Document: D4D - CM4AI.docx
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[0] Style: normal
Text: Dataset:

[1] Style: normal
Text: id: doi:10.18130/V3/B35XWX

[2] Style: normal
Text: title: "Cell Maps for Artificial Intelligence - March 2025 Data Release (Beta)"

[3] Style: normal
Text: version: "1.4"

[4] Style: normal
Text: date_published: "2025-03-03"

[5] Style: normal
Text: data_creation_date: "2025-02-27"

[6] Style: normal
Text: deposit_date: "2025-02-27"

[7] Style: normal
Text: production_locations:

[8] Style: normal
Text: - "University of California San Diego"

[9] Style: normal
Text: - "University of California San Francisco"

[10] Style: normal
Text: - "Stanford University"

[11] Style: normal
Text: - "University of Virginia"

[12] Style: normal
Text: funding_information:

[13] Style: normal
Text: - "National Institutes of Health: 1OT2OD032742-01"

[14] Style: normal
Text: depositor: "Niestroy, Justin"

[15] Style: normal
Text: point_of_contact:

[16] Style: normal
Text: name: "Ideker, Trey"

[17] Style: normal
Text: affiliation: "University of California San Diego"

[19] Style: normal
Text: description: >

[20] Style: normal
Text: This dataset is the March 2025 Data Release of Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org),

[21] Style: normal
Text: the Functional Genomics Grand Challenge in the NIH Bridge2AI program. This Beta release includes perturb-seq

[22] Style: normal
Text: data in undifferentiated KOLF2.1J iPSCs; SEC-MS data in undifferentiated KOLF2.1J iPSCs and iPSC-derived NPCs,

[23] Style: normal
Text: neurons, and cardiomyocytes; and IF images in MDA-MB-468 breast cancer cells in the presence and absence of

[24] Style: normal
Text: chemotherapy (vorinostat and paclitaxel). CM4AI output data are packaged with provenance graphs and rich

[25] Style: normal
Text: metadata as AI-ready datasets in RO-Crate format using the FAIRSCAPE framework. Data presented here will

[26] Style: normal
Text: be augmented regularly through the end of the project. CM4AI is a collaboration of UCSD, UCSF, Stanford, UVA,

[27] Style: normal
Text: Yale, UA Birmingham, Simon Fraser University, and the Hastings Center. This data is Copyright (c) 2025

[28] Style: normal
Text: The Regents of the University of California except where otherwise noted. Spatial proteomics raw image data

[29] Style: normal
Text: is copyright (c) 2025 The Board of Trustees of the Leland Stanford Junior University. Dataset licensed for

[30] Style: normal
Text: reuse under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license

[31] Style: normal
Text: (https://creativecommons.org/licenses/by-nc-sa/4.0/). Attribution is required to the copyright holders

[32] Style: normal
Text: and the authors. Any publications referencing this data or derived products should cite the Related

[33] Style: normal
Text: Publication below, as well as directly citing this data collection (2025-03-04). (2025-03-07)

[35] Style: normal
Text: subjects:

[36] Style: normal
Text: - "Medicine, Health and Life Sciences"

[37] Style: normal
Text: keywords:

[38] Style: normal
Text: - label: "AI"

[39] Style: normal
Text: ontology_label: "artificial intelligence"

[40] Style: normal
Text: ontology_iri: "http://purl.obolibrary.org/obo/NCIT_C16309"

[41] Style: normal
Text: - label: "affinity purification"

[42] Style: normal
Text: ontology_label: "affinity purification"

[43] Style: normal
Text: ontology_iri: "http://www.bioassayontology.org/bao#BAO_0002603"

[44] Style: normal
Text: - label: "AP-MS"

[45] Style: normal
Text: ontology_iri: "http://www.ebi.ac.uk/swo/SWO_1100012"

[46] Style: normal
Text: - label: "breast cancer"

[47] Style: normal
Text: ontology_iri: "http://purl.bioontology.org/ontology/LNC/LA14283-8"

[48] Style: normal
Text: - label: "cardiomyocyte"

