FAIR Dataset Landing Pages for LINCS and BD2K

Date

Thu Jan 12th 10:00am to 11:00am PST

Presenter

Stephan Schurer

Abstract

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).  The consortium has already published over 280 datasets with rich metadata annotation, which are accessible via the LINCS Data Portal (LDP).  LDP provides various options to explore, query, and download LINCS dataset packages and reagents that have been described using the LINCS data standards.

We recently introduced LINCS Dataset Landing Pages to provide integrated access to important content for each LINCS dataset.  The landing pages provide deep metadata for each LINCS dataset including description of the assays, authors, data analysis pipelines, and standardized reagents such as small molecules cell lines, antibodies, etc, with important annotations.  The landing pages are a key component to make LINCS data persistent and reusable, by integrating LINCS datasets, data processing pipelines, analytes, perturbations, model systems and related concepts as uniquely identifiable digital research objects.  LINCS dataset landing pages also provide mapping of LINCS content to various external resources and they are indexed in BioCaddie DataMed.

The BD2K LINCS DCIC also has been developing a suite of software tools to enable the research community to leverage LINCS data for biological research.

This talk will provide an overview of the LINCS data processing infrastructure and operations to maximize FAIRness of LINCS data.

Bios

Dr Stephan Schürer is Director of Drug Discovery at the Center for Computational Science and Associate Professor in the Department of Pharmacology at the University of Miami. He is also adjunct Associate Professor at the at the Scripps Research Institute Florida where he previously headed HTS- and drug discovery chemoinformatics development.  In prior industry positions Dr. Schürer was Sr. Director at Eidogen-Sertanty, a developer of life science information technology and scientific content products. At Libraria Inc. he was directing content operations to develop chemistry and SAR knowledge bases.

The research focus of the Schürer group is in systems drug discovery. The group integrates and models small molecule-protein interaction, systems biology ‘omics’, and chemistry data to improve translation of disease models into novel functional small molecules. Using distributed and parallelized big data analytics, bio- and chemoinformatics tools Dr. Schürer’s group has built sophisticated modeling pipelines to understand and predict drug mechanism of action, promiscuity and polypharmacology with a particular focus on kinases and epigenetic bromodomain reader proteins. In several focused as well as larger-scale projects, they have developed formal ontologies (e.g. BioAssay Ontology, Drug Target Ontology), data standards, and end-user multi-tier software applications. Several drug discovery collaborations ranging from cancer to neurological disorders are ongoing.

Dr Schürer is a PI in two national Consortia, the Library of Integrated Network-based Cellular Signatures (LINCS) project (http://bd2k-lincs.org/), which is also part of the Big Data to Knowledge (BD2K) program (https://datascience.nih.gov/bd2k), and the Illuminating the Druggable Genome (IDG) project (http://targetcentral.org/).

Stephan Schürer received his Ph.D. in synthetic organic chemistry from the Technical University of Berlin and studied chemistry at Humboldt University-Berlin and University of California Berkeley.

 

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