LINKING DISEASE-RELATED GENE TO THE IGTC KNOCKOUT DATABASE

该子项目是利用NIH/NCRR资助的中心赠款提供的资源的许多研究子项目之一。子项目和研究者（PI）可能从另一个NIH来源获得主要资金，因此可以在其他CRISP条目中表示。所列机构为中心，不一定是研究者所在机构。作为对小鼠胚胎干细胞中基因敲除的注释的一部分，BayGenomics（www.baygenomics.ucsf.edu）提供了与这些基因的人类直系同源物相关的医学术语的链接。这是通过使用医学主题词（MeSH）与描述相关基因的PubMed摘要链接来实现的。一个名为Meshlinker的工具用于浏览BayGenomics网站上的结果。该功能适用于BayGenomics数据库中敲除的基因，但尚未移植到国际基因陷阱联盟数据库（www.genetrap.org）。最初，我的研究项目是为IGTC网站创建Meshlinker的实现。这包括：为Meshlinker设计一个修改后的数据库模式，以符合BayGenomics和IGTC数据库之间的差异，加载数据本身以允许在IGTC网站上进行全功能数据挖掘，并将加载过程集成到IGTC管道中，以允许未来的自动运行。进一步的方向将包括将MeSH以外的医学术语本体与敲除基因联系起来，并利用这些联系提出有趣的生物学问题。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. As part of its annotation of genes knocked out in mouse embryonic stem cells, BayGenomics (www.baygenomics.ucsf.edu) provides links to medical terms with which the human orthologs of the genes are associated. This is accomplished by using the Medical Subject Headings (MeSH) linked with PubMed abstracts that describe the gene in question. A tool called Meshlinker is used to browse the results on the BayGenomics site. This functionality is in place for genes knocked out in the BayGenomics database but has not yet been ported to the International Gene Trap Consortium database (www.genetrap.org). Initially, my research project is to create an implementation of Meshlinker for the IGTC web site. This involves: designing a modified database schema for Meshlinker to correspond with the differences between the BayGenomics and IGTC databases, load the data itself to allow for fully functional data mining on the IGTC site, and integrate the loading process into the IGTC pipeline to allow for future automated runs. Further direction will include linking medical terminology ontologies other than MeSH to knocked-out genes and using these linkages to ask interesting biological questions.