Document: D4D-Metadata -- CM4AI biorxiv.docx
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PARAGRAPHS:
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[0] Style: normal
Text: Returned a filled out json record conforming to this schema below -- and to fill out the schema use the text further below:


Schema:

Text:

[1] Style: normal
Text: https://www.biorxiv.org/content/10.1101/2024.05.21.589311v1.full.pdf

[4] Style: normal
Text: Output:

[5] Style: normal
Text: {

[6] Style: normal
Text: "@context": "https://w3id.org/bridge2ai/data-sheets-schema/minimal",

[7] Style: normal
Text: "@type": "DatasetCollection",

[8] Style: normal
Text: "id": "ark:12345/cm4ai-collection",

[9] Style: normal
Text: "title": "Cell Maps for Artificial Intelligence (CM4AI): AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines",

[10] Style: normal
Text: "description": "This dataset collection contains multiple CM4AI data releases, including proteomics, imaging, and genetic perturbation data for MDA-MB-468 breast cancer cells (treated and untreated) and differentiated and naive KOLF2.1J iPSCs. Data and metadata are packaged with FAIRSCAPE for AI-readiness and ethical dissemination under a CC-BY-NC-ND 4.0 International license.",

[11] Style: normal
Text: "keywords": [

[12] Style: normal
Text: "Cell Maps",

[13] Style: normal
Text: "Artificial Intelligence",

[14] Style: normal
Text: "Cancer",

[15] Style: normal
Text: "iPSC",

[16] Style: normal
Text: "Proteomics",

[17] Style: normal
Text: "Spatial Proteomics",

[18] Style: normal
Text: "CRISPR"

[19] Style: normal
Text: ],

[20] Style: normal
Text: "language": [

[21] Style: normal
Text: "en"

[22] Style: normal
Text: ],

[23] Style: normal
Text: "license": "CC-BY-NC-ND 4.0 International",

[24] Style: normal
Text: "version": "v0.5-alpha",

[25] Style: normal
Text: "created_on": "2024-05-24T00:00:00Z",

[26] Style: normal
Text: "created_by": [

[27] Style: normal
Text: "Timothy Clark",

[28] Style: normal
Text: "Jillian Mohan",

[29] Style: normal
Text: "Leah Schaffer",

[30] Style: normal
Text: "Trey Ideker (corresponding)",

[31] Style: normal
Text: "CM4AI Collaboration"

[32] Style: normal
Text: ],

[33] Style: normal
Text: "last_updated_on": "2024-05-24T00:00:00Z",

[34] Style: normal
Text: "modified_by": [

[35] Style: normal
Text: "CM4AI Tools Module",

[36] Style: normal
Text: "CM4AI Standards Module"

[37] Style: normal
Text: ],

[38] Style: normal
Text: "doi": "https://doi.org/10.1101/2024.05.21.589311",

[39] Style: normal
Text: "conforms_to": "https://w3id.org/bridge2ai/data-sheets-schema/minimal",

[40] Style: normal
Text: "resources": [

[41] Style: normal
Text: {

[42] Style: normal
Text: "@type": "Dataset",

[43] Style: normal
Text: "id": "ark:12345/cm4ai-protein-interactions",

[44] Style: normal
Text: "title": "CM4AI Protein-Protein Interaction Data (AP-MS, SEC-MS)",

[45] Style: normal
Text: "description": "Affinity purification mass spectrometry (AP-MS) and size-exclusion chromatography mass spectrometry (SEC-MS) data capturing protein-protein interactions, focusing on 100 chromatin regulators in MDA-MB-468 cells (untreated, paclitaxel, vorinostat) and KOLF2.1J iPSCs (undifferentiated, neurons, cardiomyocytes).",

[46] Style: normal
Text: "keywords": [

[47] Style: normal
Text: "Protein-Protein Interaction",

[48] Style: normal
Text: "Mass Spectrometry",

[49] Style: normal
Text: "Chromatin Regulators"

[50] Style: normal
Text: ],

[51] Style: normal
Text: "language": [

[52] Style: normal
Text: "en"

[53] Style: normal
Text: ],

[54] Style: normal
Text: "license": "CC-BY-NC-ND 4.0 International",

[55] Style: normal
Text: "version": "v0.5-alpha",

[56] Style: normal
Text: "created_on": "2024-05-24T00:00:00Z",

[57] Style: normal
Text: "created_by": [

[58] Style: normal
Text: "CM4AI Data Module"

