Journal Article

LungMAP Portal Ecosystem: Systems-level Exploration of the Lung

Heathorn, Trevor, Du, Yina, Korte, Jeff, Prasath, V. B. Surya, Ardini-Poleske, Maryanne E., Bardes, Eric E., Adkins, Joshua, Loos, Stephanie, Xu, Yan, Whitsett, Jeffrey A., Tabar, Scott, Pryhuber, Gloria S., Burns, Kevin, Huo, Bing-Xing, Guo, Minzhe, Iyer, Balaji, Aronow, Bruce J., Jin, Kang, Kouril, Michal, Fortriede, Joshua, Salomonis, Nathan, Smith, Victoria, Paten, Benedict, Carson, James P., Bhattacharjee, Anukana, Gaddis, Nathan, Herbst, Andrew, Munshi, Ruchi, Kitzmiller, Joseph A., Misra, Ravi, Sun, Xin, Tickle, Tim, Morrisey, Edward E., Schnell, Daniel, Clair, Geremy C.

2024

Overview

An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire of molecular omics, cellular imaging, and pathological datasets. To centralize and standardize information across broad lung research efforts, we expanded the LungMAP.net website into a new gateway portal. This portal connects a broad spectrum of research networks, bulk and single-cell multiomics data, and a diverse collection of image data that span mammalian lung development and disease. The data are standardized across species and technologies using harmonized data and metadata models that leverage recent advances, including those from the Human Cell Atlas, diverse ontologies, and the LungMAP CellCards initiative. To cultivate future discoveries, we have aggregated a diverse collection of single-cell atlases for multiple species (human, rhesus, and mouse) to enable consistent queries across technologies, cohorts, age, disease, and drug treatment. These atlases are provided as independent and integrated queryable datasets, with an emphasis on dynamic visualization, figure generation, reanalysis, cell-type curation, and automated reference-based classification of user-provided single-cell genomics datasets (Azimuth). As this resource grows, we intend to increase the breadth of available interactive interfaces, supported data types, data portals and datasets from LungMAP, and external research efforts.

• Publisher: Oxford University Press,American Thoracic Society
• Subject: Animals / Data collection / Datasets / Ecosystems / genomics / Genomics - methods / human cell atlas / Humans / Lung / lung (human) / Lung diseases / LungMAP / Lungs / Mammals / Mice / omics / Organogenesis / Original Research / portal / proteomics / single-cell atlas