Research and Construction of Genetic Knowledge Graph of Milk Yield Traits in Dairy Cows

doi:10.3778/j.issn.1002-8331.2108-0005

Abstract

Abstract: Milk yield has always been one of the traits that experts pay attention to in dairy cow production traits. The improvement of milk yield is of great significance to the development of economy and people’s livelihood. Therefore, the research on the influencing factors of milk yield has become the focus of improving milk yield and milk quality. In view of the lack of cow milk yield gene knowledge graph, it firstly uses the crawler technology based on PubMed biomedical literature database to construct the related literature data set of milk yield trait omics data of dairy cows. Then, the relevant influencing factors of cow milk yield are extracted based on knowledge extraction technology, including 140 gene influencing factors. Finally, the Neo4j graph database is used for data storage, the knowledge graph related to milk yield traits of dairy cows is constructed, and the visual platform of milk yield traits data knowledge base is formed.

Key words: literature mining, knowledge graph, milk yield, knowledge extraction

摘要： 奶牛生产性状中产奶量一直是相关领域专家重点关注的性状之一，产奶量的提高对于经济和民生发展具有重要意义，因此产奶量的相关影响因素成为了研究提高奶产量和奶质量的焦点。针对目前缺少奶牛产奶量-基因知识图谱的问题，以PubMed生物医学文献库为相关来源，利用爬虫技术构建奶牛产奶量性状组学数据的相关文献数据集，通过知识抽取获得与奶牛产奶量相关的大约140个基因影响因素及其他影响因素。利用Neo4j图数据库的方式进行数据存储，构建与奶牛产奶量性状相关的知识图谱，最后形成奶牛产奶量性状数据知识库的可视化平台。

关键词: 文献挖掘, 知识图谱, 奶牛产奶量, 知识抽取

HU Hao, GAO Jing, LIU Zhenyu. Research and Construction of Genetic Knowledge Graph of Milk Yield Traits in Dairy Cows[J]. Computer Engineering and Applications, 2023, 59(2): 299-305.

胡浩, 高静, 刘振羽. 奶牛产奶量性状相关基因知识图谱的研究与构建[J]. 计算机工程与应用, 2023, 59(2): 299-305.

References

[1] STANTON J A L，MACGREGOR A B，MASON C，et al.Building comparative gene expression databases for the mouse preimplantation embryo using a pipeline approach to UniGene[J].Molecular Human Reproduction，2007，13（10）：713-720.
[2] STENSON P D，MORT M，BALL E V，et al.The human gene mutation database：building a comprehensive mutation repository for clinical and molecular genetics，diagnostic testing and personalized genomic medicine[J].Human Genetics，2014，133（1）：1-9.
[3] KAMINSKI S，RUSC A，MALEWSKI T.Single nucleotide polimorphism database of candidate genes associated with cow milk protein biosynthesis[J].Journal of Animal and Feed Sciences，2004，13（1）：51-64.
[4] OGOREVC J，KUNEJ T，RAZPET A，et al.Database of cattlecandidate genes and genetic markers for milk production and mastitis[J].Animal Genetics，2009，40（6）：832-851.
[5] QIN X，YAO X，XIA J.A novel metric to quantify the effect of pathway enrichment evaluation with respect to biomedical text-mined terms：development and feasibility study[J].JMIR Medical Informatics，2021，9（6）：28247.
[6] 佟凡.面向精准医学知识库的基因-变异-疾病关系抽取技术研究[D].北京：军事科学院，2019.
TONG F.Research on gene-mutation-disease relationshipextraction technology for Precision Medicine knowledge base[D].Beijing：Academy of Military Sciences，2019.
[7] 付义报.基于深度学习的出生缺陷关系抽取及知识图谱的构建[D].上海：华东师范大学，2020.
FU Y B.Deep learning-based relationship extraction of birth defects and construction of knowledge graph[D].Shanghai：East China Normal University，2020.
[8] PERERA N，DEHMER M，EMMERT-STREIB F.Named entity recognition and relation detection for biomedical information extraction[J].Frontiers in Cell and Developmental Biology，2020，8：673.
[9] 曹皓伟，徐建良，窦方坤.基于Neo4j生物医药知识图谱的构建[J].计算机时代，2020（6）：35-38.
CAO H W，XU J L，DOU F K.Building biomedical knowledge graph with Neo4j database[J].Computer Era，2020（6）：35-38.
[10] 柴神.知识图谱构建简介[DB/OL].（2020-11-07）[2021-07-22].https：//myblog.blog.csdn.net/article/details/109550502.
CHAI S.Introduction to knowledge graph construction[DB/OL].（2020-11-07）[2021-07-22].https：//myblog.blog.csdn.net/article/details/10955002.
[11] 漆桂林，高桓，吴天星.知识图谱研究进展[J].情报工程，2017，3（1）：4-25.
QI G L，GAO H，WU T X.The research advances of knowledge graph[J].Technology Intelligence Engineering，2017，3（1）：4-25.
[12] ZHOU H W，LIU Z，LANG C K，et al.Improving the recall of biomedical named entity recognition with label re-correction and knowledge distillation[J].BMC Bioinformatics，2021，22（1）：295.
[13] WEI C H，ALLOT A，LEAMAN R，et al.PubTator central：automated concept annotation for biomedical full text articles[J].Nucleic Acids Research，2019，47（W1）：W587-W593.
[14] WEI C H，KAO H Y，LU Z Y.PubTator：a web-based text mining tool for assisting biocuration[J].Nucleic Acids Research，2013，41（W1）：W518-W522.
[15] 薛丽娟，席梦隆，王梦婕，等.基于规则推理引擎的实体关系抽取研究[J].计算机科学与探索，2016，10（9）：1310-1319.
XUE L J，XI M L，WANG M J，et al.Entity relationship extraction based on rule inference engine[J].Journal of Frontiers of Computer Science and Technology，2016，10（9）：1310-1319.
[16] 廖建新.大数据技术的应用现状与展望[J].电信科学，2015，31（7）：7-18.

LIAO J X.Big data technology：current applications and prospects[J].Telecommunications Science，2015，31（7）：7-18.

[17] SESTAK M，HERICKO M，DRUZOVEC T W，et al.Applying k-vertex cardinality constraints on a Neo4j graph database[J].Future Generation Computer Systems-the International Journal of Escience，2021，115：459-474.