[49] Style: normal
Text: ontology_iri: "http://purl.obolibrary.org/obo/CL_0000746"

[50] Style: normal
Text: - label: "CRISPR/Cas9"

[51] Style: normal
Text: ontology_iri: "http://www.bioassayontology.org/bao#BAO_0010249"

[52] Style: normal
Text: - label: "induced pluripotent stem cell"

[53] Style: normal
Text: ontology_label: "iPSC"

[54] Style: normal
Text: ontology_iri: "http://www.ebi.ac.uk/efo/EFO_0004905"

[55] Style: normal
Text: - label: "machine learning"

[56] Style: normal
Text: ontology_iri: "http://purl.obolibrary.org/obo/OBI_0002587"

[57] Style: normal
Text: - label: "mass spectroscopy"

[58] Style: normal
Text: ontology_iri: "http://purl.bioontology.org/ontology/MESH/D013058"

[59] Style: normal
Text: - label: "neural progenitor cell"

[60] Style: normal
Text: ontology_label: "NPC"

[61] Style: normal
Text: ontology_iri: "http://purl.obolibrary.org/obo/CL_0011020"

[62] Style: normal
Text: - label: "neuron"

[63] Style: normal
Text: ontology_iri: "http://purl.obolibrary.org/obo/CL_0000540"

[64] Style: normal
Text: - label: "paclitaxel"

[65] Style: normal
Text: ontology_iri: "http://purl.obolibrary.org/obo/CHEBI_45863"

[66] Style: normal
Text: - label: "perturb-seq"

[67] Style: normal
Text: ontology_iri: "http://www.ebi.ac.uk/efo/EFO_0008860"

[68] Style: normal
Text: - label: "protein-protein interaction"

[69] Style: normal
Text: ontology_iri: "http://purl.obolibrary.org/obo/NCIT_C18469"

[70] Style: normal
Text: - label: "protein localization"

[71] Style: normal
Text: ontology_iri: "http://purl.obolibrary.org/obo/GO_0008104"

[72] Style: normal
Text: - label: "single-cell RNA sequencing"

[73] Style: normal
Text: ontology_label: "scRNAseq"

[74] Style: normal
Text: ontology_iri: "http://www.ebi.ac.uk/efo/EFO_0008913"

[75] Style: normal
Text: - label: "vorinostat"

[76] Style: normal
Text: ontology_iri: "http://purl.obolibrary.org/obo/CHEBI_45716"

[77] Style: normal
Text: - label: "Bridge2AI"

[78] Style: normal
Text: - label: "CM4AI"

[79] Style: normal
Text: - label: "KOLF2.1J"

[80] Style: normal
Text: - label: "MDA-MB-468"

[81] Style: normal
Text: - label: "SEC-MS"

[82] Style: normal
Text: - label: "size exclusion chromatography"

[83] Style: normal
Text: - label: "subcellular imaging"

[85] Style: normal
Text: license:

[86] Style: normal
Text: name: "Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International"

[87] Style: normal
Text: abbreviation: "CC BY-NC-SA 4.0"

[88] Style: normal
Text: url: "https://creativecommons.org/licenses/by-nc-sa/4.0/"

[90] Style: normal
Text: related_publications:

[91] Style: normal
Text: - citation: >

[92] Style: normal
Text: Clark T, Parker J, Schaffer L, Obernier K, Al Manir S, Churas CP, Dailamy A, Doctor Y, Forget A,

[93] Style: normal
Text: Hansen JN, Hu M, Lenkiewicz J, Levinson MA, Marquez C, Nourreddine S, Niestroy J, Pratt D, Qian G, Thaker S,

[94] Style: normal
Text: Bélisle-Pipon JC, Brandt C, Chen J, Ding Y, Fodeh S, Krogan N, Lundberg E, Mali P, Payne-Foster P,

[95] Style: normal
Text: Ratcliffe S, Ravitsky V, Sali A, Schulz W, Ideker T. Cell Maps for Artificial Intelligence: AI-Ready Maps of

[96] Style: normal
Text: Human Cell Architecture from Disease-Relevant Cell Lines. 2024.

[97] Style: normal
Text: doi: "http://doi.org/10.1101/2024.05.21.589311"

[98] Style: normal
Text: - citation: >

[99] Style: normal
Text: Nourreddine S, Doctor Y, Dailamy A, Forget A, Lee YH, Chinn B, Khaliq H, Polacco B, Muralidharan M, Pan E, Zhang Y,

[100] Style: normal
Text: Sigaeva A, Hansen JN, Gao J, Parker JA, Obernier K, Clark T, Chen JY, Metallo C, Lundberg E, Ideker T, Krogan N, Mali P.

[101] Style: normal
Text: A PERTURBATION CELL ATLAS OF HUMAN INDUCED PLURIPOTENT STEM CELLS. bioRxiv. 2024 Nov 4;2024.11.03.621734.

[102] Style: normal
Text: doi: "https://doi.org/10.1101/2024.11.03.621734"

[104] Style: normal
Text: creators:

[105] Style: normal
Text: - name: "Clark, T"

[106] Style: normal
Text: affiliation: "University of Virginia"

[107] Style: normal
Text: orcid: "https://orcid.org/0000-0003-4060-7360"

[108] Style: normal
Text: - name: "Parker, J"

[109] Style: normal
Text: affiliation: "University of California, San Diego"

[110] Style: normal
Text: orcid: "https://orcid.org/0000-0003-4535-3486"

[111] Style: normal
Text: - name: "Al Manir, S"

[112] Style: normal
Text: affiliation: "University of Virginia"

[113] Style: normal
Text: orcid: "https://orcid.org/0000-0003-4647-3877"

[114] Style: normal
Text: - name: "Axelsson, U"

[115] Style: normal
Text: affiliation: "KTH Royal Institute of Technology"

[116] Style: normal
Text: - name: "Ballllosero Navarro, F"

[117] Style: normal
Text: affiliation: "Stanford University"

[118] Style: normal
Text: orcid: "https://orcid.org/0000-0002-4180-422X"

[119] Style: normal
Text: - name: "Chinn, B"

[120] Style: normal
Text: affiliation: "University of California San Diego"

[121] Style: normal
Text: - name: "Churas, CP"

[122] Style: normal
Text: affiliation: "University of California San Diego"

[123] Style: normal
Text: orcid: "https://orcid.org/0000-0001-9998-705X"

[124] Style: normal
Text: - name: "Dailamy, A"

[125] Style: normal
Text: affiliation: "University of California, San Diego"

[126] Style: normal
Text: orcid: "https://orcid.org/0000-0002-6711-8260"

[127] Style: normal
Text: - name: "Doctor, Y"

[128] Style: normal
Text: affiliation: "University of California, San Diego"

[129] Style: normal
Text: orcid: "https://orcid.org/0009-0009-0483-7506"

[130] Style: normal
Text: - name: "Fall, J"

[131] Style: normal
Text: affiliation: "KTH - Royal Institute of Technology"

[132] Style: normal
Text: - name: "Forget, A"

[133] Style: normal
Text: affiliation: "University of California San Francisco"

[134] Style: normal
Text: orcid: "https://orcid.org/0000-0003-0223-0312"

[135] Style: normal
Text: - name: "Gao, J"

[136] Style: normal
Text: affiliation: "University of California San Diego"

[137] Style: normal
Text: orcid: "https://orcid.org/0000-0002-6311-3526"

[138] Style: normal
Text: - name: "Hansen, JN"

[139] Style: normal
Text: affiliation: "Stanford University"

[140] Style: normal
Text: orcid: "https://orcid.org/0000-0002-4650-9094"

[141] Style: normal
Text: - name: "Hu, M"

[142] Style: normal
Text: affiliation: "University of California San Diego"

[143] Style: normal
Text: orcid: "https://orcid.org/0000-0002-1571-8029"

[144] Style: normal
Text: - name: "Johannesson, A"

[145] Style: normal
Text: affiliation: "KTH - Royal Institute of Technology"

[146] Style: normal
Text: - name: "Khaliq, H"

[147] Style: normal
Text: affiliation: "University of California San Diego"

