Welcome to the Translator Ambassadors and Champions Program!

Agenda

ROVER Working Group

(Relationships and Outreach for Visible Engagement and Resources) rover-relations@lists.renci.org

Meet the ROVER Working Group Members

Karamarie (Kara) Fecho

• Founder and CEO, Copperline Professional Solutions, a biomedical data science and communications consulting firm; Research Affiliate, RENCI/UNC
• I’ve been engaged with the Translator program since its inception in 2016, serving in a variety of roles (Clinical Data Committee Chair, Publications Committee Chair, ROVER WG Lead, etc)
• My scientific background spans a wide range of clinical and translational science domains (e.g., neurobiology, anesthesiology, immunology, toxicology, pharmacology) and runs the gamut from basic science research to clinical research to patient safety research to hospital QA/QI (Anesthesiology); complementing this domain expertise, I have expertise in open team science, community engagement, data governance, data integration, data analytics, FAIR principles, data privacy and security, federated knowledge systems, and sustainable biomedical data ecosystems; I also have extensive teaching experience

Simon King

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Kelyne (KK) Noel

• Research Project Manager at RENCI at the University of North Carolina at Chapel Hill, where I lead a variety of projects across biomedical research, AI, data science, biology and public health,.I am the project manager of the Translator UEIC as well as ROVER. I have Master of Public Health from UNC Gillings School of Global Public Health. My background is in microbiology; I’ve worked in pharmaceuticals, medical devices, as well as consumer germkill products.

Kihwa Kang

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Ayushi Agrawal

• Member of Translator User Engagement and Senior Bioinformatician at the Gladstone Institutes. My research collaborations span diverse biomedical domains and a broad spectrum of data types, including multi-omics, imaging, and other high-dimensional datasets. I enjoy working at the intersection of biology, data science, and statistics to help researchers extract meaningful insights from complex data, and I am passionate about mentoring and bioinformatics education.

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Reese Rose

• Translator UI Team Product / UX Designer, interested in intersection of healthcare + technology, from DC Metro area & now living near St. Pete, FL

Guangrong Qin

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Andy Crouse

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What is Translator?

• Translator is NOT Google
• Translator is NOT an LLM, AI, agentic AI, …
• Translator is a knowledge graph (KG) system that aims to radically change the concept of “disease” from one that is symptom-based and narrowly-focused to one that is mechanism-based and considers, for example, the interplay between biomedical entities and biological systems, the relationship between rare and common disease, and the impact of social and environmental determinants of health and disease
• Translator aims to achieve this goal through the integration, harmonization, and exploration across hundreds of open clinical and biomedical data sources, using a KG–based approach to discovery, where the answers are fully qualified with evidence and provenance

Announcing the Translator System!

“This is the vision of the Biomedical Data Translator: to bridge the current symptom-based diagnosis of disease with research-based molecular and cellular characterizations through an informatics platform that enables interrogation of relationships across the full spectrum of data types, from disease names, clinical signs and symptoms, to organ and cell pathology, genomics, and drug effects.”

— Dr. Christopher Austin, former Director of NCATS

Translator Architecture

• Two main entry points:
• User Interface (80%)
• Translator Component Toolkit (TCT) (20%)

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Glossary of terms

ARAs

KPs

*High-level architectural diagram remains under development; please contact @Gaurav Vaidya with questions

Translator Ambassadors & Champions Program

• Translator Ambassadors and Champions are clinical and translational scientists, software developers, semantic engineers, bioinformaticians, or computational biologists who are eager to use Translator to advance their translational research and technical skills/research
• They are translational scientists and technical professionals motivated to engage their research communities and willing to spread awareness of and information about the Translator System and Consortium

Program Background

• Modeled on the highly successful “Ambassadors & Champions” program developed by the Center for Scientific Collaboration and Community Engagement (CSCCE) and adopted by the National Microbiome Data Collaborative (NMDC)

Program Commitment

• 4–12 hours per month, 9–12 months minimum commitment
• BUT program is flexible and does not have an established end date

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We want you to become regular Translator users and members of the broader Translator Consortium!

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• Must focus on a specific project, using the Translator UI and/or the Translator Component Toolkit
• Project may emerge organically or through brainstorming with ROVER WG members and/or among yourselves

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Goal is to identify a project that interests and excites you and that you can present at a meeting or conference of your peers and/or publish in a journal article or another communications forum!

