AGAC Portal

undefined , “Annotation of Genes with Alteration-Centric function changes”. — A customized corpus for mining functions caused by mutations.

—Main Data Service—

❏ AD-LitPathoNet. English ☞. 中文 ☞

❏ Cancer-Alterome ☞

❏ Rice-Alterome ☞

—Links to undefined Corpus and Resources—

❏ 语料库数据说明

❏ 标注说明和语料库开发相关

❏ 基于语料库的疾病知识发现的应用场景

❏ 语料库数据公开、BioNLP任务和推广

  • 2019 BioNLP Open Shared Task (2019年BioNLP开放共享任务) Visit this page!
  • Covid-19 Hackathon Project (参与BLAH7 Hackathon项目) Visit this page!
  • GDAS Track, CHIP 2022 (2022年中国健康信息会议——GDAS测评任务数据集) Visit this page!
  • 收录于Tianchi天池数据集 (面向“基因-疾病”关联机理的科学文献挖掘任务(AGAC)数据集) Visit this page!
  • Corpus-ET, BLAH8 (参与BLAH8 Hackathon项目) Visit this page!
  • Rice-Alterome, BLAH8 (参与BLAH8 Hackathon项目) Visit this page!

—Developing History—

❏ Tutorial Videos

Why did we annotate AGAC? BLAH, 2018. (时长: 16’11”/讲解: 英文/字幕:无.)

Presenter: Jingbo Xia
Youtube video AGAC in BLAH 4, Tokyo, 2017
(Idea of AGAC annotation)

Apply AGAC in LitCovid. BLAH, 2021. (时长: 4’11”/讲解: 英文/字幕:无.)

Presenter: Yuxing Wang
Youtube Video AGAC in BLAH 7, Tokyo, 2021
(Aggregate LitCovid with AGAC)
B站镜像：Bilibili视频

❏ Publications

◆ Sizhuo Ouyang, Xinzhi Yao, Yuxing Wang, Qianqian Peng, Zhihan He, Jingbo Xia*. Text Mining Task for “Gene-Disease” Association Semantics in CHIP 2022. In: Tang, B., et al. Health Information Processing. Evaluation Track Papers. CHIP 2022. Communications in Computer and Information Science, 2023, 1773:3-13. Springer, Singapore.

◆ 欧阳思卓，姚昕智，王宇星，彭钱钱，贺芷涵，夏静波*. 评测纵览：面向“基因-疾病”的关联语义挖掘任务 [J].医学信息学杂志，2022，43(12):6-9.

◆ Kaiyin Zhou, Sheng Zhang, Yuxing Wang, Kevin Bretonnel Cohen, Jin-Dong Kim, Qi Luo, Xinzhi Yao, Xingyu Zhou, Jingbo Xia*. High-quality Gene/Disease Embedding in A Multi-relational Heterogeneous Graph After A Joint Matrix/tensor Decomposition. Journal of Biomedical Informatics. 2022, 126:103973.

◆  Sizhuo Ouyang, Yuxing Wang, Kaiyin Zhou, Jingbo Xia*. LitCovid-AGAC: Cellular and Molecular Level Annotation Data Set Based on Covid-19. Genomics and Informatics, 2021; 19(3): e23.

◆  Kaiyin Zhou#, Yuxing Wang#, Kevin Bretonnel Cohen, Jin-Dong Kim, Xiaohang Ma, Zhixue Shen, Xiangyu Meng, Jingbo Xia*. Bridging Heterogeneous Mutation Data to Enhance Disease-Gene Discovery. Briefing in Bioinformatics, 2021, bbab079.

◆  Yuxing Wang, Kaiyin Zhou, Jin-Dong Kim, Kevin Cohen, Mina Gachloo, Yuxin Ren, Shanghui Nie, Xuan Qin, Panzhong Lu, Jingbo Xia*. An Active Gene Annotation Corpus and Its Application on Anti-epilepsy Drug Discovery. BIBM 2019: International Conference on Bioinformatics & Biomedicine. Page: 512-519, San Diego, U.S, Nov, 2019.

◆  Yuxing Wang, Kaiyin Zhou, Mina Gachloo, Jingbo Xia*. An Overview of the Active Gene Annotation Corpus and the BioNLP OST 2019 AGAC Track Tasks. BioNLP Open Shared Task 2019, workshop in EMNLP-IJCNLP 2019. Page: 62-71, Hong Kong, 2019.

◆  Mina Gachloo, Yuxing Wang, Jingbo Xia*. A Review of Drug Knowledge Discovery by Using BioNLP and Tensor or Matrix Decomposition. Genomics and Informatics, 2019, 17(2): e18.

◆  Kaiyin Zhou, Yuxing Wang, Sheng Zhang, Mina Gachloo, Jin-Dong Kim, Qi Luo, Kevin Bretonnel Cohen, Jingbo Xia*. GOF/LOF Knowledge Inference with Tensor Decomposition in Support of High order Link Discovery for Gene, Mutation and Disease. Mathematical Biosciences and Engineering, 2019, 16(3): 1376-1391.

◆  Yuxing Wang, Xinzhi Yao, Kaiyin Zhou, Xuan Qin, Jin-Dong Kim, Kevin Bretonnel Cohen, Jingbo Xia*. Guideline Design of an Active Gene Annotation Corpus for the Purpose of Drug Repurposing. 2018 11th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI 2018), pp:1-5, Oct, 2018, Beijing.

Links to lab projects: