Rice Trait Ontology

水稻性状本体开发和文献知识挖掘

Relevant Links

  • [Ontology] Static webpage for RTO items list. (RTO1.0 静态网页展示) Link.
  • [Ontology] Expert annotation page for RTO. (RTO 专家交互工作页面) Link.
  • [DATABASE] Rice-Alterome (水稻变异体分子事件数据库) Link.
  • [TOOL] enrRiceTrait (基于RTO的水稻性状富集Python包) Link.

History

  • We released RTO (format version 1.1, referenced ontologies: TO, WTO). Download the RTO obo file here. (12/23/2020)
  • We reported RTO in Bio-Ontologies, ISMB, 2022. (Aug, 2022)

Tutorial Videos

❏ NLP methodology. Gene-to-trait association extraction (GTAE) pipeline

Narrator: Yun Liu
Youtube Video  Group discussion, 2020
(Mining gene-trait associations,)
B站镜像：Bilibili视频

❏ enrRiceTrait, an ontology-based tool for rice trait enrichment

Narrator: Yun Liu
Youtube Video  Group discussion, 2021
(A python package for rice trait enrichment,)
B站镜像：Bilibili视频

❏ RTO development. About the ontology

Narrator: Yufei Shen
Youtube Video Bio-Ontologies, ISMB, 2022
(Ontology development of RTO,)
B站镜像：Bilibili视频

Developers, Collabrations and References

❏ Main Developers (Alphabet order)

  • Ontology: Qidong Deng, Yun Liu, Yufei Shen, Xinzhi Yao.
  • Coding: Zhihan He, Xinchen Ma, Yusha Liu.

❏ Collaborations with multiple labs (Alphabet order)

  • Zaiwen Feng‘ lab (HZAU), on rice knowledge graph.
  • Pierre Larmande‘ lab (IRD, University of Montpellier), on OryzaGP.
  • Claire Nédellec‘ lab (INRAE), on RTO.
  • Jianwei Zhang’ lab (HZAU), on RTO.

❏ References

◆ Xinzhi Yao, Yun Liu, Qidong Deng, Yusha Liu, Xinchen Ma, Yufei Shen, Qianqian Peng, Zaiwen Feng, Jingbo Xia*. RTO, A Specific Crop Ontology for Rice Trait Concepts. Annual International Conference on International Society for Computational Biology (ISMB), Madison, WI, 10-14 July 2022 (Session Bio-Ontologies COSI). https://doi.org/10.5281/zenodo.6950749

◆ Pierre Larmande, Yusha Liu, Xinzhi Yao, Jingbo Xia. OryzaGP 2021 update: a rice gene and protein dataset for named-entity recognition. Genomics and Informatics, 2021, 19(3):e27.

◆ Old RTO page.

Links to lab projects: