Document: D4D - Minimal - CM4AI RO-Crate.docx
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Text: { "@type": "DatasetCollection", "id": "https://doi.org/10.18130/V3/B35XWX", "title": "Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)", "description": "This dataset is the March 2025 Data Release of Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org), the Functional Genomics Grand Challenge in the NIH Bridge2AI program. This Beta release includes perturb-seq data in undifferentiated KOLF2.1J iPSCs; SEC-MS data in undifferentiated KOLF2.1J iPSCs and iPSC-derived NPCs, neurons, and cardiomyocytes; and IF images in MDA-MB-468 breast cancer cells in the presence and absence of chemotherapy (vorinostat and paclitaxel). CM4AI output data are packaged with provenance graphs and rich metadata as AI-ready datasets in RO-Crate format using the FAIRSCAPE framework. Data presented here will be augmented regularly through the end of the project. CM4AI is a collaboration of UCSD, UCSF, Stanford, UVA, Yale, UA Birmingham, Simon Fraser University, and the Hastings Center. This data is Copyright (c) 2025 The Regents of the University of California except where otherwise noted. Spatial proteomics raw image data is copyright (c) 2025 The Board of Trustees of the Leland Stanford Junior University. Dataset licensed for reuse under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license (https://creativecommons.org/licenses/by-nc-sa/4.0/). Attribution is required to the copyright holders and the authors. Any publications referencing this data or derived products should cite the Related Publication below, as well as directly citing this data collection (2025-03-04). (2025-03-07)", "keywords": [ "AI", "affinity purification", "AP-MS", "artificial intelligence", "breast cancer", "Bridge2AI", "cardiomyocyte", "CM4AI", "CRISPR/Cas9", "induced pluripotent stem cell", "iPSC", "KOLF2.1J", "machine learning", "mass spectroscopy", "MDA-MB-468", "neural progenitor cell", "NPC", "neuron", "paclitaxel", "perturb-seq", "perturbation sequencing", "protein-protein interaction", "protein localization", "single-cell RNA sequencing", "scRNAseq", "SEC-MS", "size exclusion chromatography", "subcellular imaging", "vorinostat" ], "language": [ "en" ], "license": "https://creativecommons.org/licenses/by-nc-sa/4.0/", "version": "1.4 (Beta)", "created_on": "2025-03-03", "created_by": [ "Clark T", "Parker J", "Al Manir S", "Axelsson U", "Ballllosero Navarro F", "Chinn B", "Churas CP", "Dailamy A", "Doctor Y", "Fall J", "Forget A", "Gao J", "Hansen JN", "Hu M", "Johannesson A", "Khaliq H", "Lee YH", "Lenkiewicz J", "Levinson MA", "Marquez C", "Metallo C", "Muralidharan M", "Nourreddine S", "Niestroy J", "Obernier K", "Pan E", "Polacco B", "Pratt D", "Qian G", "Schaffer L", "Sigaeva A", "Thaker S", "Zhang Y", "Bélisle-Pipon JC", "Brandt C", "Chen JY", "Ding Y", "Fodeh S", "Krogan N", "Lundberg E", "Mali P", "Payne-Foster P", "Ratcliffe S", "Ravitsky V", "Sali A", "Schulz W", "Ideker T" ], "last_updated_on": "2025-03-07", "modified_by": [], "doi": "doi:10.18130/V3/B35XWX", "conforms_to": "https://w3id.org/bridge2ai/data-sheets-schema/minimal", "resources": [ { "@type": "Dataset", "id": "doi:10.18130/V3/B35XWX#crispr-cell-atlas", "title": "ro-crate-metadata.json (CRISPR Perturbation Cell Atlas)", "description": "This dataset represents an expressed genome-scale CRISPRi Perturbation Cell Atlas in undifferentiated KOLF2.1J human induced pluripotent stem cells (hiPSCs) mapping transcriptional and fitness phenotypes associated with 11,739 targeted genes, as part of the Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org) Functional Genomics Grand Challenge.", "keywords": [ "CRISPR Perturbation Cell Atlas", "CRISPRi", "perturbation sequencing", "hiPSCs", "CM4AI" ], "language": [ "en" ], "license": "https://creativecommons.org/licenses/by-nc-sa/4.0/", "version": "1.4 (Beta)", "created_on": "2025-03-03", "created_by": [], "last_updated_on": null, "modified_by": [], "doi": null, "conforms_to": null, "download_url": null, "path": "CRISPR Perturbation Cell Atlas/ro-crate-metadata.json", "format": "JSON", "encoding": null, "compression": null, "media_type": "application/json", "bytes": null, "hash": null, "md5": "cbd...818", "sha256": null }, { "@type": "Dataset", "id": "doi:10.18130/V3/B35XWX#crispr-rna-sequences", "title": "ro-crate-metadata.json (CRISPR Perturbation RNA Sequences - Raw Sequences)", "description": "Raw sequence data from an expressed genome-scale CRISPRi Perturbation Cell Atlas in KOLF2.1J hiPSCs mapping transcriptional and fitness phenotypes associated with 11,739 targeted genes, part of the CM4AI Functional Genomics Grand Challenge.", "keywords": [ "CRISPR Perturbation Cell Atlas", "CRISPRi", "raw sequences", "CM4AI" ], "language": [ "en" ], "license": "https://creativecommons.org/licenses/by-nc-sa/4.0/", "version": "1.4 (Beta)", "created_on": "2025-03-03", "created_by": [], "last_updated_on": null, "modified_by": [], "doi": null, "conforms_to": null, "download_url": null, "path": "CRISPR Perturbation RNA Sequences - Raw Sequences/ro-crate-metadata.json", "format": "JSON", "encoding": null, "compression": null, "media_type": "application/json", "bytes": null, "hash": null, "md5": "1ca...f5c", "sha256": null }, { "@type": "Dataset", "id": "doi:10.18130/V3/B35XWX#if-paclitaxel", "title": "cm4ai-v0.6-beta-if-images-paclitaxel.zip", "description": "This data set displays the spatial localization of 563 proteins of interest in cells of the breast cancer cell line MDA-MB-468 treated with paclitaxel as imaged by immunofluorescence-based staining (ICC-IF) and confocal microscopy, as part of CM4AI.", "keywords": [ "immunofluorescence", "paclitaxel", "MDA-MB-468", "protein localization", "CM4AI" ], "language": [ "en" ], "license": "https://creativecommons.org/licenses/by-nc-sa/4.0/", "version": "1.4 (Beta)", "created_on": "2025-03-03", "created_by": [], "last_updated_on": null, "modified_by": [], "doi": null, "conforms_to": null, "download_url": null, "path": "Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-paclitaxel.zip", "format": "ZIP", "encoding": null, "compression": "zip", "media_type": "application/zip", "bytes": null, "hash": null, "md5": "942...043", "sha256": null }, { "@type": "Dataset", "id": "doi:10.18130/V3/B35XWX#if-untreated", "title": "cm4ai-v0.6-beta-if-images-untreated.zip", "description": "This data set displays the spatial localization of 563 proteins of interest in untreated MDA-MB-468 cells by immunofluorescence-based staining (ICC-IF) and confocal microscopy, as part of CM4AI.", "keywords": [ "immunofluorescence", "untreated", "MDA-MB-468", "protein localization", "CM4AI" ], "language": [ "en" ], "license": "https://creativecommons.org/licenses/by-nc-sa/4.0/", "version": "1.4 (Beta)", "created_on": "2025-03-03", "created_by": [], "last_updated_on": null, "modified_by": [], "doi": null, "conforms_to": null, "download_url": null, "path": "Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-untreated.zip", "format": "ZIP", "encoding": null, "compression": "zip", "media_type": "application/zip", "bytes": null, "hash": null, "md5": "0b4...ef7", "sha256": null }, { "@type": "Dataset", "id": "doi:10.18130/V3/B35XWX#if-vorinostat", "title": "cm4ai-v0.6-beta-if-images-vorinostat.zip", "description": "This data set displays the spatial localization of 563 proteins of interest in cells of the breast cancer cell line MDA-MB-468 treated with vorinostat as imaged by immunofluorescence-based staining (ICC-IF) and confocal microscopy, as part of CM4AI.", "keywords": [ "immunofluorescence", "vorinostat", "MDA-MB-468", "protein localization", "CM4AI" ], "language": [ "en" ], "license": "https://creativecommons.org/licenses/by-nc-sa/4.0/", "version": "1.4 (Beta)", "created_on": "2025-03-03", "created_by": [], "last_updated_on": null, "modified_by": [], "doi": null, "conforms_to": null, "download_url": null, "path": "Protein Localization Subcellular Images/cm4ai-v0.6-beta-if-images-vorinostat.zip", "format": "ZIP", "encoding": null, "compression": "zip", "media_type": "application/zip", "bytes": null, "hash": null, "md5": "ac5...d52", "sha256": null }, { "@type": "Dataset", "id": "doi:10.18130/V3/B35XWX#sec-ms", "title": "ro-crate-metadata.json (Protein-protein Interaction SEC-MS)", "description": "This dataset was generated by size exclusion chromatography-mass spectroscopy (SEC-MS) on undifferentiated KOLF2.1J human iPSCs, in the Nevan Krogan laboratory at UCSF, as part of the CM4AI Functional Genomics Grand Challenge.", "keywords": [ "protein-protein interaction", "SEC-MS", "KOLF2.1J", "CM4AI" ], "language": [ "en" ], "license": "https://creativecommons.org/licenses/by-nc-sa/4.0/", "version": "1.4 (Beta)", "created_on": "2025-03-03", "created_by": [], "last_updated_on": null, "modified_by": [], "doi": null, "conforms_to": null, "download_url": null, "path": "Protein-protein Interaction SEC-MS/ro-crate-metadata.json", "format": "JSON", "encoding": null, "compression": null, "media_type": "application/json", "bytes": null, "hash": null, "md5": "cb6...032", "sha256": null } ] }


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