TY - JOUR
T1 - Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program
T2 - Integrated access to diverse large-scale cellular perturbation response data
AU - Koleti, Amar
AU - Terryn, Raymond
AU - Stathias, Vasileios
AU - Chung, Caty
AU - Cooper, Daniel J.
AU - Turner, John P.
AU - VidoviÄ ‡, Dušica
AU - Forlin, Michele
AU - Kelley, Tanya T.
AU - D'Urso, Alessandro
AU - Allen, Bryce K.
AU - Torre, Denis
AU - Jagodnik, Kathleen M.
AU - Wang, Lily
AU - Jenkins, Sherry L.
AU - Mader, Christopher
AU - Niu, Wen
AU - Fazel, Mehdi
AU - Mahi, Naim
AU - Pilarczyk, Marcin
AU - Clark, Nicholas
AU - Shamsaei, Behrouz
AU - Meller, Jarek
AU - Vasiliauskas, Juozas
AU - Reichard, John
AU - Medvedovic, Mario
AU - Ma'Ayan, Avi
AU - Pillai, Ajay
AU - Schürer, Stephan C.
N1 - Funding Information:
1Center for Computational Science, University of Miami, FL, USA, 2BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA, 3Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA, 4Department of Human Genetics and Genomics, Miller School of Medicine, University of Miami, FL, USA, 5Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 6Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA and 7Division of Genome Sciences, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Funding Information:
The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses. Integration of, and unified access to LINCS data has therefore been particularly challenging. The Big Data to Knowledge (BD2K) LINCS Data Coordination and Integration Center (DCIC) has developed data standards specifications, data processing pipelines, and a suite of end-user software tools to integrate and annotate LINCS-generated data, to make LINCS signatures searchable and usable for different types of users. Here, we describe the LINCS Data Portal (LDP) (http://lincsportal.ccs.miami.edu/), a unified web interface to access datasets generated by the LINCS DSGCs, and its underlying database, LINCS Data Registry (LDR). LINCS data served on the LDP contains extensive metadata and curated annotations. We highlight the features of the LDP user interface that is designed to enable search, browsing, exploration, download and analysis of LINCS data and related curated content.
Funding Information:
National Heart, Lung, and Blood Institute through funds provided by the National Institutes of Health Translational Research [U54HL127624]; Library of Integrated Network-based Cellular Signatures (LINCS) Program (http://www. lincsproject.org/); National Institutes of Health Translational Research Big Data to Knowledge (BD2K) initiative (http://www.bd2k.nih.gov/). Funding for open access charge: NIH [U54HL127624]. Conflict of interest statement. None declared.
Publisher Copyright:
© 2017 The Author(s) .
PY - 2018/1/1
Y1 - 2018/1/1
N2 - The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses. Integration of, and unified access to LINCS data has therefore been particularly challenging. The Big Data to Knowledge (BD2K) LINCS Data Coordination and Integration Center (DCIC) has developed data standards specifications, data processing pipelines, and a suite of end-user software tools to integrate and annotate LINCS-generated data, to make LINCS signatures searchable and usable for different types of users. Here, we describe the LINCS Data Portal (LDP) (http://lincsportal.ccs.miami.edu/), a unified web interface to access datasets generated by the LINCS DSGCs, and its underlying database, LINCS Data Registry (LDR). LINCS data served on the LDP contains extensive metadata and curated annotations. We highlight the features of the LDP user interface that is designed to enable search, browsing, exploration, download and analysis of LINCS data and related curated content.
AB - The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses. Integration of, and unified access to LINCS data has therefore been particularly challenging. The Big Data to Knowledge (BD2K) LINCS Data Coordination and Integration Center (DCIC) has developed data standards specifications, data processing pipelines, and a suite of end-user software tools to integrate and annotate LINCS-generated data, to make LINCS signatures searchable and usable for different types of users. Here, we describe the LINCS Data Portal (LDP) (http://lincsportal.ccs.miami.edu/), a unified web interface to access datasets generated by the LINCS DSGCs, and its underlying database, LINCS Data Registry (LDR). LINCS data served on the LDP contains extensive metadata and curated annotations. We highlight the features of the LDP user interface that is designed to enable search, browsing, exploration, download and analysis of LINCS data and related curated content.
UR - http://www.scopus.com/inward/record.url?scp=85040904200&partnerID=8YFLogxK
U2 - 10.1093/nar/gkx1063
DO - 10.1093/nar/gkx1063
M3 - Article
C2 - 29140462
AN - SCOPUS:85040904200
SN - 0305-1048
VL - 46
SP - D558-D566
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -