The National Institutes of Health Library of Integrated Network-based Cellular 
Signatures (LINCS) program is generating extensive multidimensional data sets, 
including biochemical, genome-wide transcriptional, and phenotypic cellular 
response signatures to a variety of small-molecule and genetic perturbations 
with the goal of creating a sustainable, widely applicable, and readily 
accessible systems biology knowledge resource. Integration and analysis of 
diverse LINCS data sets depend on the availability of sufficient metadata to 
describe the assays and screening results and on their syntactic, structural, 
and semantic consistency. Here we report metadata specifications for the most 
important molecular and cellular components and recommend them for adoption 
beyond the LINCS project. We focus on the minimum required information to model 
LINCS assays and results based on a number of use cases, and we recommend 
controlled terminologies and ontologies to annotate assays with syntactic 
consistency and semantic integrity. We also report specifications for a simple 
annotation format (SAF) to describe assays and screening results based on our 
metadata specifications with explicit controlled vocabularies. SAF specifically 
serves to programmatically access and exchange LINCS data as a prerequisite for 
a distributed information management infrastructure. We applied the metadata 
specifications to annotate large numbers of LINCS cell lines, proteins, and 
small molecules. The resources generated and presented here are freely 
available.