| 1 |
ADHD-KG
|
[13]ADHD-KG
|
[14]ADHD-KG: a knowledge graph of attention deficit hyperactivity disorder
|
GitHub [15]ADHD-KG
|
.n3 / .nt [16]ADHD-KG [17]ADHD-KG v1.0
|
2022
|
School of Computing and Engineering, University of Huddersfield [18]School of Computing and Engineering
|
| 2 |
BIKG
|
-
|
[19]Biological Insights Knowledge Graph: an integrated knowledge graph to support drug development
|
-
|
-
|
2022
|
Company: AstraZeneca [20]AI and knowledge graphs for drug discovery [21]AstraZeneca
|
| 3 |
BIOS
|
[22]Biomedical Informatics Ontology System - BIOS@IDEA
|
[23]BIOS: An Algorithmically Generated Biomedical Knowledge Graph
|
GitHub [24]BIOS NER [25]BIOS EntityClassification
|
.txt [26]Biomedical Informatics Ontology System - BIOS@IDEA
|
2022
|
International Digital Economy Academy [27]International Digital Economy Academy (IDEA) , Center for Statistical Science, Tsinghua University [28]Center for Statistical Science , Individuals from other research institutes
|
| 4 |
BY-COVID-KG
|
-
|
-
|
GitHub [29]COVID-19 Knowledge Graph: A comprehensive representation of chemical and biological entities associated with COVID-19
|
.pkl / .csv / .graphml / .sif [30]BY-COVID Knowledge Graph: A comprehensive network integrating various data resources of BY-COVID project - BioModels
|
2022
|
BeYond-COVID (BY-COVID) project, various European research institutes [31]BY-COVID
|
| 5 |
Bio2RDF
|
[32]Bio2RDF v2.7a [33]Bio2RDF Home
|
[34]Bio2RDF: Towards a mashup to build bioinformatics knowledge systems [35]Bio2RDF release 3: a larger connected network of linked data for the life sciences
|
GitHub [36]Bio2RDF-scripts
|
.nq / .owl [37]Bio2RDF Release 3 [38]File Browser , SPARQL endpoint [39]OpenLink Virtuoso SPARQL Query Editor
|
2014
|
Individuals from various research institutes
|
| 6 |
Bio4j
|
[40]Bio4j
|
[41]Bio4j: a high-performance cloud-enabled graph-based data platform
|
GitHub [42]Bio4j bioinformatics graph data platform [43]Bio4j Titan
|
.dmp (TitanDB) [44]bio4j-titan/docs/Bio4jAWSReleases.md at master · bio4j/bio4j-titan [45]bio4j-titan/docs/ImportingTitanBio4j.md at master · bio4j/bio4j-titan
|
2014
|
Company: Era7 Bioinformatics [46]Oh no sequences! Research Group - Era7 Bioinformatics
|
| 7 |
BioGrakn
|
[47]Tomas Sabat
|
[48]BioGrakn: A Knowledge Graph-Based Semantic Database for Biomedical Sciences
|
GitHub [49]BioGrakn
|
.zip (Grakn) [50]Releases · vaticle/biograkn · GitHub
|
2018
|
Company: Vaticle Ltd [51]Vaticle · GitHub
|
| 8 |
BioGraph
|
[52]BioGraph
|
[53]BioGraph: Data Model for Linking and Querying Diverse Biological Metadata
|
GitHub [54]BioGraph
|
.zip (Neo4J) [55]biograph/biograph-backend/importers at master · aleksandar-veljkovic/biograph · GitHub
|
2023
|
Individuals from various research institutes
|
| 9 |
BioKG
|
-
|
[56]BioKG: A Knowledge Graph for Relational Learning On Biological Data
|
GitHub [57]biokg [58]biodblinker , PyPI [59]biodblinker · PyPI
|
.tsv [60]Release biokg-v1.0.0 · dsi-bdi/biokg
|
2020
|
Biomedical Discovery Informatics Unit, NUI Galway [61]Data Science Institute - University of Galway [62]DSI - Biomedical Discovery Informatics
|
| 10 |
Biomedical Data Translator
|
[63]Biomedical Data Translator - National Center for Advancing Translational Sciences [64]Translator Developer Documentation
|
[65]The Biomedical Data Translator Program: Conception, Culture, and Community [66]Progress toward a universal biomedical data translator
|
GitHub [67]ReasonerAPI [68]Knowledge Graph Exchange (KGE) Archive and Registry Working Group [69]TranslatorTechnicalDocumentation
