BioKG v1.0

BioKG v1.0 图谱概览

BioKG v1.0 的整体概览与来源构成，用于项目展示与合作交流。

Partner View

BioKG v1.0 Biomedical Knowledge Graph Overview

页面聚焦图谱整体规模、主要来源数据库与结构特征， 便于在项目沟通中快速形成统一认知。

数据库直查 小时级缓存 对外展示口径
数据库 bio_kg_v2
统计时间 2026-09-07 23:51:16
缓存周期 1 小时

Special Disease Hub

专病库入口已就绪

已接入阿尔茨海默病、渐冻症、胰腺癌和代谢子专题的统一筛查结果，可直接进入单病页查看结构与缺口。

进入专病库

Core Metrics

图谱整体状态

以下指标用于概览当前图谱规模、关系复杂度与整体连接水平。

节点总数 69,724,776

nodes 表当前总行数。

边总数 404,875,821

edges 表当前总行数。

节点类型数 74

nodes.category 的当前类别数。

边类型数 81

edges.type 的当前类别数。

图密度 8.33 x 10^-8

按当前节点数和边数计算的整体连接密度。

边/节点比 5.81

平均每个节点对应多少条边。

Source Breakdown

数据来源构成

节点按 `provided_by` 聚合，边按 `primary_knowledge_source` 聚合，便于合作方快速理解图谱组成。

节点来源数据库

按 nodes.provided_by 聚合 / 共 86 个来源
01
UCSC 16,066,459 · 23.0%
02
rna_b_editing_20260830_003 15,078,032 · 21.6%
03
rna_b_props_20260831_002_p1 6,763,655 · 9.7%
04
4DN 5,288,081 · 7.6%
05
ClinVar 4,294,684 · 6.2%
展开完整来源列表（86 个）
数据库 节点数 占比
UCSC 16,066,459 23.0%
rna_b_editing_20260830_003 15,078,032 21.6%
rna_b_props_20260831_002_p1 6,763,655 9.7%
4DN 5,288,081 7.6%
ClinVar 4,294,684 6.2%
gene_b_phase6_20260818_025 3,917,917 5.6%
ChEMBL 2,978,426 4.3%
rna_b_four_classes_20260830_004 2,757,793 4.0%
rna_a_props_20260824 2,659,140 3.8%
rna_b_props_20260831_002_p2 1,322,952 1.9%
Ensembl 1,236,932 1.8%
gene_b_phase4_20260818_013_p4 1,002,847 1.4%
drug_b_scafnet_20260901 947,325 1.4%
drug_b_scaffold_20260830 891,526 1.3%
UniProtKB 600,753 0.9%
PolyASite 569,005 0.8%
drug_b_brics_20260901 422,465 0.6%
r3_parts_a_20260811_001 314,096 0.5%
rna_a_coding_potential_20260827 276,379 0.4%
LncBook 261,004 0.4%
gene_b_tss_20260818_005 241,049 0.3%
