LIFE is addressing a range of technical and scientific challenges related to collecting, integrating, searching, visualizing and analyzing large and feature-rich (big) data. All LINCS experimental assays can be searched using a simple User Interface LIFEwrx, which indexes the data from all the LINCS platforms. LIFEwrx is the project demonstration that connects KINOMEScan profiles, KiNativ profiles, broad cancer cell line growth inhibition profiles, cue signal response profiles, very large-scale gene expression signatures, phosphoproteomics signatures, single cell metabolomics profiles, single cell protein secretion profiles and other datasets. LIFE is a knowledge based search system with an underlying ontology that semantically integrates the various LINCS signatures generated at different Centers based on relevant molecular entities (such as small molecules, genes, proteins), model systems (such as cell lines) and other concepts (such as diseases). LINCS data is further enriched and cross-referenced by various external data sources.
The LINCS Data Working Group for the development of LINCS standards to define and annotate the metadata.The LINCS metadata specifications were used for a simple annotation format (SAF) to describe assays and screening results with explicit controlled vocabularies. To view the LINCS metadata standards click here. A recent publication on the LINCS metadata standards and SAF is available in PMID: 24518066 doi:10.1177/1087057114522514
Dr. Shamu and team at Harvard Medical School (HMS) LINCS Center (U54) have been key on the understanding of the complex assays in their platform, metadata annotations and the implementation of SAF into the HMS DB API.
The cancer cell lines was manual curation led by Dr. Benes (MGH), the effort has been a collaborative effort between Harvard Medical School (HMS) LINCS Center, Massachusset General Hospital (MGH) and University of Miami LINCS Center.
Our work is based on the inspiration of being able to contribute back to the community by providing useful tools to address scientific questions.