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炭疽病知识图谱：基于知识图谱的炭疽病知识库，从生物医学文献中挖掘而来。

AnthraxKP: a knowledge graph-based, Anthrax Knowledge Portal mined from biomedical literature.

机构信息

College of Computer and Information Engineering, Inner Mongolia Agricultural University, Erdos East Street No. 29, Hohhot 010011, China.

Inner Mongolia Autonomous Region Key Laboratory of Big Data Research and Application for Agriculture and Animal Husbandry, Zhaowuda Road No. 306, Hohhot 010018, China.

出版信息

Database (Oxford). 2022 Jun 2;2022. doi: 10.1093/database/baac037.

DOI:10.1093/database/baac037
PMID:35653350
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9216567/
Abstract

Anthrax is a zoonotic infectious disease caused by Bacillus anthracis (anthrax bacterium) that affects not only domestic and wild animals worldwide but also human health. As the study develops in-depth, a large quantity of related biomedical publications emerge. Acquiring knowledge from the literature is essential for gaining insight into anthrax etiology, diagnosis, treatment and research. In this study, we used a set of text mining tools to identify nearly 14 000 entities of 29 categories, such as genes, diseases, chemicals, species, vaccines and proteins, from nearly 8000 anthrax biomedical literature and extracted 281 categories of association relationships among the entities. We curated Anthrax-related Entities Dictionary and Anthrax Ontology. We formed Anthrax Knowledge Graph (AnthraxKG) containing more than 6000 nodes, 6000 edges and 32 000 properties. An interactive visualized Anthrax Knowledge Portal(AnthraxKP) was also developed based on AnthraxKG by using Web technology. AnthraxKP in this study provides rich and authentic relevant knowledge in many forms, which can help researchers carry out research more efficiently. Database URL: AnthraxKP is permitted users to query and download data at http://139.224.212.120:18095/.

摘要

炭疽是一种由炭疽杆菌（炭疽细菌）引起的人畜共患传染病，不仅影响全球的家畜和野生动物，也影响人类健康。随着研究的深入，大量相关的生物医学文献不断涌现。从文献中获取知识对于深入了解炭疽的病因、诊断、治疗和研究至关重要。在这项研究中，我们使用了一组文本挖掘工具，从近 8000 篇炭疽生物医学文献中识别出近 14000 个属于 29 个类别的实体，如基因、疾病、化学物质、物种、疫苗和蛋白质，并提取了 281 类实体之间的关联关系。我们整理了炭疽相关实体词典和炭疽本体。我们形成了包含 6000 多个节点、6000 条边和 32000 个属性的炭疽知识图谱（AnthraxKG）。还基于 AnthraxKG 使用 Web 技术开发了交互式可视化炭疽知识门户（AnthraxKP）。本研究中的 AnthraxKP 以多种形式提供丰富、真实的相关知识，有助于研究人员更高效地开展研究。数据库网址：AnthraxKP 允许用户在 http://139.224.212.120:18095/ 进行查询和下载数据。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a2f/9216567/8a437d69529c/baac037f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a2f/9216567/15b4a8972855/baac037f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a2f/9216567/182de4655b2b/baac037f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a2f/9216567/8a437d69529c/baac037f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a2f/9216567/15b4a8972855/baac037f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a2f/9216567/182de4655b2b/baac037f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7a2f/9216567/8a437d69529c/baac037f4.jpg

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本文引用的文献

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2
Database resources of the National Center for Biotechnology Information.国家生物技术信息中心数据库资源。
Nucleic Acids Res. 2021 Jan 8;49(D1):D10-D17. doi: 10.1093/nar/gkaa892.
3
Constructing knowledge graphs and their biomedical applications.构建知识图谱及其生物医学应用。
Comput Struct Biotechnol J. 2020 Jun 2;18:1414-1428. doi: 10.1016/j.csbj.2020.05.017. eCollection 2020.
4
OpenBioLink: a benchmarking framework for large-scale biomedical link prediction.OpenBioLink：大规模生物医学链接预测的基准测试框架。
Bioinformatics. 2020 Jul 1;36(13):4097-4098. doi: 10.1093/bioinformatics/btaa274.
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Discovering protein drug targets using knowledge graph embeddings.利用知识图嵌入发现蛋白药物靶点。
Bioinformatics. 2020 Jan 15;36(2):603-610. doi: 10.1093/bioinformatics/btz600.
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PubTator central: automated concept annotation for biomedical full text articles.PubTator 中心：用于生物医学全文文章的自动概念标注。
Nucleic Acids Res. 2019 Jul 2;47(W1):W587-W593. doi: 10.1093/nar/gkz389.
7
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.人类表型本体（HPO）知识库和资源的扩展。
Nucleic Acids Res. 2019 Jan 8;47(D1):D1018-D1027. doi: 10.1093/nar/gky1105.
8
OMIM.org: leveraging knowledge across phenotype-gene relationships.OMIM.org：利用表型-基因关系中的知识。
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COSMIC: the Catalogue Of Somatic Mutations In Cancer.COSMIC：癌症体细胞突变目录。
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