COLLABORATIVE: ABI Development: Methodology for Pattern Creation, Imprint Validation, and Discovery from the Annotated Biological Web

马里兰大学、爱荷华大学和圣博纳文图尔大学获得了合作资助，以开发一种利用注释知识财富的方法，特别是拟南芥基因的基因本体（GO）和植物本体（PO）注释。由于有丰富而尚未充分利用的基因注释集合，该项目旨在促进发现隐藏的知识，这可能是进一步科学研究的基础。该方法将从注释图中提取感兴趣的模式（模式发现）。基于文献的方法将提取验证这些模式背后的生物学意义的句子（模式验证）。为了演示该方法，将为拟南芥定制PattArAn工具（拟南芥注释中的模式）。PattArAn将为用户提供拟南芥基因模式的图形展示以及相关的GO和PO CV术语。图数据挖掘技术和有效的算法解决方案，以识别密集子图（DSG）和执行图摘要（GS）将被开发。将开发算法来挖掘文献中提取的模式（称为印记）的相关句子。PattArAn将实现迭代探索，并将整合相关步骤，如咨询基因功能预测。该项目将涉及与生物学家合作，构建和改进注释图，并验证模式以确保与他们的研究相关。该项目为拟南芥群落做出了广泛的贡献。PattArAn可以帮助拟南芥管理员管理GO-PO注释，并补充现有的工具，如Textpresso和AraNet。它也可以用来为其他物种的基因组序列信息是可用的，引导一个注释数据库。该项目为研究生（马里兰大学和爱荷华大学）和本科生（圣博纳文蒂尔大学）提供了重要的研究和教育经验。小组成员将继续指导来自代表性不足社区的妇女和学生，参加外联活动，领导一个期刊俱乐部等。该研究项目的成果将通过生物学和生物信息学场所传播。更多信息可访问项目网站：https://wiki.umiacs.umd.edu/clip/pattaran/。

Collaborative grants have been awarded to the University of Maryland, the University of Iowa and St. Bonaventure University to develop a methodology that exploits the wealth of annotation knowledge, notably Gene Ontology (GO) and Plant Ontology (PO) annotations of Arabidopsis genes. Motivated by the availability of rich and as yet insufficiently tapped collections of gene annotations, the project aims to facilitate the discovery of hidden knowledge that could be the basis of further scientific research. The methodology will extract patterns of interest from annotation graphs (pattern discovery). Literature-based methods will extract sentences that validate the biological meaning underlying these patterns (pattern validation). To demonstrate the methodology, the PattArAn tool (Patterns in Arabidopsis Annotations) will be customized for Arabidopsis. PattArAn will provide the user with a graphical presentation of patterns of Arabidopsis genes and associated GO and PO CV terms. Graph data mining techniques and efficient algorithmic solutions to identify dense subgraphs (DSG) and to perform graph summarization (GS) will be developed. Algorithms to mine the literature for relevant sentences for an extracted pattern (referred to as the imprint) will be developed. PattArAn will enable iterative exploration and will incorporate allied steps such as consulting gene function prediction. The project will involve collaboration with biologists for building and refining annotation graphs, and validating patterns to ensure relevance to their research.The project makes broad contributions to the Arabidopsis thaliana community. PattArAn may assist Arabidopsis curators to manage GO-PO annotations and complement existing tools such as Textpresso and AraNet. It can also be used to bootstrap an annotation database for other plant species given that their genome sequence information is available. The project offers significant research and educational experiences for graduate students (University of Maryland and Iowa) and undergraduate students (St. Bonaventure University). Team members will continue to mentor women and students from under-represented communities, participate in outreach activities, lead a Journal Club, etc. The outcomes from this research project will be disseminated via biology and bioinformatics venues. More information may be obtained at the project website: https://wiki.umiacs.umd.edu/clip/pattaran/.