基于图数据库的农业多本体解析导入方法

doi:10.19788/j.issn.2096-6369.000125

农业大数据学报 ›› 2025, Vol. 7 ›› Issue (4): 431-445.doi: 10.19788/j.issn.2096-6369.000125

基于图数据库的农业多本体解析导入方法

陈晓静¹^,²(), 李威¹^,²(), 樊景超¹^,², 闫燊³, 张建华¹^,²^,^*(), 周国民¹^,²^,⁴^,⁵^,^*()

1.中国农业科学院农业信息研究所/农业农村部农业大数据重点实验室/国家农业科学数据中心，北京 100081
2.中国农业科学院国家南繁研究院，海南三亚 572024
3.中国农业科学院作物科学研究所，北京 100081
4.农业农村部南京农业机械化研究所，南京 210014
5.中国农业科学院西部农业研究中心，，新疆昌吉 831100

收稿日期:2025-07-29 修回日期:2025-10-20 出版日期:2025-12-26 发布日期:2025-12-26
通讯作者: 周国民，E-mail：zhouguomin@caas.cn；
张建华，E-mail：zhangjianhua@caas.cn。
作者简介:陈晓静，E-mail：82101225580@caas.cn；
李威，E-mail：yjzltd@qq.com。
基金资助:
国家重点研发计划(2022YFF0711800);中国农业科学院国家南繁研究院南繁专项(YBXM2448);中国农业科学院国家南繁研究院南繁专项(YBXM2340);中国农业科学院国家南繁研究院南繁专项(YBXM2409);中国农业科学院国家南繁研究院南繁专项(YBXM2410);中国农业科学院国家南繁研究院南繁专项(YBXM2430);中国农业科学院国家南繁研究院南繁专项(YBXM2508);中国农业科学院国家南繁研究院南繁专项(YBXM2509);中央级公益性科研院所基本科研业务费专项(JBYW-AII-2025-05);中央级公益性科研院所基本科研业务费专项(Y2025YC90);国家农业科学数据中心项目(NASDC2025XM11)

A Method for Parsing and Importing Agricultural Multi-Ontologies Based on Graph Databases

CHEN XiaoJing¹^,²(), LI Wei¹^,²(), FAN JingChao¹^,², YAN Shen³, ZHANG JianHua¹^,²^,^*(), ZHOU GuoMin¹^,²^,⁴^,⁵^,^*()

1. Agricultural Information Institute of CAAS / Key Laboratory of Agricultural Big Data, Ministry of Agriculture and Rural Affairs / National Agriculture Science Data Center, Beijing 100081, China
2. National Nanfan Research Institute of CAAS, Sanya 572024, Hainan, China
3. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
4. Nanjing Research Institute of Agricultural Mechanization, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
5. Western Research Institute, CAAS, Changji 831100, Xinjiang, China

Received:2025-07-29 Revised:2025-10-20 Published:2025-12-26 Online:2025-12-26

摘要/Abstract

摘要：

统一组织结构复杂、规模庞大的农业本体，对于消除平台之间的数据孤岛、优化农业知识的标准化表达以及提高信息检索效率具有重要意义。本研究利用图数据库在存储本体方面的天然结构优势，创新性提出一种将面向OBO和OWL两种格式的大规模农业本体数据导入图数据库的方法。该方法首先按语义信息拆分解析OBO本体，同时通过消除冗余概念和前缀资源解析OWL本体，其次，在减少存储压力的需求下，进一步设计了编码方案和基于共现次数的属性关系筛选，最后智能化建模和映射，将本体存储进图数据库中，完成具备167 887个实体和249 603条关系的农业多本体数据库的构建。实体和关系对比分析结果表明，该方法在保留本体内部结构的同时，也保留了广泛的本体间知识链接，案例分析结果证明，多本体解析融合机制可以直观有效地构建跨本体知识交互。该方法有助于进一步推动农业本体的重用和共享，有效提升了农业信息资源标准化程度，所构建的农业多本体集成知识库为农业语义搜索、知识深度挖掘和智能化农业管理决策奠定了坚实的数据基础。

关键词: 农业本体, 图数据库, 本体解析, 知识集成

Abstract:

Integrating complex and large-scale agricultural ontologies into a unified framework is crucial for eliminating data silos across platforms, optimizing the standardization of agricultural knowledge representation, and enhancing information retrieval efficiency. Leveraging the inherent structural advantages of graph databases in ontology storage, this study proposes an innovative method for importing large-scale agricultural ontology data in both OBO and OWL formats into a graph database. The method first involves semantically parsing and splitting OBO ontologies, while simultaneously processing OWL ontologies through the elimination of redundant concepts and resolution of prefixed resources. To reduce storage overhead, an encoding scheme and a co-occurrence frequency-based attribute-relation filtering strategy are further designed. Finally, intelligent modeling and mapping are performed to store the ontologies within the graph database, resulting in the construction of an agricultural multi-ontology database comprising 167,887 entities and 249,603 relationships. Comparative analysis of entities and relationships demonstrates that the proposed method effectively preserves both internal ontological structures and extensive inter-ontological knowledge links. Case studies confirm that the multi-ontology parsing and integration mechanism enables intuitive and effective cross-ontology knowledge interaction. This approach facilitates the reuse and sharing of agricultural ontologies, significantly improving the standardization of agricultural information resources. The constructed integrated agricultural multi-ontology knowledge base provides a robust data foundation for semantic search, deep knowledge mining, and intelligent decision-making in agriculture.

Key words: agricultural ontology, graph database, ontology parsing, knowledge integration

陈晓静, 李威, 樊景超, 闫燊, 张建华, 周国民. 基于图数据库的农业多本体解析导入方法[J]. 农业大数据学报, 2025, 7(4): 431-445.

CHEN XiaoJing, LI Wei, FAN JingChao, YAN Shen, ZHANG JianHua, ZHOU GuoMin. A Method for Parsing and Importing Agricultural Multi-Ontologies Based on Graph Databases[J]. Journal of Agricultural Big Data, 2025, 7(4): 431-445.

图/表 18

表1

公开的主要农业本体及网址"

英文名称	中文名称和简称	本体格式	网址
OBO Metadata Ontology	OBO 元数据本体(OMO)	OBO	https://obofoundry.org
Sequence Ontology	序列本体(SO)	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
Gene Ontology	基因本体(GO)	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
ChEBI Ontology	生化实体本体(CHEBI)	OBO	https://www.ebi.ac.uk/chebi/init.do
Protein Ontology	蛋白质本体(PRO)	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
Cell Ontology	细胞本体(CL)	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
Anatomical Entity Ontology	解剖实体本体(AEO)	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
Plant Ontology	植物本体(PO)	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
Environment Ontology	环境本体(ENVO)	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
Plant Experimental Conditions Ontology	植物实验条件本体(PECO)	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
Agronomy Ontology	农学本体(AGRO)	OWL	https://bigdata.cgiar.org/ontologies-for-agriculture/
Small-scale fisheries & aquaculture ontology	小规模渔业和水产养殖本体（SSFAO）	OWL	https://bigdata.cgiar.org/ontologies-for-agriculture/
Phenotype And Trait Ontology	表型和性状本体(PATO)	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
Plant Trait ontology	特质本体(TO)	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
Animal Trait Ontology for Livestock	牲畜的动物性状本体(ATOL)	OWL	https://bigdata.cgiar.org/ontologies-for-agriculture/
Food Ontology	食品本体(FOODON)	OWL	https://bigdata.cgiar.org/ontologies-for-agriculture/
Compositional Dietary Nutrition Ontology	组合膳食营养本体(CDNO)	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
SEONT	SEONT农业住户调查本体	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
EMBRACE Data and Methods Ontology	EMBRACE 数据和方法本体（EDAM）	OBO	https://bigdata.cgiar.org/ontologies-for-agriculture/
An ontology of core ecological entities	核心生态实体的本体(ecocore)	OBO	https://obofoundry.org
Soil food web ontology	土壤食物网本体(SFWO)	OBO	https://github.com/soilfoodwebontology/sfwo
Relation Ontology	关系本体（RO）	OBO	https://basic-formal-ontology.org/users.html
Bioinformatics Web Services ontology	生物信息学 Web 服务本体（OBIWS）	OWL	https://basic-formal-ontology.org/users.html
Environment Ontology for Livestock	畜牧业环境本体(EOL)	OWL	https://agroportal.lirmm.fr/ontologies/EOL
Flora Phenotype Ontology	菌群表型本体(FLOPO)	OWL	https://obofoundry.org
Livestock Breed Ontology	牲畜品种本体（LBO）	OBO	https://agroportal.lirmm.fr/ontologies/LBO
Livestock Product Trait Ontology	畜产品性状本体（LPT）	OBO	https://agroportal.lirmm.fr/ontologies/LPT
Plant Stress Ontology	植物胁迫本体(PSO)	OBO	https://obofoundry.org

