Cell Maps for Artificial Intelligence - U2OS Cell Map

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Description

This dataset is the U2OS Cell Map Release of Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org), the Functional Genomics Grand Challenge in the NIH Bridge2AI program. It provides an AI-ready, provenance-tracked reconstruction of a multi-scale map of human cell architecture for the U2OS (osteosarcoma) cell line, integrating protein subcellular localization from Human Protein Atlas (HPA) immunofluorescence (IF) imaging with protein-protein interaction (PPI) data from BioPlex affinity purification mass spectrometry (AP-MS), following the methodology of Schaffer, Hu, Qian et al. (Nature, 2025), "Multimodal cell maps as a foundation for structural and functional genomics."

The release is delivered as a chain of FAIRSCAPE RO-Crates, each packaging its software, inputs, outputs, and computations with full provenance. It comprises:

• HPA IF image download for U2OS (cellmaps_imagedownloader)
• BioPlex U2OS PPI edgelist construction (cellmaps_ppidownloader)
• ResNet IF image embeddings across two folds (cellmaps_image_embedding)
• Node2Vec PPI embeddings (cellmaps_ppi_embedding)
• MUSE co-embedding of the image and PPI modalities across two folds (cellmaps_coembedding)
• HiDeF multi-scale hierarchy generation (cellmaps_generate_hierarchy)
• Enrichment-based hierarchy evaluation against CORUM, GO Cellular Component, and HPA (cellmaps_hierarchyeval)
• Figure-reproduction provenance for the Schaffer et al. (Nature, 2025) publication

Data Governance & Ethics

• Human Subjects: No — data derived from commercially available, de-identified human cell lines
• FDA Regulated: No
• Confidentiality Level: Unrestricted
• Data Governance Committee: Jillian Parker (jillianparker@health.ucsd.edu)
• Ethical Review: Vardit Ravitsky (ravitskyv@thehastingscenter.org) and Jean-Christophe Bélisle-Pipon (jean-christophe_belisle-pipon@sfu.ca)
• License: CC BY-NC-SA 4.0. Attribution to the copyright holders and authors is required; publications using this data or derived products should cite the related publications and this data collection directly.

Completeness

• The PPI (BioPlex AP-MS) and protein localization (HPA IF imaging) inputs interrogate protein sets that only partially overlap
• 5,147 proteins are jointly represented in both modalities — roughly half of the detectable U2OS proteome — and only these flow into the co-embedding and downstream hierarchy
• This release covers the U2OS cell line only

Maintenance Plan

• This is a one-time cell map release and is not planned to be updated.
• Additional CM4AI cell map releases are anticipated, but they will be issued as separate datasets rather than updates to this one
• Long-term preservation in the University of Virginia Dataverse, supported by committed institutional funds

Intended Use

• AI-ready datasets to support research in functional genomics
• Protein complex mapping and multi-scale cell architecture modeling
• Multimodal representation learning and graph embedding
• Training, validation, and benchmarking of methods that integrate imaging and interaction data, including interpretable biology-informed ML models

Limitations

Researchers should be aware of inherent limitations:

• Scope is limited to the U2OS cell line and may not generalize to other cell types
• Input IF imaging covers 10,348 proteins (20,660 images) from the HPA; the input PPI network covers 7,543 proteins and 36,842 interactions from BioPlex U2OS AP-MS; only the 5,147 proteins shared by both assays appear in the integrated map
• AP-MS interactions reflect co-purification and may include indirect interactions; IF localization reflects antibody-accessible epitopes
• Requires domain expertise for meaningful analysis

Prohibited Uses

• These laboratory data are not to be used in clinical decision-making or in any context involving patient care without appropriate regulatory oversight and approval

Potential Sources of Bias

Users should be aware of potential biases:

• Data are derived from a single commercially available osteosarcoma cell line (U2OS) and do not represent biological variation across tissues, donors, or disease states
• Well-studied proteins, and those with available HPA antibodies or BioPlex bait clones, are over-represented relative to the full U2OS proteome