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