ChEBI 216,787 0.3%
rna_a_refseq_ingest_20260826 194,361 0.3%
protein_a_pdb_nodes_20260831_001 191,002 0.3%
r3_nodeside_d_20260812_001 189,465 0.3%
NCBI Gene 148,760 0.2%
OpenTargets_Genetics 143,904 0.2%
rna_b_codons_20260830_001 136,588 0.2%
r3_sites_b_20260812_001 113,479 0.2%
InterPro 51,489 0.1%
Gene Ontology 45,272 0.1%
HGNC 45,129 0.1%
OpenTargets 44,023 0.1%
protein_disulfide_sites_20260819_081 36,314 0.1%
r2_nodeside_n2_20260810_001 31,854 0.0%
r2_nodeside_n3_20260810_001 28,146 0.0%
drug_b_ring_20260901 27,288 0.0%
Reactome 23,671 0.0%
HPO 19,933 0.0%
DrugBank 16,581 0.0%
rmsk_family_20260818_062 15,674 0.0%
huMAP3.0 15,284 0.0%
MONDO 15,073 0.0%
UBERON 10,522 0.0%
SIDER 9,497 0.0%
SilencerDB 8,818 0.0%
r2_nodeside_n1_20260810_001 5,605 0.0%
ATC 5,579 0.0%
ComplexPortal 4,446 0.0%
AlzKB 3,409 0.0%
Cell Ontology 3,335 0.0%
HENA 2,994 0.0%
Hetionet 2,606 0.0%
ADVP 2,556 0.0%
gene_smallfix_20260818_015_c 2,410 0.0%
PSI-MOD 2,116 0.0%
rna_pre_precursor_083_20260819 1,862 0.0%
r2_closeout_d_patch_20260810_001 1,678 0.0%
PCL 1,660 0.0%
source_unknown 1,652 0.0%
NCBI RefSeq 1,612 0.0%
HPA 1,441 0.0%
PrimeKG 1,267 0.0%
AlzData 1,247 0.0%
drug_b_alert_20260901 1,139 0.0%
cytoband_20260818_027 1,128 0.0%
SIGNOR 1,095 0.0%
ICELLNET 1,092 0.0%
GTEx 725 0.0%
SEA_AD 549 0.0%
TCGA 464 0.0%
CPTAC-3 414 0.0%
AD Multi-Region 356 0.0%
HsapDv 239 0.0%
HMDB 219 0.0%
RNAct 82 0.0%
PATO 70 0.0%
BioKG_Root 69 0.0%
CellMark 69 0.0%
miRTarBase 57 0.0%
FMA 46 0.0%
omics_od1_20260810T104520Z 27 0.0%
drug_b_warhead_20260901 23 0.0%
Perturb-seq 2 0.0%
HP 1 0.0%
omics_ne1_20260818T074644Z 1 0.0%

边来源数据库

按 edges.primary_knowledge_source 聚合 / 共 114 个来源
01
4dn 89,526,751 · 22.1%
02
rediportal 49,490,708 · 12.2%
03
rdkit 40,272,571 · 9.9%
04
Ensembl 39,622,766 · 9.8%
05
ucsc-tables 37,861,229 · 9.4%
展开完整来源列表（114 个）
数据库 边数 占比
4dn 89,526,751 22.1%
rediportal 49,490,708 12.2%
rdkit 40,272,571 9.9%
Ensembl 39,622,766 9.8%
ucsc-tables 37,861,229 9.4%
HENA 23,657,643 5.8%
ORnament 15,114,581 3.7%
RefSeq 12,143,244 3.0%
tflink 10,666,320 2.6%
ClinVar 9,929,054 2.5%
remap 8,994,882 2.2%
polyasite 6,967,489 1.7%
InterPro 4,763,737 1.2%
uorfdb 3,255,334 0.8%
DG-Miner 2,910,491 0.7%
rnacentral 2,693,893 0.7%
ChEMBL 2,279,162 0.6%
Hetionet 1,936,640 0.5%
BioGRID 1,877,516 0.5%
miRDB 1,875,944 0.5%
scimodom 1,741,649 0.4%
mercer 1,708,643 0.4%
rnact 1,696,789 0.4%
AlzKB 1,630,850 0.4%
ChEMBL 1,570,926 0.4%
HPA 1,459,421 0.4%
lncbook 1,256,993 0.3%
reftss 1,141,130 0.3%
Reactome 1,049,154 0.3%
abc 936,782 0.2%
oreganno 847,955 0.2%
PrimeKG 798,336 0.2%
OpenTargets 762,466 0.2%
epimap 704,513 0.2%
ensembl.gtf_116.transcripts 646,499 0.2%
encode-re2g 555,575 0.1%
IntAct 545,235 0.1%
CTD 536,467 0.1%
STITCH 487,827 0.1%
BindingDB 486,487 0.1%
dorothea 481,202 0.1%
STRING 448,272 0.1%
noncode 430,121 0.1%
Perturb-seq 408,745 0.1%
sifts 404,636 0.1%
UniProtKB 364,387 0.1%
hgnc-hcop 346,657 0.1%
ChEBI 297,824 0.1%
ensembl-compara 283,017 0.1%
GCST 268,777 0.1%
HPO 217,390 0.1%
cell-ontology 206,096 0.1%
DrugCentral 145,015 0.0%
covalentindb 129,579 0.0%
SIDER 123,591 0.0%
rmbase 121,904 0.0%
complexportal 120,803 0.0%
NEALE 79,054 0.0%
AlzData 71,943 0.0%
GO 64,717 0.0%
HPO_annotations 63,900 0.0%
encori 60,442 0.0%
NPInter 59,369 0.0%
biokg_etl 53,669 0.0%
HuRI 50,445 0.0%
Reactome 49,864 0.0%
cellxgene-census 45,070 0.0%
hgnc 38,779 0.0%
MONDO 36,649 0.0%
ad-multi-region 36,348 0.0%
ComplexPortal 35,392 0.0%
OmniPath 32,235 0.0%
NIAGADS 31,583 0.0%
silencerdb 30,532 0.0%
SIGNOR 28,697 0.0%
Monarch Initiative 27,258 0.0%
drugbank 26,294 0.0%
rnadisease 23,053 0.0%
HP 22,393 0.0%
GWAS Catalog 20,431 0.0%
alzkb 18,969 0.0%
sea-ad 17,739 0.0%
gdc 15,582 0.0%
alzdata 13,579 0.0%
WikiPathways 12,875 0.0%
alzgps 11,978 0.0%
DTC 10,730 0.0%
miRTarBase 10,017 0.0%
hra 8,428 0.0%
TRRUST 8,345 0.0%
FINNGEN 8,078 0.0%
UBERON 7,701 0.0%
PrimeKG 7,227 0.0%
mirbase 5,592 0.0%
MONDO 4,740 0.0%
PharmGKB 4,657 0.0%
HPA 2,397 0.0%
pdac-kg-omics 2,073 0.0%
SAIGE 1,960 0.0%
chembl_36_sqlite.tar 1,834 0.0%
icellnet 1,712 0.0%
pcl 1,418 0.0%
SIGNOR 1,203 0.0%
ucsc 1,128 0.0%
iresbase 1,105 0.0%
gtex 1,086 0.0%
RISE 1,064 0.0%
hsapdv 457 0.0%
AD_Multi_Region 435 0.0%
GENCODE 337 0.0%
TTD 329 0.0%
TDG Clinical Trial 185 0.0%
DGIdb 149 0.0%
BioKG Engine 62 0.0%

Pending Sources

待入库/下载清单

这个区域只读取一份待办清单文件，适合让 agent 自动维护“已找到但还没下载或还没完成入库”的候选库。

待入库/下载清单

最近同步 2026-04-26T16:53:00+08:00 / 共 21 个
数据库 下载
starBase / ENCORI ✔
POSTAR3 -
RISE ✔
DIANA-LncBase v3 -
hTFtarget -
展开完整待下载列表（21 个）
数据库 下载
starBase / ENCORI ✔
POSTAR3 -
RISE ✔
DIANA-LncBase v3 -
hTFtarget -
CellPhoneDB ✔
HMDB -
MINERVA disease maps -
COVID-19 Disease Map -
LncRNA2Target -
MNDR -
circBank -
RNAInter -
ATtRACT ✔
RBPDB -
EuRBPDB -
CLIPdb -
ADSP -
OpenNeuro ds004504 ✔
OpenNeuro ds006036 ✔
SEA-AD ✔