[148] Style: normal
Text: - name: "Lee, YH"

[149] Style: normal
Text: affiliation: "University of California San Diego"

[150] Style: normal
Text: orcid: "https://orcid.org/0000-0003-0917-355X"

[151] Style: normal
Text: - name: "Lenkiewicz, J"

[152] Style: normal
Text: affiliation: "University of California San Diego"

[153] Style: normal
Text: orcid: "https://orcid.org/0000-0001-7252-8638"

[154] Style: normal
Text: - name: "Levinson, MA"

[155] Style: normal
Text: affiliation: "University of Virginia"

[156] Style: normal
Text: orcid: "https://orcid.org/0000-0003-0384-8499"

[157] Style: normal
Text: - name: "Marquez, C"

[158] Style: normal
Text: affiliation: "University of California San Diego"

[159] Style: normal
Text: orcid: "0000-0003-3960-420X"

[160] Style: normal
Text: - name: "Metallo, C"

[161] Style: normal
Text: affiliation: "University of California San Diego"

[162] Style: normal
Text: orcid: "https://orcid.org/0000-0003-2404-3040"

[163] Style: normal
Text: - name: "Muralidharan, M"

[164] Style: normal
Text: affiliation: "University of California San Francisco"

[165] Style: normal
Text: - name: "Nourreddine, S"

[166] Style: normal
Text: affiliation: "University of California San Diego"

[167] Style: normal
Text: orcid: "https://orcid.org/0000-0003-3881-7588"

[168] Style: normal
Text: - name: "Niestroy, J"

[169] Style: normal
Text: affiliation: "University of Virginia"

[170] Style: normal
Text: orcid: "https://orcid.org/0000-0002-1103-3882"

[171] Style: normal
Text: - name: "Obernier, K"

[172] Style: normal
Text: affiliation: "University of California San Francisco"

[173] Style: normal
Text: orcid: "https://orcid.org/0000-0002-4025-1299"

[174] Style: normal
Text: - name: "Pan, E"

[175] Style: normal
Text: affiliation: "University of California San Diego"

[176] Style: normal
Text: - name: "Polacco, B"

[177] Style: normal
Text: affiliation: "University of California San Francisco"

[178] Style: normal
Text: - name: "Pratt, D"

[179] Style: normal
Text: affiliation: "University of California San Diego"

[180] Style: normal
Text: orcid: "https://orcid.org/0000-0002-1471-9513"

[181] Style: normal
Text: - name: "Qian, G"

[182] Style: normal
Text: affiliation: "University of California San Diego"

[183] Style: normal
Text: orcid: "https://orcid.org/0009-0005-4217-2745"

[184] Style: normal
Text: - name: "Schaffer, L"

[185] Style: normal
Text: affiliation: "University of California San Diego"

[186] Style: normal
Text: orcid: "https://orcid.org/0000-0001-6339-9141"

[187] Style: normal
Text: - name: "Sigaeva, A"

[188] Style: normal
Text: affiliation: "KTH Royal Institute of Technology"

[189] Style: normal
Text: orcid: "https://orcid.org/0000-0003-3361-3797"

[190] Style: normal
Text: - name: "Thaker, S"

[191] Style: normal
Text: affiliation: "University of Alabama at Birmingham"

[192] Style: normal
Text: orcid: "https://orcid.org/0000-0001-6730-2773"

[193] Style: normal
Text: - name: "Zhang, Y"

[194] Style: normal
Text: affiliation: "University of California San Diego"

[195] Style: normal
Text: - name: "Bélisle-Pipon, JC"

[196] Style: normal
Text: affiliation: "Simon Fraser University"

[197] Style: normal
Text: orcid: "https://orcid.org/0000-0002-8965-8153"

[198] Style: normal
Text: - name: "Brandt, C"

[199] Style: normal
Text: affiliation: "Yale University"

[200] Style: normal
Text: orcid: "https://orcid.org/0000-0001-8179-1796"

[201] Style: normal
Text: - name: "Chen, JY"

[202] Style: normal
Text: affiliation: "The University of Alabama at Birmingham"

