LINCS Extended Metadata Standard: Small molecules
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LINCS Extended Metadata Standard: Small molecules
metasource: Fairsharing.org
version: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Small molecules
metasource: Fairsharing.org
version: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
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LINCS Extended Metadata Standard: Small molecules
metasource: Fairsharing.orgversion: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Small molecules
metasource: Fairsharing.orgversion: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Names
More detailed information about this field from each metasource.
LINCS Extended Metadata Standard: Small molecules
metasource: Fairsharing.orgversion: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Small molecules
metasource: Fairsharing.orgversion: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to model LINCS assays and results and have been recommended by LINCS for adoption beyond the LINCS project. Small molecules are used as perturbagens in LINCS experiments. Small-molecule metadata also include substance-specific batch information, such as compound provider, salt form, molecular mass, purity, and aqueous solubility. For Food and Drug Administration–approved drugs, they proposed reporting additional information, such as drug indication and mechanism of action. If available, Protein Data Bank identifiers of corresponding target small-molecule co-crystal structures should also be reported.
Description
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LINCS Production Phase 2 Extended Metadata Standards were developed by the LINCS consortium with the goal of generating an integrated view across the diverse LINCS data resources. These guidelines are focused on the minimum required information to model LINCS assays and results and have been recommended by LINCS for adoption beyond the LINCS project. Small molecules are used as perturbagens in LINCS experiments. Small-molecule metadata also include substance-specific batch information, such as compound provider, salt form, molecular mass, purity, and aqueous solubility. For Food and Drug Administration–approved drugs, they proposed reporting additional information, such as drug indication and mechanism of action. If available, Protein Data Bank identifiers of corresponding target small-molecule co-crystal structures should also be reported.
metasource: Fairsharing.orgversion: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Webpage:
http://www.lincsproject.org/LINCS/data/standardsWebpage
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http://www.lincsproject.org/LINCS/data/standards
metasource: Fairsharing.orgversion: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications:
Publications
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Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS)
PMID: 24518066
metasource: Fairsharing.org
version: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications
More detailed information about this field from each metasource.
Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS)
PMID: 24518066
metasource: Fairsharing.org
version: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
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Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS)
PubMed citations: 43.
43 articles citing: Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS)
An Integrated In Silico, In Vitro and Tumor Tissues Study Identified Selenoprotein S (SELENOS) and Valosin-Containing Protein (VCP/p97) as Novel Potential Associated Prognostic Biomarkers in Triple Negative Breast Cancer. PMID:35158912
Lessons learned from SARS-CoV-2 measurements in wastewater. PMID:34375259
Downregulation of Salivary Proteins, Protective against Dental Caries, in Type 1 Diabetes. PMID:34287355
Repurposing of Anticancer Stem Cell Drugs in Brain Tumors. PMID:34165342
Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project. PMID:32939051
Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes. PMID:31809632
Annot: a Django-based sample, reagent, and experiment metadata tracking system. PMID:31675914
EdgeScaping: Mapping the spatial distribution of pairwise gene expression intensities. PMID:31386677
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. PMID:31272389
L1000 Viewer: A Search Engine and Web Interface for the LINCS Data Repository. PMID:31258549
Biomedical Image Processing with Containers and Deep Learning: An Automated Analysis Pipeline: Data architecture, artificial intelligence, automated processing, containerization, and clusters orchestration ease the transition from data acquisition to insights in medium-to-large datasets. PMID:31094000
Model-Based Clustering With Data Correction For Removing Artifacts In Gene Expression Data. PMID:30740193
Gene Expression Analysis Reveals Novel Gene Signatures Between Young and Old Adults in Human Prefrontal Cortex. PMID:30210331
A novel method of using Deep Belief Networks and genetic perturbation data to search for yeast signaling pathways. PMID:30208101
The GCTx format and cmap{Py, R, M, J} packages: resources for optimized storage and integrated traversal of annotated dense matrices. PMID:30203022
Bioinformatic and biological avenues for understanding alcohol use disorder. PMID:30144960
Therapeutic Effect of Repurposed Temsirolimus in Lung Adenocarcinoma Model. PMID:30087612
Master Regulators Connectivity Map: A Transcription Factors-Centered Approach to Drug Repositioning. PMID:30034338
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
Saliva Proteomics Analysis Offers Insights on Type 1 Diabetes Pathology in a Pediatric Population. PMID:29755368
EMUDRA: Ensemble of Multiple Drug Repositioning Approaches to improve prediction accuracy. PMID:29688306
Drug Repositioning in Glioblastoma: A Pathway Perspective. PMID:29615902
Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses. PMID:29322930
The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. PMID:29199020
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. PMID:29140462
Drug target ontology to classify and integrate drug discovery data. PMID:29122012
PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens. PMID:28740083
Characterization of transcriptional modules related to fibrosing-NAFLD progression. PMID:28684781
Transcriptomic profiling of human hippocampal progenitor cells treated with antidepressants and its application in drug repositioning. PMID:28208023
The ChEMBL database in 2017. PMID:27899562
Systematic Quality Control Analysis of LINCS Data. PMID:27796074
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. PMID:27377652
Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways. PMID:27364358
RegenBase: a knowledge base of spinal cord injury biology for translational research. PMID:27055827
Predicting target proteins for drug candidate compounds based on drug-induced gene expression data in a chemical structure-independent manner. PMID:26684652
Inferring Infection Patterns Based on a Connectivity Map of Host Transcriptional Responses. PMID:26508266
Metadata management for high content screening in OMERO. PMID:26476368
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
The Disease Ontology: fostering interoperability between biological and clinical human disease-related data. PMID:26093607
TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples. PMID:25638808
Systematic evaluation of connectivity map for disease indications. PMID:25606058
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. PMID:25348409
Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action. PMID:25324859
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catalytic activity
metasource: Fairsharing.org
version: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
cellular assay
metasource: Fairsharing.org
version: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
reaction data
metasource: Fairsharing.org
version: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
small molecule
metasource: Fairsharing.org
version: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
Tags
More detailed information about this field from each metasource.
catalytic activity
metasource: Fairsharing.orgversion: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
cellular assay
metasource: Fairsharing.orgversion: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
reaction data
metasource: Fairsharing.orgversion: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
small molecule
metasource: Fairsharing.orgversion: FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Jan. 8, 2019, 1:40 p.m.; Last accessed: Jan 03 2022 7:11 p.m.
catalytic activity cellular assay gene expression reaction data small molecule
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