CRISPR-Cas systems not only play key roles in prokaryotic acquired immunity, but can also be adapted as powerful genome editing tools. Understanding the native role of CRISPR-Cas systems in providing adaptive immunity can lead to new CRISPR-based technologies. Here, we develop CRISPRminer, a knowledge base and web server to comprehensively collect and investigate the knowledge of CRISPR-Cas systems and generate instructive annotations, including CRISPR arrays and Cas protein annotation, CRISPR-Cas system classification, self-targeting events detection, microbe–phage interaction inference, and anti-CRISPR annotation. CRISPRminer is user-friendly and freely available at http://www.microbiome-bigdata.com/CRISPRminer.
Existing OIE (Open Information Extraction) algorithms are independent of each other such that there exist lots of redundant works; the featured strategies are not reusable and not adaptive to new tasks. This paper proposes a new pipeline to build OIE systems, where an Open-domain Information eXpression (OIX) task is proposed to provide a platform for all OIE strategies. The OIX is an OIE friendly expression of a sentence without information loss. The generation procedure of OIX contains shared works of OIE algorithms so that OIE strategies can be developed on the platform of OIX as inference operations focusing on more critical problems. Based on the same platform of OIX, the OIE strategies are reusable, and people can select a set of strategies to assemble their algorithm for a specific task so that the adaptability may be significantly increased. This paper focuses on the task of OIX and propose a solution -Open Information Annotation (OIA). OIA is a predicate-function-argument annotation for sentences. We label a data set of sentence-OIA pairs and propose a dependency-based rule system to generate OIA annotations from sentences. The evaluation results reveal that learning the OIA from a sentence is a challenge owing to the complexity of natural language sentences, and it is worthy of attracting more attention from the research community.
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