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It provides an AI-ready, provenance-tracked\n  reconstruction of a multi-scale map of human cell architecture for the U2OS\n  (osteosarcoma) cell line, integrating protein subcellular localization from\n  Human Protein Atlas (HPA) immunofluorescence (IF) imaging with\n  protein-protein interaction (PPI) data from BioPlex affinity purification\n  mass spectrometry (AP-MS), following the methodology of Schaffer, Hu, Qian\n  et al. (Nature, 2025), \"Multimodal cell maps as a foundation for structural\n  and functional genomics.\"</p>\n  <p>The release is delivered as a chain of FAIRSCAPE RO-Crates, each packaging its software, inputs, outputs, and\n  computations with full provenance. It comprises:</p>\n  <ul>\n      <li><strong>HPA IF image download</strong> for U2OS\n  (cellmaps_imagedownloader)</li>\n      <li><strong>BioPlex U2OS PPI edgelist construction</strong>\n  (cellmaps_ppidownloader)</li>\n      <li><strong>ResNet IF image embeddings</strong> across two folds\n  (cellmaps_image_embedding)</li>\n      <li><strong>Node2Vec PPI embeddings</strong>\n  (cellmaps_ppi_embedding)</li>\n      <li><strong>MUSE co-embedding</strong> of the image and PPI modalities\n  across two folds (cellmaps_coembedding)</li>\n      <li><strong>HiDeF multi-scale hierarchy generation</strong>\n  (cellmaps_generate_hierarchy)</li>\n      <li><strong>Enrichment-based hierarchy evaluation</strong> against\n  CORUM, GO Cellular Component, and HPA (cellmaps_hierarchyeval)</li>\n      <li><strong>Figure-reproduction provenance</strong> for the Schaffer et\n  al. (Nature, 2025) publication</li>\n  </ul>\n  <hr>\n  <h3>Data Governance & Ethics</h3>\n  <ul>\n      <li><strong>Human Subjects:</strong> No &mdash; data derived from\n  commercially available, de-identified human cell lines</li>\n      <li><strong>FDA Regulated:</strong> No</li>\n      <li><strong>Confidentiality Level:</strong> Unrestricted</li>\n      <li><strong>Data Governance Committee:</strong> Jillian Parker\n  (jillianparker@health.ucsd.edu)</li>\n      <li><strong>Ethical Review:</strong> Vardit Ravitsky\n  (ravitskyv@thehastingscenter.org) and Jean-Christophe B&eacute;lisle-Pipon\n  (jean-christophe_belisle-pipon@sfu.ca)</li>\n      <li><strong>License:</strong> CC BY-NC-SA 4.0. Attribution to the\n  copyright holders and authors is required; publications using this data or\n  derived products should cite the related publications and this data\n  collection directly.</li>\n  </ul>\n  <h3>Completeness</h3>\n  <ul>\n      <li>The PPI (BioPlex AP-MS) and protein localization (HPA IF imaging)\n  inputs interrogate protein sets that only partially overlap</li>\n      <li>5,147 proteins are jointly represented in both modalities &mdash;\n  roughly half of the detectable U2OS proteome &mdash; and only these flow\n  into the co-embedding and downstream hierarchy</li>\n      <li>This release covers the U2OS cell line only</li>\n  </ul>\n  <h3>Maintenance Plan</h3>\n  <ul>\n      <li>This is a one-time cell map release and is not planned to be\n  updated.</li>\n      <li>Additional CM4AI cell map releases are anticipated, but they will be\n  issued as separate datasets rather than updates to this one</li>\n      <li>Long-term preservation in the University of Virginia Dataverse,\n  supported by committed institutional funds</li>\n  </ul>\n  <h3>Intended Use</h3>\n  <ul>\n      <li>AI-ready datasets to support research in functional genomics</li>\n      <li>Protein complex mapping and multi-scale cell architecture\n  modeling</li>\n      <li>Multimodal representation learning and graph embedding</li>\n      <li>Training, validation, and benchmarking of methods that integrate\n  imaging and interaction data, including interpretable biology-informed ML\n  models</li>\n  </ul>\n  <h3>Limitations</h3>\n  <p><strong>Researchers should be aware of inherent limitations:</strong></p>\n  <ul>\n      <li>Scope is limited to the U2OS cell line and may not generalize to\n  other cell types</li>\n      <li>Input IF imaging covers 10,348 proteins (20,660 images) from the\n  HPA; the input PPI network covers 7,543 proteins and 36,842 interactions\n  from BioPlex U2OS AP-MS; only the 5,147 proteins shared by both assays\n  appear in the integrated map</li>\n      <li>AP-MS interactions reflect co-purification and may include indirect\n  interactions; IF localization reflects antibody-accessible epitopes</li>\n      <li>Requires domain expertise for meaningful analysis</li>\n  </ul>\n  <h3>Prohibited Uses</h3>\n  <ul>\n      <li><strong>These laboratory data are not to be used in clinical\n  decision-making or in any context involving patient care without appropriate\n  regulatory oversight and approval</strong></li>\n  </ul>\n  <h3>Potential Sources of Bias</h3>\n  <p>Users should be aware of potential biases:</p>\n  <ul>\n      <li>Data are derived from a single commercially available osteosarcoma\n  cell line (U2OS) and do not represent biological variation across tissues,\n  donors, or disease states</li>\n      <li>Well-studied proteins, and those with available HPA antibodies or\n  BioPlex bait clones, are over-represented relative to the full U2OS\n  proteome</li>\n  </ul>","citation:dsDescriptionDate":"2025-06-30"},"grantNumber":{"citation:grantNumberAgency":"National Institutes of Health","citation:grantNumberValue":"1OT2OD032742-01"},"publication":[{"publicationCitation":"Schaffer, L.V., Hu, M., Qian, G. et al. 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