|
REST API [70]SmartAPI - Translator , Web UI [71]NCATS Biomedical Data Translator
|
2023
|
National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH) [72]National Center for Advancing Translational Sciences
|
| 11 |
Bioteque
|
[73]BIOTEQUE: Metapath Explorer
|
[74]Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque [75]BQsupports: systematic assessment of the support and novelty of new biomedical associations
|
GitLab [76]bioteque / Bioteque
|
.tsv [77]BIOTEQUE: Downloads
|
2022
|
Structural Bioinformatics and Network Biology Group, IRB Barcelona [78]Structural Bioinformatics and Network Biology Group
|
| 12 |
Biozon
|
[79]Biozon
|
[80]BIOZON: a hub of heterogeneous biological data [81]BIOZON: a system for unification, management and analysis of heterogeneous biological data
|
Website [82]Biozon : Download files and software
|
.sql (PostgreSQL) [83]Biozon : Download files and software
|
2005
|
Department of Developmental Biology, Stanford University [84]Stanford Developmental Biology
|
| 13 |
COVID-19 Knowledge Graph
|
[85]COVID-19 Knowledge Graph
|
[86]COVID-19 Knowledge Graph from semantic integration of biomedical literature and databases
|
GitHub [87]covid19kg_rdf
|
.ttl [88]COVID-19 Knowledge Graph - RDF Dumps , REST API [89]COVID-19 Knowledge Graph - RESTful API , SPARQL GUI [90]COVID-19 Knowledge Graph - YASGUI SPARQL GUI
|
2022
|
Department of Computer and Information Sciences, University of Delaware [91]Computer & Information Sciences at the University of Delaware
|
| 14 |
COVID-19-Net
|
[92]Peter Rose - COVID Information Commons
|
-
|
GitHub [93]Covid-19-Community
|
Neo4j Browser [94]reader@neo4j://132.249.238.185:7687 - Neo4j Browser
|
2022
|
Individuals from various research institutes
|
| 15 |
COVID-KG
|
[95]BLENDER Lab - Software
|
[96]COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation
|
-
|
.csv [97]Wayback Machine: KG.zip
|
2020
|
BLENDER Lab, University of Illinois [98]BLENDER Lab
|
| 16 |
CROssBAR
|
[99]CROssBAR Project [100]CROssBAR Knowledge Graphs
|
[101]CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations
|
GitHub [102]CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations
|
.csv / .tsv [103]CROssBAR integrated knowledge graphs (KG) · cansyl/CROssBAR
|
2023
|
Cancer Systems Biology Laboratory (CanSyL), METU [104]CanSyL - Cancer Systems Biology Laboratory , Protein Function Development Team, EMBL-EBI [105]Protein Function Development – Services for protein sequences and their function
|
| 17 |
Chem2Bio2RDF
|
[106]chem2bio2rdf
|
[107]Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data
|
-
|
RDF [108]Wayback machine: chem2bio2rdf datasets
|
2010
|
School of Informatics and Computing, Indiana University [109]IU School of Informatics, Computing, and Engineering
|
| 18 |
Clinical Knowledge Graph (CKG)
|
[110]Clinical Knowledge Graph — ClinicalKnowledgeGraph 1.0 documentation
|
[111]Clinical Knowledge Graph Integrates Proteomics Data into Clinical Decision-Making [112]A knowledge graph to interpret clinical proteomics data
|
GitHub [113]CKG
|
.dump (Neo4j) [114]Clinical Knowledge Graph
|
2021
|
NNF Center for Protein Research, University of Copenhagen [115]Novo Nordisk Foundation Center for Protein Research
|
| 19 |
CovidGraph
|
[116]HealthECCO [117]CovidGraph - a COVID-19 Knowledge Graph - HealthECCO [118]CovidGraph Documentation
|
[119]CovidGraph: a graph to fight COVID-19
|
GitHub [120]documentation
|
Web UI [121]CovidGraph Explorer , Neo4j Browser [122]Neo4j Browser
