Lantern: a semi-automated pipeline and repository for annotating lncRNAs with ontologies

Abstract

With advancements in in omics technologies, the range of biological processes long non-coding RNAs (lncRNAs) are involved in is expanding extensively [1,2). The accelerating rate of evidence discovery of lncRNAs' role in various critical biochemical, cellular, and physiological processes is necessitating a robust platform of lncRNA annotation resources. Available resources with lncRNA ontology annotations are rare: despite a plethora of resources for annotating genes, and an extensive body of lncRNA literature. Here, we present a lncRNA annotation extractor and repository (Lantern), was developed using PubMed's abstract retrieval engine and NCBO's recommender annotation system [3]. Between 1-150 abstracts were extracted per lncRNA, which were subsequently used for extracting annotations with respect to each ontology by querying NCBO's recommender system via Application Programming Interface (API). To evaluate the quality of annotations in Lantern, benchmarking analysis was performed by deploying Lantern's pipeline over 182 lncRNAs from lncRNAdb [4) and compared the extracted annotations against annotations mapped onto the lncRNAdb's manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8 based on manual verification of ontology annotations for 50 lncRNAs. Additionally, lncRNAs were also annotated with multiple omics information, like: RBP-interaction, tissue specific expression, protein c-expression, coding potential, sub-cellular localization and SNPs for around 11000 lncRNAs; retrieved and analyzed by robust NGS tools and pipelines. The extracted annotations for 11000 lncRNAs are available at http://www.iupui.edu/~sysbio/lantern/.