Node Landscape

节点类型概览

从节点类型分布可以快速看出当前图谱主要由哪些生物医学实体构成。

节点类型概览

按 nodes.category 聚合 / 共 74 类
RnaEditingSite 21.6%

15,078,032

ConservedRegion 14.8%

10,350,729

RepeatRegion 8.2%

5,683,690

Exon 6.6%

4,628,515

Variant 6.4%

4,437,152

TADBoundary 5.2%

3,643,895

biolink:RegulatoryRegion 4.6%

3,220,454

RNA 4.6%

3,197,693

展开完整节点类型列表（74 类）
节点类型 节点数 占比
RnaEditingSite 15,078,032 21.6%
ConservedRegion 10,350,729 14.8%
RepeatRegion 5,683,690 8.2%
Exon 4,628,515 6.6%
Variant 4,437,152 6.4%
TADBoundary 3,643,895 5.2%
biolink:RegulatoryRegion 3,220,454 4.6%
RNA 3,197,693 4.6%
SmallMolecule 3,083,116 4.4%
biolink:ChemicalEntity 2,289,766 3.3%
RnaModificationSite 1,863,553 2.7%
LaminaAssociatedDomain 1,644,186 2.4%
UORF 1,627,667 2.3%
SpliceSite 1,070,316 1.5%
Protein 1,054,892 1.5%
biolink:TranscriptionFactorBindingSite 1,002,762 1.4%
TandemRepeat 768,546 1.1%
Gene 720,976 1.0%
Intron 698,612 1.0%
PolyASiteCluster 569,005 0.8%
CodingSequence 383,119 0.5%
biolink:TranscriptionTerminationSite 358,678 0.5%
ThreePrimeUTR 312,869 0.4%
Transcript 274,238 0.4%
ProteinSite 262,433 0.4%
biolink:TranscriptionStartSite 241,049 0.3%
ProteinRegion 201,456 0.3%
FivePrimeUTR 199,939 0.3%
MacromolecularStructure 192,680 0.3%
StopCodon 104,988 0.2%
Treatment 59,954 0.1%
BranchSite 59,302 0.1%
ProteinFeature 51,489 0.1%
Phenotype 42,094 0.1%
Disease 37,943 0.1%
Drug 33,438 0.0%
CpGIsland 32,038 0.0%
StartCodon 31,600 0.0%
BiologicalProcess 29,140 0.0%
Pathway 27,828 0.0%
ProteinIsoform 24,772 0.0%
Peptide 22,870 0.0%
Complex 21,513 0.0%
RepeatName 15,600 0.0%
MolecularFunction 11,811 0.0%
Anatomy 11,406 0.0%
Measurement 8,437 0.0%
DrugClass 7,246 0.0%
SideEffect 6,060 0.0%
CellularComponent 4,321 0.0%
CellType 4,169 0.0%
Sample 2,415 0.0%
GeneFamily 2,410 0.0%
PosttranslationalModification 2,116 0.0%
Chromosome 1,691 0.0%
CellSubtype 1,175 0.0%
biolink:Cytoband 1,128 0.0%
GeneSet 1,024 0.0%
Antibody 890 0.0%
CellState 733 0.0%
Case 715 0.0%
TranscriptionFactor 519 0.0%
IRES 508 0.0%
Symptom 508 0.0%
PharmacologicClass 329 0.0%
DevelopmentalStage 239 0.0%
ProteinFamily 184 0.0%
RepeatFamily 58 0.0%
CellGroup 53 0.0%
RepeatClass 16 0.0%
CellClass 15 0.0%
Assembly 8 0.0%
Cohort 3 0.0%
CellLine 2 0.0%

Schema Graph

类型关系示意图

图中仅展示现有节点类型以及它们之间的总体连接结构，不展开到底层实例节点。

Schema Visualization

仅保留主要类型，并合并双向连接
正在加载类型关系图...
节点大小表示节点规模 连线粗细表示连接强度 大节点位于内圈，小节点位于外圈 可拖拽 / 可缩放 / 点击高亮

Connectivity Matrix

节点类型连接矩阵

横纵轴顺序与现有类型矩阵图保持一致，用来查看不同节点类型之间的连接强度。

类型连接矩阵

读取预生成统计结果
正在加载连接矩阵...

统计口径

以当前库内结果为准

当前页面展示基于 BioKG 数据库快照统计结果，仅保留概览场景最常用的核心指标与来源拆解。

刷新策略

按小时更新

页面按小时级节奏更新，适合作为稳定的项目概览入口，而非高频监控界面。