Program Requirements

Translational Science Ambassadors and Technical Champions are expected to:

• Share contact information, affiliation, and professional interests with other program participants and the broader Translator Consortium (pinned to Slack channel)
• Create a Translator user account at https://ui.transltr.io
• Participate in user engagement sessions
• One-hour follow-up meetings
• Usability testing, feature testing
• Program determination of participant interests and potential projects
• Present your project at one approved meeting, conference, or workshop in field of interest OR publish your project in an approved journal or other communications forum
• Funding support is provided for program graduation!
• Agree to abide by all Translator Consortium guidelines

Program Rewards

• Travel support for one approved scientific or technical meeting OR APC charges for one approved scientific or technical publication
• Maximum = $2500 per participant (10 participant cap)
• Training in use of Translator UI and Translator Component Toolkit
• Participation in Translator hackathons
• Opportunities to highlight project during Translator hackathons and other Translator events
• Networking opportunities with other program participants, broader Translator Consortium, and NCATS program leadership
• Promotion on Translator website (if possible)
• Scientific authorship and/or recognition for code contribution (when appropriate)

Program Support

• Welcoming package
• Overview of program and commitment
• ROVER WG member contact information
• Key Translator publications
• Translator tutorial (see video in https://ascpt.onlinelibrary.wiley.com/doi/10.1111/cts.70284 - noting that the UI has been updated since the tutorial was published!)
• Glossary of terms
• ROVER WG listserv: rover-relations@lists.renci.org
• Contact information for individual members can be found in welcoming package
• Dedicated slack channel: #translator-ambassadors-champions
• Monthly A&C check-in calls
• Monthly A&C HELP desk calls
• Handy tools, for example: Name Resolver and Node Normalizer

Your feedback is welcome!

Meet your fellow A&C Participants

Terence Egbelo

• Postdoctoral Fellow, Evotec; Recent PhD graduate from the University of Sheffield, England
• Using the Translator Tier 0 KG to validate a biomedical KG completion algorithm

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Natalie Gil

• Bioinformatician, Gladstone Institutes Bioinformatics Core
• Using the TCT to develop a new Translator tool, GeneSet Translator, that aims to make high-dimensional, multi-gene input, pathfinder query results interpretable

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Ginnie Hench

• Director, Open BioData Modeling
• Using the UI + the TCT to derive evidence in support of select key event relationships (KER) in the AOP-wiki

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Julie Horvath

• Senior Research Scientist, Renaissance Computing Institute; Director of RENCI-Museum Partnership, NC Museum of Natural Sciences; Adjunct Faculty, Biological Sciences, NC State University; Associate Director, Triangle Center for Evolutionary Medicine
• Using UI + TCT to explore the relationship between the gene ABCC11 and the skin microbiome

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Luna Li

• Graduate Student, Biomedical and Health Informatics, University of Washington
• Using the Translator Tier 0 KG and the TCT to identify causal regulatory (activation/inhibition) gene-gene relationships to construct or augment gene regulatory networks

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Sepid Mazrouee

• Data Scholar, NIAID/NIH
• Contributing a curated, NIAID monoclonal antibody dataset to Translator as a new knowledge source

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Julia McAfee

• Graduate Student, Chemistry, University of Virginia
• Using the UI and a new Canvas workspace feature to identify genes that up/downregulate H₂O₂ and/or HOCl in acute myeloid leukemia cells

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Reuben Thomas

• Director, Bioinformatics Core, Gladstone Institutes
• Using the UI + the TCT to augment high-dimensional assay results and protein-protein interaction networks in the context of Long COVID and HIV

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Michela Traglia

• Senior Statistician, Gladstone Institute of Data Science and Biotechnology
• Using the UI to search for chemicals that increase/decrease the expression/activity of select mitochondrial complex genes, variants of which were found to be associated with decreased risk of PD and AD in UK BioBank data

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Q&A

Roundtable Introductions

We are excited to get to know you! Please provide a brief introduction.

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• What is your name, including your preferred name?
• What is your position and affiliation?
• Anything else you’d like to share regarding your professional background?
• Why did you enroll in the Translator Ambassadors and Champions program?
• Do you have an idea(s) for a Translator project?

Meet the new A&C participants

Kenneth Bruskiewicz

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Massimiliano Cocca

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Ameera Jailani

• Postdoctoral Research Associate, University of Sheffield (cancer drug discovery, tumour microenvironment)
• Using UI to explore the relationship between select G protein-coupled receptors and pancreatic cancer
• Problem: Some G protein-coupled receptors couple to accessory proteins (receptor activity-modifying proteins) to become the functional receptor complex - will get in touch with helpdesk + Guangrong Qin (for help navigating cancer datasets)

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Saumya Jaiswal

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Saurav Kumar

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Zulekha Lakhani

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Maureen Pittman

* Postdoctoral Associate, University of North Carolina Chapel Hill

* Using the UI and TCT to explore Epithelial-Mesenchymal Transition (EMT) gene programs dysregulated in Crohn's and Ulcerative Colitis, and identifying factors that may initiate or contribute to Adverse Outcome Pathways in the digestive tract.

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Jonathan Senn

- Software Engineer at Mango Inc. Biotech startup developing an instrument that automates microbial testing for quality control.

- Previously a research assistant under Dr. Holly Mortensen at EPA ORD. Authored AOP DB v2.

- Recruited by Dr. Mortensen to shelter AOP DB from the winds of political change

- Update and migrate AOP DB either as a knowledge source for the Translator project or integrate it into another application.

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Hana Smith

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Zhenwei Song

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