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We introduce RLIMS-P version 2.0, an enhanced rule-based information extraction (IE) system for mining kinase, substrate, and phosphorylation site information from scientific literature. Consisting of natural language processing and IE modules, the system has integrated several new features, including the capability of processing full-text articles and generalizability towards different post-translational...
Figures play an important role in illustrating concepts, methodology and results in biomedicai literature. However, figures in biomedicai literature are often composed of multiple subfigures (panels), which may illustrate diverse methodologies or results. Robust and accurate panel partitioning is crucial to support article categorization based on methods or experimental results and to provide the...
Gallus Reactome provides a manually curated reference database for chicken signaling and metabolic pathways. Providing such a high-quality reference database requires significant time input from both curators and pathway experts. This paper describes the application of orthology prediction, computational linguistic tools including text mining and information extraction applications, along with resources...
Figures in biomedical articles often constitute direct evidence of experimental results. Image analysis methods can be coupled with text-based methods to improve knowledge discovery. However, automatically harvesting figures along with their associated captions from full-text articles remains challenging. In this paper, we present an automatic system for robustly harvesting figures from biomedical...
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