LINCS Data Portal: Unified interface to search, query, explore, analyze, and download LINCS data

The Library of Integrated Network-based Signatures (LINCS, http://lincsproject.org/) 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. The BD2K LINCS Data Coordination and Integration Center (DCIC) has been developing a collection of tools including data standards specifications, data processing pipelines and infrastructure, a metadata registration system, and a diverse suite of end-user software tools to support and implement an end-to-end solution from submitting LINCS datasets by the Data and Signature Generation Centers (DSGCs) to dataset publication via a Data Portal followed by integrated data analytics enabled by easy to use web-based tools.The LINCS Data Portal (LDP) presents a unified interface to access LINCS datasets and metadata with mappings to many external resources. LDP provides various options to explore, query, and download LINCS dataset packages and reagents that have been described using the LINCS metadata standards.The LINCS Data Portal dataset 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 rich 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. Dataset citation is now integrated into LDP.We recently added new curated content and search functionality for small molecules and many new features to further improve the utility of LDP.LDP is built on a robust API and is integrated with the MetaData Registry and interfaces with other components of the Integrated Knowledge Environment (IKE) developed in our Center. All LINCS datasets are also indexed in bioCADDIE DataMed and omicsDI.