[203] Style: normal
Text: orcid: "https://orcid.org/0000-0002-6112-415X"

[204] Style: normal
Text: - name: "Ding, Y"

[205] Style: normal
Text: affiliation: "University of Texas at Austin"

[206] Style: normal
Text: orcid: "https://orcid.org/0000-0003-2567-2009"

[207] Style: normal
Text: - name: "Fodeh, S"

[208] Style: normal
Text: affiliation: "Yale University"

[209] Style: normal
Text: orcid: "https://orcid.org/0000-0003-4664-3143"

[210] Style: normal
Text: - name: "Krogan, N"

[211] Style: normal
Text: affiliation: "University of California San Francisco"

[212] Style: normal
Text: orcid: "https://orcid.org/0000-0003-4902-337X"

[213] Style: normal
Text: - name: "Lundberg, E"

[214] Style: normal
Text: affiliation: "Stanford University"

[215] Style: normal
Text: orcid: "https://orcid.org/0000-0001-7034-0850"

[216] Style: normal
Text: - name: "Mali, P"

[217] Style: normal
Text: affiliation: "University of California San Diego"

[218] Style: normal
Text: orcid: "https://orcid.org/0000-0002-3383-1287"

[219] Style: normal
Text: - name: "Payne-Foster, P"

[220] Style: normal
Text: affiliation: "University of Alabama"

[221] Style: normal
Text: orcid: "https://orcid.org/0000-0002-3508-3577"

[222] Style: normal
Text: - name: "Ratcliffe, S"

[223] Style: normal
Text: affiliation: "University of Virginia"

[224] Style: normal
Text: orcid: "https://orcid.org/0000-0002-6644-8284"

[225] Style: normal
Text: - name: "Ravitsky, V"

[226] Style: normal
Text: affiliation: "University of Montreal"

[227] Style: normal
Text: orcid: "https://orcid.org/0000-0002-7080-8801"

[228] Style: normal
Text: - name: "Sali, A"

[229] Style: normal
Text: affiliation: "University of California San Diego"

[230] Style: normal
Text: orcid: "https://orcid.org/0000-0003-0435-6197"

[231] Style: normal
Text: - name: "Schulz, W"

[232] Style: normal
Text: affiliation: "Yale University"

[233] Style: normal
Text: orcid: "https://orcid.org/0000-0002-2048-4028"

[234] Style: normal
Text: - name: "Ideker, T"

[235] Style: normal
Text: affiliation: "University of California San Diego"

[236] Style: normal
Text: orcid: "https://orcid.org/0000-0002-1708-8454"

[238] Style: normal
Text: files:

[239] Style: normal
Text: -

[240] Style: normal
Text: filename: "ro-crate-metadata.json"

[241] Style: normal
Text: path: "CRISPR Perturbation Cell Atlas/"

[242] Style: normal
Text: file_format: "JSON"

[243] Style: normal
Text: file_size: "31.1 KB"

[244] Style: normal
Text: md5_checksum: "cbd...818"

[245] Style: normal
Text: date_published: "2025-03-03"

[246] Style: normal
Text: downloads: 11

[247] Style: normal
Text: description: >

[248] Style: normal
Text: This dataset represents an expressed genome-scale CRISPRi Perturbation Cell Atlas

[249] Style: normal
Text: in undifferentiated KOLF2.1J human induced pluripotent stem cells (hiPSCs) mapping

[250] Style: normal
Text: transcriptional and fitness phenotypes associated with 11,739 targeted genes, as part of

[251] Style: normal
Text: the Cell Maps for Artificial Intelligence (CM4AI; CM4AI.org) Functional Genomics Grand Challenge.