|
2022
|
Covidgraph.org Team, Individuals from various research institutes [123]Covidgraph.org Team
|
| 20 |
CovidPubKG
|
-
|
[124]CovidPubGraph: A FAIR Knowledge Graph of COVID-19 Publications
|
GitHub [125]CovidPubKG: A FAIR Knowledge Graph of COVID-19 Publications
|
.nt / .ttl [126]/datasets/CovidPubGraph/archive/ [127]CovidPubGraph: A FAIR Knowledge Graph of COVID-19 Publications , SPARQL endpoint [128]Virtuoso SPARQL Query Editor
|
2021
|
DICE group, Paderborn University [129]The Data Science (DICE) group
|
| 21 |
DDI-BLKG
|
-
|
[130]Drug-Drug Interaction Prediction on a Biomedical Literature Knowledge Graph
|
GitHub [131]Drug-Drug Interaction Prediction on a Biomedical Literature Knowledge Graph (DDI-BLKG)
|
.txt [132]ownCloud - A safe home for all your data
|
2020
|
Institute of Informatics and Telecommunications, NCSR Demokritos [133]National Centre for Scientific Research "Demokritos"
|
| 22 |
DRKG
|
-
|
[134]DRKG/DRKG Drug Repurposing Knowledge Graph.pdf at master · gnn4dr/DRKG
|
GitHub [135]Drug Repurposing Knowledge Graph (DRKG)
|
.tsv / .npy [136]GitHub - gnn4dr/DRKG: A knowledge graph and a set of tools for drug repurposing
|
2022
|
Individuals from various research institutes
|
| 23 |
DeepKG
|
[137]COVID-19 KG
|
[138]DeepKG: an end-to-end deep learning-based workflow for biomedical knowledge graph extraction, optimization and applications
|
-
|
Triplets [139]COVID-19 KG
|
2021
|
Individuals from various research institutes
|
| 24 |
DisGeNET-RDF
|
[140]DisGeNET - a database of gene-disease associations [141]DisGeNET RDF
|
[142]DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes [143]DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases [144]The DisGeNET knowledge platform for disease genomics: 2019 update
|
Bitbucket [145]disgenet2r — Bitbucket [146]disgenet-app — Bitbucket
|
.ttl [147]Index of /download , SPARQL endpoint [148]Virtuoso SPARQL Query Editor [149]SPARQL Explorer , .tsv / .sql (SQLite) [150]DisGeNET - a database of gene-disease associations , REST API [151]DisGeNET Programmatic Access
|
2020
|
Integrative Biomedical Informatics (IBI) group, Research Programme on Biomedical Informatics (GRIB) [152]Integrative Biomedical Informatics - Research - Grib
|
| 25 |
Drug-CoV
|
-
|
[153]Drug-CoV: a drug-origin knowledge graph discovering drug repurposing targeting COVID-19
|
GitHub [154]kg
|
.csv [155]kg/Drug-CoV at main · SRL94/kg
|
2023
|
School of Information Technology, Murdoch University [156]School of Information Technology - Murdoch University
|
| 26 |
DrugMechDB
|
[157]Indication Mechanism of Action Database - DrugMechDB
|
[158]DrugMechDB: A Curated Database of Drug Mechanisms [159]Design and application of a knowledge network for automatic prioritization of drug mechanisms
|
GitHub [160]DrugMechDB
|
-
|
2023
|
Su Lab, Scripps Research Institute [161]The Su Lab - Quantitative methods in biomedical discovery
|
| 27 |
DrugRep-HeSiaGraph
|
-
|
[162]DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing
|
GitHub [163]DrugRep-HeSiaGraph
|
.csv [164]DrugRep-HeSiaGraph
|
2023
|
CBRC Lab, Amirkabir University Of Technology [165]CBRC
|
| 28 |
DrugRep-KG
|
-
|
[166]DrugRep-KG: Toward Learning a Unified Latent Space for Drug Repurposing Using Knowledge Graphs
|
GitHub [167]DrugRep-KG
|
.csv / .txt [168]DrugRep-KG/DRP-KGE-Data and Code at main · CBRC-lab/DrugRep-KG · GitHub
|
2023
|
CBRC Lab, Amirkabir University Of Technology [169]CBRC
|
| 29 |
EmBiology
|
[170]EmBiology - Biological data structured for insights - Elsevier
