate the creation and re-use of FAIR metadata standards and machine-ready metadata templates. The M4M workshops have adopted CEDAR to provide the metadata capabilities for the initial workshops.

 

The M4M workshops are agile events that bring together domain experts, metadata specialists, and technical developers to define metadata elements and standards, create machine-actionable templates for collecting metadata according to those standards, and register the templates for open access, discovery, and re-use. CEDAR has worked with the Leiden-based GO FAIR team for over a year to demonstrate and evaluate the CEDAR technologies for these tasks, and participated in two recent M4M workshops. At the second of these, two national science funders—the Health Research Board of Ireland (HRB) and the Netherlands Organisation for Health Research and Development (ZonMW)—took the first steps toward a complete life cycle of FAIR metadata for their communities by creating CEDAR templates to capture metadata of interest to research funding agencies.

 

In coming months, CEDAR expects to participate in several more M4M workshops, and advance the FAIR Funder pilot program (depicted in the diagram) through many more of the 7 stages shown in the diagram. CEDAR initially provided services to define metadata elements (1), create machine-actionable templates (2), and register the templates in the CEDAR repository for later re-use (3), and CEDAR enhancements already under way will provide advanced search and open publication for the CEDAR metadatda resources that have been developed, and integrated metadata authoring in coordination with the DSL Data Wizard (4). Also important to GO FAIR: CEDAR already provides rigorous semantic capabilities that let CEDAR metadata be published as JSON-LD or simple RDF triples, two highly interoperable formats for sharing research metadata.

 

The CEDAR technologies adopted by GO FAIR's M4M workshops and the FAIR Funder pilot program are helping the GO FAIR community move metadata management from ad-hoc, individually developed solutions to a more rigorous, structured, and user-friendly approach to metadata. 

https://www.go-fair.org/resources/go-fair-workshop-series/metadata-for-machines-workshops/

https://arxiv.org/abs/1902.11162

https://www.go-fair.org/

 

Explore BMIR

At BMIR, we develop computatiional methods for biomedical discovery that influence medical decisions.

Learn more about the cutting-edge ways we are advancing technology and biomedicine to improve human health.

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Notable Projects and Services

CEDAR is making data submission smarter and faster, so biomedical researchers and analysts create and use better metadata.

 

Diagnostics - Infectious Diseases

EteRNA, an online puzzle, enlists video gamers to try to design a sensor module that could make diagnosing TB as easy as taking a home pregnancy test.

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The NCBO manages a repository of all the world’s publicly available biomedical ontologies and terminologies—now more than 390 in number.

Green Button

Green button: the promise of personalizing medical practice guidelines in real time

Protégé is the most widely used ontology-development system in the world.

CoINcIDE

CoINcIDE, is a novel methodological framework for the discovery of patient subtypes across multiple datasets that requires no between dataset transformations.

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