FAIR LINCS Data and Metadata powered by the CEDAR Framework

Presenting Author Information 

Name

Raymond Terryn

Institution

University of Miami

BD2K Grant Number

U54 HL127624

PI

Stephan Schürer

Email

sschurer@med.miami.edu

Phone Number

(305) 243-4842

Additional Author Information 

Names and affiliations of additional authors

Raymond Terryn [1,7]
Amar Koleti [1,7]
Rafael S. Gonçalves [6, 8]
Vasileios Stathias [1,7]
Michele Forlin [1,7]
Wen Niu [5,7]
Caroline Monteiro [4,7]
Daniel Cooper [7]
Christopher Mader [1,7]
Vance Lemmon [1,7]
Dusica Vidovic [1,7]
Csongor I. Nyulas [6, 8]
Martin J. O'Connor [6, 8]
Mario Medvedovic [5,7]
Avi Ma’ayan [4,7]
Caty Chung [1,7]
John Graybeal [6, 8]
Mark A. Musen [6, 8]
Stephan Schürer [1,2,5]

1 Center for Computational Science and University of Miami, Miami, FL;
2 Department of Molecular and Cellular Pharmacology, University of Miami, Miami, FL;
3 Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami FL;
4 Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1215, New York, NY;
5 Division of Biostatistics and Bioinformatics, Environmental Health Department, University of Cincinnati; Cincinnati, OH;
6 Stanford Center for Biomedical Informatics Research Stanford; Palo Alto, CA;
7 BD2K LINCS Data Coordination and Integration Center
8 BD2K CEDAR The Center for Expanded Data Annotation and Retrieval

Is there an additional contact person?

Yes

Name of additional contact

Caty Chung

Email address of additional contact

c.chung@miami.edu

Additional information 

Please choose the topic that best fits your abstract (posters will be grouped according to your selection). Detailed session descriptions can be found in the Abstract Guidelines.

Collaborations

Please consider my abstract for a (See Presentation Guidelines)

Poster only

Abstract Information

Poster presentations may be submitted electronically in order to reach a wider audience and be available after the All hands meeting. Do you plan to submit your poster as a digital submission in addition to bringing a physical copy?

Yes

Abstract Title

FAIR LINCS Data and Metadata powered by the CEDAR Framework

Abstract Description

The Library of Integrated Network-based Signatures (LINCS) program generates a wide variety of cell-based perturbation-response signatures using diverse assay technologies. For example, LINCS includes large-scale transcriptional profiling of genetic and small molecule perturbations, and various proteomics and imaging datasets. We have developed data processing pipelines, and supporting informatics infrastructure to access, standardize and harmonize, register and publish LINCS datasets and metadata from all Data and Signature Generating Centers (DSGC’s). Metadata standards specifications provide a foundation for harmonizing and integrating LINCS data. Here we introduce a CEDAR-based LINCS Community Metadata Environment, to support end-to-end metadata management framework that supports authoring, curation, validation, management, and sharing of LINCS metadata, while building upon the existing LINCS metadata standards and data-release workflows. Following this initial validation, our goal is to create reusable metadata modules with user friendly templates for each of the LINCS metadata categories and to make our suite of tools compatible with the CEDAR metadata technologies. This should further simplify metadata handling in the LINCS consortium and facilitate a global metadata repository at CEDAR. As other projects apply the same approach, many more datasets will become cross-searchable and can be linked optimizing the metadata pathway from submission to discovery.