|
[171]EmBiology
|
-
|
Commercial access
|
2023
|
Company: Elsevier [172]Elsevier - An Information Analytics Business
|
| 30 |
EpiGraphDB
|
[173]EpiGraphDB
|
[174]EpiGraphDB: a database and data mining platform for health data science
|
GitHub [175]epigraphdb [176]epigraphdb-r
|
Neo4j build pipeline [177]neo4j-build-pipeline , REST API [178]EpiGraphDB API - Swagger UI
|
2021
|
MRC Integrative Epidemiology Unit, University of Bristol [179]MRC Integrative Epidemiology Unit - University of Bristol
|
| 31 |
GP-KG
|
-
|
[180]KG-Predict: A knowledge graph computational framework for drug repurposing
|
File server [181]Index of /public/data/GPKG-Predict
|
.txt [182]Index of /public/data/GPKG-Predict/data
|
2022
|
Center for Artificial Intelligence in Drug Discovery, Case Western Reserve University [183]Center for Artificial Intelligence in Drug Discovery - Case Western Reserve University
|
| 32 |
GenomicKB
|
[184]GenomicKB
|
[185]GenomicKB: a knowledge graph for the human genome
|
-
|
.dump (Neo4j) [186]Database Download :: GKB Documentation
|
2023
|
Liu Lab, University of Michigan [187]Liu Lab
|
| 33 |
Google Health Knowledge Graph
|
[188]A remedy for your health-related questions: health info in the Knowledge Graph [189]A reintroduction to our Knowledge Graph and knowledge panels
|
-
|
-
|
REST API with JSON-LD responses [190]Google Knowledge Graph Search API [191]Google Knowledge Graph Search API - Enterprise Knowledge Graph
|
2020
|
Company: Google [192]Google - About Google, Our Culture & Company News
|
| 34 |
GrEDeL
|
-
|
[193]GrEDeL: A Knowledge Graph Embedding Based Method for Drug Discovery From Biomedical Literatures
|
[194]GitHub - ShengtianSang/GrEDeL: GrEDeL
|
-
|
2019
|
Individuals from various research institutes
|
| 35 |
HALD
|
[195]HALD
|
[196]HALD, a human aging and longevity knowledge graph for precision gerontology and geroscience analyses
|
GitHub [197]hald
|
.json / .csv [198]HALD, a human aging and longevity knowledge graph for precision gerontology and geroscience analyses
|
2023
|
Ming Chen's Group of Bioinformatics, Zhejiang University [199]Ming Chen's Group of Bioinformatics!
|
| 36 |
HemeKG
|
[200]HemeKG v0.0.1-dev
|
[201]A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders
|
GitHub [202]HemeKG , PyPI [203]hemekg · PyPI
|
.json (BEL JSON) [204]hemekg/hemekg at master · hemekg/hemekg · GitHub
|
2021
|
Pharmaceutical Biochemistry and Bioanalytics, University of Bonn [205]Department of Pharmaceutical Biochemistry and Bioanalytics , Department of Bioinformatics, Fraunhofer SCAI [206]Bioinformatics - Fraunhofer SCAI
|
| 37 |
Hetionet
|
[207]Hetionet - An integrative network of biomedical knowledge
|
[208]Systematic integration of biomedical knowledge prioritizes drugs for repurposing [209]Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
|
Website [210]Het.io - Software , GitHub [211]hetio/hetionet: Data repository containing Hetionet downloads [212]hetio/hetnetpy repository: Hetnets in Python , PyPI [213]hetio · PyPI [214]hetnetpy · PyPI
|
.json / .tsv / .dump (Neo4j) / .npy (NumPy) [215]Het.io - Explore Neo4j Browser [216]Hetionet in Neo4j
|
2018
|
Baranzini Lab, UCSF [217]Baranzini Lab , Greene Lab, University of Pennsylvania [218]Greene Lab
|
| 38 |
HuadingKG
|
-
|
[219]HKGB: An Inclusive, Extensible, Intelligent, Semi-auto-constructed Knowledge Graph Framework for Healthcare with Clinicians’ Expertise Incorporated
|
GitHub [220]huadingkg
|
RDF (Apache Jena) [221]huadingkg
|
2019
|