表1

图1

图2

图3

表2

OBO本体文件内容与格式转换结果示例"

OBO格式本体文本内容	格式转换结果
[Term] id: GO:0000070 name: mitotic sister chromatid segregation namespace: biological_process alt_id: GO:0016359 def: "The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets." [GOC:ai, GOC:jl] subset: goslim_pombe synonym: "mitotic chromosome segregation" EXACT [] synonym: "mitotic sister-chromatid adhesion release" NARROW [] is_a: GO:0000819 ! sister chromatid segregation is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0098813 ! nuclear chromosome segregation intersection_of: part_of GO:0140014 ! mitotic nuclear division relationship: part_of GO:0140014 ! mitotic nuclear division namezh: 有丝分裂姐妹染色单体分离 defzh: 该细胞周期过程在有丝分裂细胞周期中对复制的同源染色体进行组织并随后物理分离和分配到两组。每个复制的染色体由两条姐妹染色单体组成，它们在细胞赤道处对齐，与同源配对伙伴配对。每种形态类型的同源染色体中的一个进入产生的染色体组中的一个。	Subject	Predicate	Object
	GO:0000070	name	mitotic sister chromatid segregation
	GO:0000070	namespace	biological_process
	GO:0000070	alt_id	GO:0016359
	GO:0000070	def	"The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets." [GOC:ai, GOC:jl]
	GO:0000070	subset	goslim_pombe
	GO:0000070	synonym	"mitotic sister-chromatid adhesion release" NARROW []
	GO:0000070	is_a	GO:1903047
	GO:0000070	intersection_of	part_of GO:0140014
	GO:0000070	part_of	GO:0140014
	GO:0000070	namezh	有丝分裂姐妹染色单体分离
	GO:0000070	defzh	该细胞周期过程在有丝分裂细胞周期中对复制的同源染色体进行组织并随后物理分离和分配到两组。每个复制的染色体由两条姐妹染色单体组成，它们在细胞赤道处对齐，与同源配对伙伴配对。每种形态类型的同源染色体中的一个进入产生的染色体组中的一个。

表2

图4

表3

表4

图5

表5

表6

表7

表8

图6

图7

图8

图9

图10

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OWL格式本体文本内容	格式转换结果
<!-- http://purl.obolibrary.org/obo/FOODON_00003552 --> <owl:Class rdf:about="&obo;FOODON_00003552"> <rdfs:subClassOf rdf:resource="&obo;FOODON_00003458"/> <obo:IAO_0000115 xml:lang="en">A white-colored spear of a white asparagus plant which grows underground, without chlorophyll.</obo:IAO_0000115> <obo:IAO_0000117 rdf:resource="http://orcid.org/0000-0002-8844-9165"/> <dcterms:contributor> https://orcid.org/0000-0001-5275-8866</dcterms: contributor> <dcterms:date rdf:datatype="&xsd;dateTime">2020-10-21T05:37:26</dcterms:date> <oboInOwl:hasExactSynonym xml:lang="en">edible ivory</oboInOwl:hasExactSynonym> <oboInOwl:hasExactSynonym xml:lang="en">royal vegetable</oboInOwl:hasExactSynonym> <oboInOwl:hasExactSynonym xml:lang="en">white asparagus</oboInOwl:hasExactSynonym> <oboInOwl:hasExactSynonym xml:lang="en">white gold asparagus</oboInOwl:hasExactSynonym> <rdfs:label xml:lang="en">white asparagus spear</rdfs:label> </owl:Class>	Subject	Predicate	Object
	FOODON_00003552	type	Class
	FOODON_00003552	subClassOf	FOODON_00003458
	FOODON_00003552	definition	A white-colored spear of a white asparagus plant which grows underground, without chlorophyll.
	FOODON_00003552	term editor	0000-0002-8844-9165
	FOODON_00003552	contributor	0000-0001-5275-8866
	FOODON_00003552	date	2020-10-21T05:37:26
	FOODON_00003552	hasExactSynonym	edible ivory
	FOODON_00003552	hasExactSynonym	royal vegetable
	FOODON_00003552	hasExactSynonym	white asparagus
	FOODON_00003552	hasExactSynonym	white gold asparagus
	FOODON_00003552	label	white asparagus spear

