Human Reference Atlas: Networks and Knowledge Graphs
Abstract
The HuBMAP Human Reference Atlas (HRA) effort aims to develop a common coordinate framework (CCF) for the healthy human body, see HRA Portal at https://humanatlas.io . An international team of organ experts (anatomists, pathologist, surgeons, biomedical researchers) and ontologists across 20+ consortia are authoring so called ASCT+B tables that capture the partonomy and typology information for anatomical structures, cell types, and biomarkers used to identify cell types. The ASCT+B tables are used to revise and extend existing CCF-relevant ontologies. In close collaboration with NIAID at NIH, a 3D Reference Object Library was compiled (https://3d.nih.gov/collections/hra ) that provides semantically annotated 3D representations of major anatomical structures captured in the ASCT+B tables. The HRA can be extended and explored using several interactive user interfaces: The Registration User Interface (RUI, https://apps.humanatlas.io/rui ) supports tissue data registration and annotation across 50+ 3D reference organs. The Exploration User Interface (EUI, https://apps.humanatlas.io/eui ) supports exploration of semantically and spatially explicit data—from the whole body to the single cell level. The Cell Distance Explorer (CDE, https://apps.humanatlas.io/cde ) computes and visualizes distance distributions between different cells, cell types, and anatomical structures and cell types and morphological features. For an introduction to HuBMAP goals, data, and code visit the Visible Human MOOC (VHMOOC, https://expand.iu.edu/browse/sice/cns/courses/hubmap-visiblehuman-mooc ). This talk details the multi-modal, multi-scale networks of the HRA, how HRA data is published as an open knowledge graph (https://humanatlas.io/api ), and how HuBMAP, SenNet, GTEx, and other tissue data is mapped to the HRA to harmonize data at scale in support of precision health and medicine.
Online (Zoom)
Link to register: https://iu.zoom.us/webinar/register/WN_02hY7XPrReyAr52wGHmb6w
Short Bio
KATY BÖRNER is the Victor H. Yngve Distinguished Professor of Engineering and Information Science in the Departments of Intelligent Systems Engineering and Information Science, Luddy School of Informatics, Computing, and Engineering; core faculty of the Cognitive Science Program; and founding director of the Cyberinfrastructure for Network Science Center (http://cns.iu.edu )—all at Indiana University in Bloomington, Indiana. She is a curator of the Mapping Science exhibit (http://scimaps.org ) and she leads the international Human Reference Atlas effort (https://humanatlas.io ). She holds an MS in electrical engineering from the University of Technology in Leipzig, and a PhD in computer science from the University of Kaiserslautern. Börner is a Fellow of the American Association for the Advancement of Science (AAAS), a Humboldt Research Fellow, an Association for Computing Machinery (ACM) Fellow, and a Network Society Fellow.