Individuals from various research institutes
|
| 39 |
IASiS Open Data Graph
|
[222]The iASiS project Knowledge Graph - IASIS
|
[223]iASiS Open Data Graph: Automated Semantic Integration of Disease-Specific Knowledge
|
GitHub [224]iASiS Open Data Graph
|
MongoDB / Neo4j build pipeline [225]iASiS Open Data Graph
|
2020
|
Institute of Informatics and Telecommunications, NCSR Demokritos [226]National Centre for Scientific Research "Demokritos"
|
| 40 |
IDSM
|
[227]IDSM - Integrated Database of Small Molecules
|
[228]IDSM ChemWebRDF: SPARQLing small-molecule datasets
|
GitLab [229]chemdb · GitLab
|
.owl / .ttl / .sql (PostgreSQL) pipeline [230]chemdb / loaders · GitLab , SPARQL endpoints [231]IDSM / SPARQL GUI [232]IDSM / SPARQL GUI [233]YASGUI
|
2023
|
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences [234]IOCB Prague - Institute of Organic Chemistry and Biochemistry of the CAS
|
| 41 |
INDRA
|
[235]INDRA [236]INDRA documentation — INDRA 1.22.0 documentation
|
[237]From word models to executable models of signaling networks using automated assembly [238]Automated assembly of molecular mechanisms at scale from text mining and curated databases
|
GitHub [239]INDRA , PyPI [240]indra · PyPI
|
.tsv [241]indra_assembly_paper/data at master · sorgerlab/indra_assembly_paper · GitHub , .pkl / .json [242]INDRA assembly Benchmark Corpus , REST API [243]INDRA REST API
|
2023
|
Sorger Lab, Harvard Medical School [244]Sorger Lab
|
| 42 |
Implicitome
|
-
|
[245]The Implicitome: A Resource for Rationalizing Gene-Disease Associations
|
GitHub [246]GeneDiseasePaper
|
.csv / .nq [247]Dryad - Data -- The implicitome: a resource for rationalizing gene-disease associations
|
2017
|
Individuals from various research institutes
|
| 43 |
KEGG50k
|
-
|
[248]Drug target discovery using knowledge graph embeddings
|
-
|
.txt [249]KEGG50k-drugtargets
|
2018
|
Data Science Institute, University of Galway [250]Data Science Institute - University of Galway
|
| 44 |
KG-COVID-19
|
[251]KG-COVID-19 documentation — kg-covid-19 1.0.0 documentation
|
[252]KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response
|
GitHub [253]kg-covid-19
|
.nt / .tsv [254]KG-COVID-19 , SPARQL endpoint [255]Blazegraph Workbench
|
2023
|
Individuals from various research institutes
|
| 45 |
KG-Hub
|
[256]Knowledge Graph Hub
|
[257]KG-Hub -- Building and Exchanging Biological Knowledge Graphs
|
GitHub [258]Knowledge-Graph-Hub
|
.nt [259]KG-Hub Index
|
2023
|
Individuals from various research institutes
|
| 46 |
KGen
|
-
|
[260]KGen: a knowledge graph generator from biomedical scientific literature
|
GitHub [261]KGen
|
.txt / .ttl [262]KGen/examples/biomedical at master · rossanez/KGen · GitHub
|
2022
|
Institute of Computing, University of Campinas [263]Institute of Computing
|
| 47 |
KIDS
|
-
|
[264]Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes
|
GitHub [265]Knowledge Integration and Decision Support (KIDS)
|
.txt / .xml [266]KIDS/kg_constructor/data at master · IBPA/KIDS · GitHub
|
2022
|
Tagkopoulos Lab, University of California [267]Integrative Biology and Predictive Analytics – @ UC DAVIS
|
| 48 |
KaBOB
|
-
|
[268]KaBOB: ontology-based semantic integration of biomedical databases
|
GitHub [269]KaBOB
|
RDF pipeline [270]KaBOB
|
2015
|
Computational Bioscience Program, University of Colorado [271]Computational Bioscience Home - School of Medicine
|
| 49 |
Knowledge4COVID-19 KG
|
-
|
[272]Knowledge4COVID-19: A semantic-based approach for constructing a COVID-19 related knowledge graph from various sources and analyzing treatments’ toxicities