[59] Style: normal
Text: ],

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Text: "last_updated_on": "2024-05-24T00:00:00Z",

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Text: "modified_by": [

[62] Style: normal
Text: "CM4AI Tools Module"

[63] Style: normal
Text: ],

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Text: "doi": "https://doi.org/10.1101/2024.05.21.589311",

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Text: "conforms_to": "https://w3id.org/bridge2ai/data-sheets-schema/minimal",

[66] Style: normal
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[67] Style: normal
Text: "path": "s3://cm4ai-bucket/data/protein_interactions_v0.5-alpha.json",

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Text: "format": "JSON",

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Text: "encoding": "UTF-8",

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[76] Style: normal
Text: },

[77] Style: normal
Text: {

[78] Style: normal
Text: "@type": "Dataset",

[79] Style: normal
Text: "id": "ark:12345/cm4ai-imaging",

[80] Style: normal
Text: "title": "CM4AI Spatial Proteomics Imaging Data (Immunofluorescence)",

[81] Style: normal
Text: "description": "High-resolution immunofluorescence (IF) images of targeted proteins in MDA-MB-468 cells (with/without drug treatment) and KOLF2.1J iPSCs (undifferentiated vs. neurons/cardiomyocytes). Generated using a standardized automated fixation and staining protocol, capturing spatial distribution of 100 chromatin regulators.",

[82] Style: normal
Text: "keywords": [

[83] Style: normal
Text: "Immunofluorescence",

[84] Style: normal
Text: "Microscopy",

[85] Style: normal
Text: "Spatial Proteomics"

[86] Style: normal
Text: ],

[87] Style: normal
Text: "language": [

[88] Style: normal
Text: "en"

[89] Style: normal
Text: ],

[90] Style: normal
Text: "license": "CC-BY-NC-ND 4.0 International",

[91] Style: normal
Text: "version": "v0.5-alpha",

[92] Style: normal
Text: "created_on": "2024-05-24T00:00:00Z",

[93] Style: normal
Text: "created_by": [

[94] Style: normal
Text: "Stanford University Team"

[95] Style: normal
Text: ],

[96] Style: normal
Text: "last_updated_on": "2024-05-24T00:00:00Z",

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[98] Style: normal
Text: "CM4AI Tools Module"

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Text: ],

[100] Style: normal
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[101] Style: normal
Text: "conforms_to": "https://w3id.org/bridge2ai/data-sheets-schema/minimal",

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[112] Style: normal
Text: },

[113] Style: normal
Text: {

[114] Style: normal
Text: "@type": "Dataset",

[115] Style: normal
Text: "id": "ark:12345/cm4ai-crispr",

[116] Style: normal
Text: "title": "CM4AI Genetic Perturbation Data (Single-Cell CRISPR Screens)",

[117] Style: normal
Text: "description": "Single-cell CRISPR-Cas9 perturbation screens targeting 100 chromatin regulators in MDA-MB-468 cells under 3 conditions (no treatment, paclitaxel, vorinostat) and in undifferentiated KOLF2.1J iPSCs. The dataset includes 10x Genomics 3’HT raw and processed files with gene expression profiles.",

[118] Style: normal
Text: "keywords": [

[119] Style: normal
Text: "CRISPR",

[120] Style: normal
Text: "Genetic Perturbation",

[121] Style: normal
Text: "Single-Cell Transcriptomics"

[122] Style: normal
Text: ],

[123] Style: normal
Text: "language": [

[124] Style: normal
Text: "en"

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[128] Style: normal
Text: "created_on": "2024-05-24T00:00:00Z",

[129] Style: normal
Text: "created_by": [

[130] Style: normal
Text: "UC San Diego Team"

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Text: "last_updated_on": "2024-05-24T00:00:00Z",

[133] Style: normal
Text: "modified_by": [

[134] Style: normal
Text: "CM4AI Tools Module"

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Text: "doi": "https://doi.org/10.1101/2024.05.21.589311",

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[138] Style: normal
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Text: "path": "s3://cm4ai-bucket/data/crispr_screens_v0.5-alpha.tar.gz",

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DOCUMENT PROPERTIES:
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Title: Word Document
Author: 
Created: None
Modified: 2025-04-16 17:44:58+00:00
