Phenopackets: Making phenotype profiles FAIR++ for disease diagnosis and discovery

<div><div><div><p>It is estimated 350 million people worldwide are afflicted with a rare disease. Because each disease is different, there are significant challenges in obtaining enough information relevant to the patient’s condition to help inform diagnosis and treatment. While great strides have been made in exchange formats for sequence data, complementary standards for phenotypes and environment are urgently needed. Patient phenotypic abnormalities are currently described in diverse places in diverse formats: publications, public databases, electronic health records, clinical testing labs, disease registries, and social media. Here we propose a new standard for exchange of patient phenotype data that is optimized for integration from these distributed contexts. The PXF standard will allow phenotypic data to be captured at the point of publication, to be transmitted in the context of diagnostic testing, to be used for exchange of data in clinical studies, and as a backbone for patient-contributed data registries and social media. Increasing the volume of computable phenotype data across a diversity of systems will support large-scale computational disease analysis using combined genotype and phenotype data - something that patients themselves will now be able to participate in.</p></div></div></div

Curation Innovation- Data integrator and standards role

Innovations in curation: Developing consistency among standards, tools, protocols; improving accuracy of text mining; integrating curation into research, publishing, reviewing workflows and laboratory information systems; existing “gold standard” curation vs alternative methods, e.g., crowdsourcing, automation. What are concrete examples where curation has added value and lack of curation has been disastrous? Do we have metrics to evaluate success? This slide presented as the data integrator and data standards developer

Getting More From Your VIVO

Workshop/tutorial slides for introducing the VIVO-ISF ontology via SPARQL queries.  No prior SPARQL experience is required

SciENcv-OpenRIF Integration

This presentation was given as part of the OpenRIF workshop on April 17, 2016 at the FORCE2016 conference.  It provides background on the SciENcv system, the goals of integrating it with OpenRIF, and some details on how the integration is being accomplished.<br

Data Managment Open House

<p>This event was the first of a two-part program aimed at understanding how libraries and librarians can facilitate data management, data publication, reproducibility, and data reuse as part of an award from Force11 to Melissa Haendel. The overall project goal is to promote interaction between librarians and research scientists to help define new roles for the OHSU library.</p

Getting More From Your VIVO: Generating Reports and Functional Datasets For Analysis

<p>Research information systems are important tools for individuals, institutions, and consortia and can inform decision making, assessment, and collaborative activities. This workshop will cover the concept of research impact and indicators of impact within the VIVO ontology, business processes, and workflow for generating reports and datasets from your VIVO. Attendees of the workshop will gain a better perspective of strategies to identify and monitor research impact using their systems and a recipe book (including sparql queries) to generate meaningful reports and data sets. Attendees will be able to participate in hands-on work with the VIVO-ISF ontology to identify existing indicators and brainstorm possible ontology extensions for incorporation into the data framework. Finally, an open discussion on consortial approaches for use of this data will conclude the session.</p

Get real: A synthetic dataset illustrating clinical and genetic covariates

Poster presentation at BD2K All Hands Meeting 2016 (https://datascience.nih.gov/bd2k/AHM) discussing BD2K funded work to develop a script to generate realistic synthetic datasets for hands-on learning in BD2K workshops

Improving Knowledge Discovery Through Development of a Big Data to Knowledge Skills Course - Research Week 2015

Poster presentation at OHSU Research Week 2015, discussing BD2K funded work to develop and implement data science skills courses at Oregon Health & Science University in Portland, Oregon.<br

CVD Risk Prediction Synthetic Dataset

This is a synthetic dataset to teach students about using clinical and genetic covariates to predict cardiovascular risk in a realistic (but synthetic) dataset.<br><p>For the workshop materials, please go here: https://github.com/laderast/cvdNight1</p><p>Contents:</p><p>1) dataDictionary.pdf - pdf file describing all covariates in the synthetic dataset.</p><p>2) fullPatientData.csv - csv file with multiple covariates</p><p>3) genoData.csv - subset of patients in fullPatientData.csv with additional SNP calls.</p><p><br></p

An ecosystem of contributions

Slides for opening of the openRIF workshop at Force2016. <div>There exists an ecosystem of different projects that aim to represent the different aspects of the research ecosystem. OpenRIF aims to bring these efforts together to help support interoperability, improved attribution, and use of research data for analytics and team science.</div