|
GitHub [273]Knowledge4COVID-19 , Zenodo [274]Knowledge4COVID-19
|
SPARQL endpoint [275]Virtuoso SPARQL Query Editor
|
2022
|
L3S Research Center, University of Hannover [276]L3S Research Center - All Projects , Individuals from various research institutes
|
| 50 |
LMKG
|
-
|
[277]LMKG: A large-scale and multi-source medical knowledge graph for intelligent medicine applications
|
GitHub [278]LMKG
|
.json [279]LMKG – Google Drive , Neo4j Browser [280]Neo4j Browser
|
2023
|
Department of Electronic Engineering, Tsinghua University [281]Department Of Electronic Engineering Tsinghua University , Individuals from various research institutes
|
| 51 |
MDKG
|
-
|
[282]An Integrated Knowledge Graph for Microbe-Disease Associations
|
GitHub [283]MDKG
|
.dict / .txt [284]MDKG/dataset.rar at master · ccszbd/MDKG · GitHub
|
2020
|
Central China Normal University [285]Central China Normal University
|
| 52 |
Monarch KG
|
[286]Monarch Initiative [287]monarch-py
|
[288]Navigating the Phenotype Frontier: The Monarch Initiative [289]The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species [290]The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species
|
GitHub [291]monarch_ingest [292]Monarch App , PyPI [293]monarch-py · PyPI
|
.nt, .jsonl, .tsv, .db (SQLite), .dump (Neo4j) [294]Directory index for https://data.monarchinitiative.org/
|
2023
|
Department of Biomedical Informatics, University of Colorado [295]Department of Biomedical Informatics , Individuals from various research institutes
|
| 53 |
Mpox Knowledge Graph
|
[296]Monkeypox Knowledge Graph: A comprehensive representation embedding chemical entities and associated biology of Monkeypox - BioModels
|
[297]Mpox Knowledge Graph: a comprehensive representation embedding chemical entities and associated biology of Mpox
|
GitHub [298]Monkeypox Knowledge Graph: A comprehensive representation of chemical and biological entities associated with Monkeypox
|
.csv / .graphml / .pkl / .sif [299]Monkeypox Knowledge Graph: A comprehensive representation embedding chemical entities and associated biology of Monkeypox - BioModels [300]Mpox Knowledge Graph: A comprehensive representation of chemical and biological entities associated with Mpox , Web UI [301]Mpox Knowledge Graph - A comprehensive representation embedding chemical entities and associated biology of Mpox
|
2022
|
Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) [302]Fraunhofer ITMP
|
| 54 |
NGLY1 Deficiency KG
|
-
|
[303]Structured reviews for data and knowledge-driven research
|
GitHub [304]The NGLY1 Deficiency Knowledge Graph [305]BioKnowledge reviewer library
|
.csv [306]ngly1-graph/neo4j-graphs at master · SuLab/ngly1-graph , Neo4j Browser [307]Neo4j Browser
|
2019
|
Su Lab, Scripps Research Institute [308]The Su Lab - Quantitative methods in biomedical discovery
|
| 55 |
NeDRex
|
[309]NeDRex
|
[310]Network medicine for disease module identification and drug repurposing with the NeDRex platform
|
GitHub [311]NeDRex [312]NeDRexApp [313]nedrexdb
|
REST API [314]NeDRexDB , Neo4j API [315]NeDRexDB - Neo4j , Cytoscape app [316]Cytoscape App Store - NeDRex
|
2021
|
Individuals from various research institutes
|
| 56 |
Neo4COVID-19
|
[317]Neo4COVID-19
|
[318]A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research
|
GitHub [319]neo4covid19
|
Neo4j Browser [320]Neo4j Data Browser
|
2022
|
National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH) [321]National Center for Advancing Translational Sciences