属性名称	数据类型	说明
Vertex_ID	Int	术语编号
ontology_id	Text	原始编码
name	Text	术语名称
subset	Text	子集
is_obsolete	Text	是否过时
def	Text	定义
synonym	Text	同义词
xref	Text	外部参照
comment	Text	注释
alt_id	Text	可替代术语（可跨本体）
created_by	Text	创建作者
creation_date	Text	创建日期
consider	Text	可参考术语
replaced_by	Text	被术语替代
namespace	Text	命名空间
namezh	Text	中文名称
defzh	Text	中文定义
property_value	Text	属性值
disjoint_from	Text	完全不重叠术语

关系名称	说明	描述
is_a	继承关系	表示一种具体概念是另一种概念的子类。
part_of	部分整体关系	表示一个概念是另一个概念的一部分。
has_part	部分整体逆向关系	表示一个概念拥有某个部分。
has_quality	属性关系	表示一个概念拥有某种性质或特性。
intersection_of	交集关系	表示某个概念是两个概念的交集。
occurs_in	时空关系	表示一个概念在特定时间和空间中发生，表示某个事件、过程或行为发生在某个特定的环境、位置或范围中。
negatively_regulates	负调节关系	表示一个概念对另一个概念的调节作用是负向的，即减少或抑制某种活动或过程。
only_in_taxon	约束关系	表示某个概念仅适用于特定的物种或类群。
positively_regulates	正调节关系	表示一个概念对另一个概念的调节作用是正向的，即促进或增强某种活动或过程。
regulates	调节关系	表示某个概念对另一个概念的调节作用，通常不指定是正向还是负向调节。
disjointWith	不相交关系	表示两个概念在本体中是完全互不相交的，即它们没有任何共享的实例。
subClassOf	继承关系	表示一个概念是另一个概念的子类，表示继承、包含或特性传递。
determined_by	因果关系	表示某个概念是由其他概念所决定或确定的。
develops_from	演变关系	表示某个概念是从另一个概念演变、发展或衍生出来的。

创建内容	示例
创建属性	schema.propertyKey("Vertex_ID").asInt().ifNotExist().create();
创建顶点类型	schema.vertexLabel("aeo") .properties("Vertex_ID", "ontology_id", "name", "subset", "is_obsolete", "def", "synonym", "xref", "comment", "alt_id", "created_by", "creation_date", "consider", "replaced_by", "namespace", "namezh", "defzh", "property_value", "disjoint_from") .primaryKeys("Vertex_ID") .ifNotExist() .create();
创建索引	schema.indexLabel("aeoByontology_id") .onV("aeo") .by("ontology_id") .secondary() .ifNotExist() .create();
创建边类型	schema.edgeLabel("aeo_has_part") .sourceLabel("aeo") .targetLabel("aeo") .ifNotExist() .create();

本体名称	实体数量（个）	本体内关系数量（条）
aeo	250	366
agro	2768	3118
assfo	252	247
atol	2172	2216
cdno	2059	2241
chebi	3051	3521
cl	15964	60879
ecocore	5047	17508
EDAM	2745	3045
envo	3247	1846
eol	624	635
flopo	24204	346
foodon	10970	7765
go	9166	9187
lbo	1113	1108
lpt	503	562
OBIws	130	61
omo	27	26
pato	1858	2121
peco	2552	3378
po	1705	2619
pro	67906	38283
pso	419	794
ro	53	49
seont	1217	1869
sfwo	368	493
so	2597	3445
to	4920	6184

基于图数据库的农业多本体解析导入方法

A Method for Parsing and Importing Agricultural Multi-Ontologies Based on Graph Databases

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