HuBMAP Human Reference Atlas Workshop

Unifying Efforts Around the Human Reference Atlas

The Human Reference Atlas (HRA) is a multiscale, multimodal, three-dimensional atlas of the anatomical structures and cells in the healthy human body. The HRA provides standard terminologies and data structures for describing specimens, biological structures, and spatial positions linked to existing ontologies.

This workshop brought together experts from the National Library of Medicine, the J. Craig Venter Institute (JCVI), and HuBMAP to share and integrate human atlas data and code across efforts.

Event Details

June 23-24, 2025

ISE Department,

Luddy School of Informatics, Computing, and Engineering

700 N Woodlawn Ave Bloomington, IN 47408

Goals

Share HRA data across atlas efforts.
Use HRA lightweight components and other HRA code in other portals.
Expand utility of existing HRA Jupyter notebooks.
Identify synergies across human atlas efforts.

Participating Teams

Experts from government, academic, and research institutions came together to share knowledge, tools, and data in support of the Human Reference Atlas initiative.

1st row: Richard Scheuermann, NLM; Bruce W. Herr II, CNS; Yun “Renee” Zhang, NLM.

2nd row: Katy Börner, CNS; Matthew Diller, NLM; Beverly Peng, J. Craig Venter Institute; Bingfang Xu, NLM.

3rd row: Andreas Bueckle, CNS; Raymond Leclair, NLM; Anne Deslattes Mays, NLM; Ajith Pankajam, NLM.

4th row: William Spear, NLM; Noam Rotenberg, NLM; Supriya Bidanta, CNS; Michael Ginda, CNS.

National Library of Medicine (NIH/NLM)

Richard H. Scheuermann, Scientific Director of the National Library of Medicine (NIH/NLM)
Bingfang Xu (NIH/NLM)
Ajith Viswanathan Asari Pankajam (NIH/NLM)
Matthew Diller (NIH/NLM)
Noam Rotenberg (NIH/NLM)
Yun (Renee) Zhang (NIH/NLM)
Anne Deslattes Mays (NIH/NLM)
Raymond Leclair (NIH/NLM)
William Spear (NIH/NLM)

J. Craig Venter Institute (JCVI)

Beverly Peng, JCVI

Indiana University Team

Katy Börner, CNS and HRA lead
Bruce W. Herr II, System Architect
Andreas Bueckle, Research Lead
Yash Yashvardhan, AI Expert
Lisel Record, HRA SOPs

Results

Over the two days, 30+ all-hands and individual meetings took place. Much data and code was exchanged. Key results include:

Integration of FR-Match into HRApop workflow.
Addition of FTU lightweight components into the NLM Cell Knowledge Network MVP.
Exploration of using HRAlit as a paper identification step for NLP performed by the NLM team.
Plans to use NS-Forest to empower ASCT+B table authors to identify best biomarkers that best characterize cell types in different tissues.
Exploration of interoperability and compatibility between HRA KG and the Cell Knowledge Network (CKN) using Linked Open Data principles.

Acknowledgements

We thank Meryl S. Jacob, Saai V. Permanand, and Gauri Markandey for event support. Michael Gallant helped with computing logistics. The event was partially funded by the Cyberinfrastructure for Network Science Center at IU.

Prior CCF/HRA Workshops