2019 spring Course
<Bio-medicine Text Mining and Knowledge discovery>
研究生课程《生物医药文本挖掘和知识发现》
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Outline oWeek 1: (28th, Feb) (Introductory Training) •Chapter 0. Introduction of BioNLP and This Course •Chapter 1. First Class of Linux and Lexicon Analysis -Alex's Case(教师Slides, download here.) •数据: Brown Corpus Sample. •5 Min Talk: 曹锴《Shell编程实现》 oWeek 2: (7th, Mar) (Basic R Package) •Chapter *. Idea of this Course •Chapter 2. R programming & Word Cloud (Slides download here) •5 Min Talk: 杨鉴舜《中文文本词云图的制作流程》git clone https://github.com/YangJianshun/Bio_TM_Practice oWeek 3: (14th, Mar) (First course in Ontology) •Chapter 3. Gene Ontology (Dataset and Text Retrieval and Ontology)(Slides download here) •Suggested link: ftp://ftp.geneontology.org/go/www/GO.tools_by_type.term_enrichment.shtml •Suggested paper: AgriGO-https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896167/ 5 Min Talk: 王丹阳 《性别差异表达基因的GoEnrichment分析》 5 Min Talk: 张纳安 《斑马鱼基因组中在多物种中相对保守的基因的功能分析》 oWeek 4: (21st, Mar) (Ontology and Enrichment) •Chapter 4. Side Effect and Human Phenotype Ontology (Case study for drug repurposing) •Instruction. <Enrichment analysis, Hypergeometric test and its drawback> •Resource: HPO disease-gene-phenotype link ref (download here). •5 Min Talk: 徐泽伟 git clone https://github.com/Nanguage/BioTMCourse •5 Min Talk: 毛沁泉《HPO的富集分析》(Slides)(Codes) oWeek 5: (28th, Mar) (Ontology and Enrichment) •Chapter 5. Clinical Trial and Its R package application (Download the slides) *Chapter 5'. NER and Shell programming. (Codes for shell was distributed in class. Please cautiously use the curl command. Please...) •Assignment: Python or R package for Clinical Trial •Assignment: Integrative enrichment analysis oWeek 6: (4th, Apr) (Dependency tree) •Chapter 6‘'. Dependency Tree and the application in triple extraction •Material and Codes Fully available : https://github.com/bionlp-hzau/tutorial4dependencytree oWeek 7: (11st, Apr) ---Hackathon night •Hackathon (Please bring your own laptop; Fight for your own task; Show time and discussion; Wrap-up) •20 Min talk. Mina Gachloo <BioNLP on drug-related knowledge discovery> oWeek 8: (18th, Apr) •Chapter 7: CRF: Mathematics in NLP-1 oWeek 9: (25th, Apr) •Chapter 7: CRF: Mathematics in NLP-2 oWeek 10: (2nd, May) •Chapter 7: CRF: Mathematics in NLP-3 oWeek 11: (9th, May) •Chances for students' wrap-up. •Conclusion Talk <History and Future of Bio Text Mining> |