[252] Style: normal
Text: -

[253] Style: normal
Text: filename: "ro-crate-metadata.json"

[254] Style: normal
Text: path: "CRISPR Perturbation RNA Sequences - Raw Sequences/"

[255] Style: normal
Text: file_format: "JSON"

[256] Style: normal
Text: file_size: "1000.1 KB"

[257] Style: normal
Text: md5_checksum: "1ca...f5c"

[258] Style: normal
Text: date_published: "2025-03-03"

[259] Style: normal
Text: downloads: 5

[260] Style: normal
Text: description: >

[261] Style: normal
Text: This dataset represents raw sequence data from an expressed genome-scale CRISPRi Perturbation

[262] Style: normal
Text: Cell Atlas in KOLF2.1J human induced pluripotent stem cells (hiPSCs) mapping transcriptional

[263] Style: normal
Text: and fitness phenotypes associated with 11,739 targeted genes, as part of the Cell Maps for

[264] Style: normal
Text: Artificial Intelligence (CM4AI; CM4AI.org).

[265] Style: normal
Text: -

[266] Style: normal
Text: filename: "cm4ai-v0.6-beta-if-images-paclitaxel.zip"

[267] Style: normal
Text: path: "Protein Localization Subcellular Images/"

[268] Style: normal
Text: file_format: "ZIP Archive"

[269] Style: normal
Text: file_size: "2.6 GB"

[270] Style: normal
Text: md5_checksum: "942...043"

[271] Style: normal
Text: date_published: "2025-03-03"

[272] Style: normal
Text: downloads: 9

[273] Style: normal
Text: description: >

[274] Style: normal
Text: Spatial localization of 563 proteins of interest in MDA-MB-468 breast cancer cells

[275] Style: normal
Text: treated with paclitaxel, imaged by immunofluorescence staining and confocal microscopy

[276] Style: normal
Text: in the Lundberg Lab at Stanford University.

[277] Style: normal
Text: -

[278] Style: normal
Text: filename: "cm4ai-v0.6-beta-if-images-untreated.zip"

[279] Style: normal
Text: path: "Protein Localization Subcellular Images/"

[280] Style: normal
Text: file_format: "ZIP Archive"

[281] Style: normal
Text: file_size: "3.2 GB"

[282] Style: normal
Text: md5_checksum: "0b4...ef7"

[283] Style: normal
Text: date_published: "2025-03-03"

[284] Style: normal
Text: downloads: 12

[285] Style: normal
Text: description: >

[286] Style: normal
Text: Spatial localization of 563 proteins of interest in untreated MDA-MB-468 breast cancer

[287] Style: normal
Text: cells, imaged by immunofluorescence staining and confocal microscopy in the Lundberg

[288] Style: normal
Text: Lab at Stanford University.

[289] Style: normal
Text: -

[290] Style: normal
Text: filename: "cm4ai-v0.6-beta-if-images-vorinostat.zip"

[291] Style: normal
Text: path: "Protein Localization Subcellular Images/"

[292] Style: normal
Text: file_format: "ZIP Archive"

[293] Style: normal
Text: file_size: "2.8 GB"

[294] Style: normal
Text: md5_checksum: "ac5...d52"

[295] Style: normal
Text: date_published: "2025-03-03"

[296] Style: normal
Text: downloads: 10

[297] Style: normal
Text: description: >

[298] Style: normal
Text: Spatial localization of 563 proteins of interest in MDA-MB-468 breast cancer cells

[299] Style: normal
Text: treated with vorinostat, imaged by immunofluorescence staining and confocal microscopy

[300] Style: normal
Text: in the Lundberg Lab at Stanford University.

[301] Style: normal
Text: -

[302] Style: normal
Text: filename: "ro-crate-metadata.json"

[303] Style: normal
Text: path: "Protein-protein Interaction SEC-MS/"

[304] Style: normal
Text: file_format: "JSON"

[305] Style: normal
Text: file_size: "2.9 KB"

[306] Style: normal
Text: md5_checksum: "cb6...032"

[307] Style: normal
Text: date_published: "2025-03-03"

[308] Style: normal
Text: downloads: 4

[309] Style: normal
Text: description: >

[310] Style: normal
Text: Dataset generated by size exclusion chromatography-mass spectroscopy (SEC-MS) on

[311] Style: normal
Text: undifferentiated KOLF2.1J human induced pluripotent stem cells (hiPSCs), from the

[312] Style: normal
Text: Nevan Krogan laboratory at UCSF, as part of the CM4AI Functional Genomics Grand Challenge.


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