AGAC Portal

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

undefined We are listing all about AGAC in this portal: Corpus annotation idea, data info, data usage in AGAC track as a shared task, baseline Python codes for AGAC track, and downstream applications with AGAC.

undefined 在这个页面中,我们列出了与AGAC语料库有关的标注规则、数据格式、代码和应用案例。

1. undefined Toy Example (标注示例)

2. undefined Corpus Guideline Book (标注指南)

3. undefined Corpus Development (语料库历史)

4. undefined Corpus Availability and BioNLP Open Shared Task (数据开放和共享任务)

5. undefined Data with Json form (数据格式)

6. undefined Baseline Python Codes (可获取的基线方法和代码)

7. undefined on Alzheimer’s Disease (AGAC在老年痴呆症的应用)

8. undefined on 84 Cancer Literature (AGAC在癌症数据的应用)

9. undefined on Covid-19 Literature (AGAC在新型冠状病毒文献挖掘的应用)

10. undefined for Covid-19 Hackathon Project (AGAC在BLAH7 Hackathon上的参与项目)

11. undefined on GDAS Track, CHIP 2022 (AGAC作为中国健康信息会议2022上的测评任务数据集)

—AGAC Story—

Why did we annotate AGAC?

Youtube video AGAC in BLAH 4, Tokyo, 2017
(Idea of AGAC annotation)

Bilibili视频 AGAC in BLAH 7, Tokyo, 2021
(Aggregate LitCovid with AGAC)


◆ 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:

▶ BioNLP 新手通道

▶ 课题组组员通道 (隐藏)

▶ 课题组课题页

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