LINCS Extended Metadata Standard: Small molecules

Abbreviation: LINCS 2: Small molecules

General Information

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.

This record replaces or incorporates the following deprecated resources:

LINCS Pilot Phase 1 Metadata Standards: Small Molecules

Homepage http://www.lincsproject.org/LINCS/data/standards

Developed in United States

Created in 2015

Taxonomic range

Scope and data types

How to cite this record FAIRsharing.org: LINCS 2: Small molecules; LINCS Extended Metadata Standard: Small molecules; DOI: https://doi.org/10.25504/FAIRsharing.7rfpgs; Last edited: Feb. 22, 2018, 2:40 p.m.; Last accessed: Nov 19 2018 9:28 a.m.

This record is maintained by cchung ORCID

Record added: April 27, 2016, 2:15 p.m.
Record updated: March 30, 2017, 1:08 a.m. by cchung.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.7rfpgs' by 'cchung' at 01:08, 30 Mar 2017 (approved):

'description' has been modified:
Before: 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 Administrationapproved 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.
After: 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 Administrationapproved 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.

Edits to 'https://fairsharing.org/FAIRsharing.7rfpgs' by 'The FAIRsharing Team' at 19:50, 22 Oct 2016 (approved):

	'homepage' has been modified:
		Before: http://www.lincsproject.org/data/data-standards/
		After: http://www.lincsproject.org/LINCS/data/standards

Edits to 'https://fairsharing.org/FAIRsharing.7rfpgs' by 'The FAIRsharing Team' at 16:34, 28 Sep 2016 (approved):

	'name' has been modified:
		Before: LINCS Production Phase 2 Extended Metadata Standard: Small molecules
		After: LINCS Extended Metadata Standard: Small molecules

In Collections

LINCS Project

Support

General

online documentation

http://www.lincsproject.org/LINCS/files/ ...

Additional Information

Contact

sherry.jenkins@mssm.edu

Tools

No tools defined

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Publications

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).

Vempati UD,Chung C,Mader C,Koleti A,Datar N,Vidovic D,Wrobel D,Erickson S,Muhlich JL,Berriz G,Benes CH,Subramanian A,Pillai A,Shamu CE,Schurer SC
J Biomol Screen 2014

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

Terminology Artifacts

No semantic standards defined

Models and Formats

No syntax standards defined

Identifier Schemas

No identifier schema standards defined

Implementing Databases (1)

Library of Integrated Network-Based Cellular Signatures Data Portal
The LINCS Data Portal provides a unified interface for searching LINCS dataset packages and reagents. LINCS data are being made openly available as a community resource through a series of data releases, so as to enable scientists to address a broad range of basic research questions and to facilitate the identification of biological targets for new disease therapies. LINCS datasets consist of assay results from cultured and primary human cells treated with bioactive small molecules, ligands such as growth factors and cytokines, or genetic perturbations. Many different assays are used to monitor cell responses, including assays measuring transcript and protein expression; cell phenotype data are captured by biochemical and imaging readouts. Assays are typically carried out on multiple cell types, and at multiple timepoints; perturbagen activity is monitored at multiple doses.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by cchung ORCID

Funds

NIH Common Fund, USA (Government body)
US National Institutes of Health (NIH) (Research institute)

LINCS Extended Metadata Standard: Small molecules

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