|
| 57 |
OREGANO
|
-
|
[322]Computational Approaches for Drug Repositioning: Towards a Holistic Perspective based on Knowledge Graphs [323]The OREGANO knowledge graph for computational drug repurposing
|
GitLab [324]oregano · GitLab
|
.tsv [325]Data_OREGANO/Graphs · oregano · GitLab [326]The OREGANO knowledge graph for computational drug repurposing [327]The OREGANO knowledge graph for computational drug repurposing , SPARQL endpoint [328]Blazegraph Workbench
|
2023
|
Population Health Research Center, University of Bordeaux [329]AHeaD - Bordeaux population health
|
| 58 |
Open Graph Benchmark: ogbl-biokg
|
[330]Link Property Prediction
|
[331]Open Graph Benchmark: Datasets for Machine Learning on Graphs
|
GitHub [332]ogb , PyPI [333]ogb · PyPI
|
.csv [334]Index of /ogb/data/linkproppred
|
2023
|
Department of Computer Science, Stanford University [335]Computer Science - Stanford University School of Engineering , Individuals from various research institutes
|
| 59 |
OpenBioLink
|
[336]OpenBioLink2021 Challenge
|
[337]OpenBioLink: a benchmarking framework for large-scale biomedical link prediction
|
GitHub [338]OpenBioLink , PyPI [339]openbiolink · PyPI
|
.tsv [340]OpenBioLink2021 Challenge , .tsv / .nt / .bel [341]OpenBioLink2020
|
2020
|
Institute of Artificial Intelligence, Medical University of Vienna [342]Section for Artificial Intelligence and Decision Support, CeMSIIS, MedUni Vienna
|
| 60 |
Otter-Knowledge
|
[343]Otter-Knowledge
|
[344]Otter-Knowledge: benchmarks of multimodal knowledge graph representation learning from different sources for drug discovery
|
GitHub [345]Otter Knowledge
|
.nt [346]ibm/otter_uniprot_bindingdb_chembl · Datasets at Hugging Face [347]ibm/otter_stitch · Datasets at Hugging Face [348]ibm/otter_primekg · Datasets at Hugging Face [349]ibm/otter_dude · Datasets at Hugging Face
|
2023
|
Company: IBM [350]International Business Machines · GitHub
|
| 61 |
PGxLOD
|
[351]PGxLOD
|
[352]Learning from biomedical linked data to suggest valid pharmacogenes [353]PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison
|
GitHub [354]RDF-data-mining [355]pgxlod-reconciliation-rules
|
SPARQL endpoint [356]Virtuoso SPARQL Query Editor , FCT Browser [357]Precision Search & Find
|
2019
|
PractiKPharma project, Loria [358]PractiKPharma Project Homepage , Loria, Joint Research Unit between CNRS, University of Lorraine, INRIA [359]Loria
|
| 62 |
PharMeBINet
|
[360]PharMeBINet
|
[361]The heterogeneous pharmacological medical biochemical network PharMeBINet
|
GitHub [362]PharMeBINet: The heterogeneous pharmacological medical biochemical network
|
.db (Neo4j) / .graphml [363]PharMeBINet: Downloads [364]PharMeBINet
|
2022
|
Bioinformatics / Medical Informatics Department, University Bielefeld [365]Bioinformatics / Medical Informatics Department
|
| 63 |
PharmKG
|
-
|
[366]PharmKG: a dedicated knowledge graph benchmark for bomedical data mining
|
GitHub [367]PharmKG
|
.tsv [368]PharmKG: A Dedicated Knowledge Graph Benchmark for Biomedical Data Mining
|
2020
|
School of Data and Computer Science, Sun Yat-sen University [369]Sun Yat-Sen University: Research Institutes
|
| 64 |
PheKnowLator
|
[370]PheKnowLator
|
[371]A Framework for Automated Construction of Heterogeneous Large-Scale Biomedical Knowledge Graphs [372]An Open-Source Knowledge Graph Ecosystem for the Life Sciences
|
GitHub [373]PheKnowLator , PyPI [374]pkt-kg · PyPI , Zenodo [375]Search PheKnowLator
|
.owl / .nt / .gpickle / .pkl / .tsv / .json [376]Archived Builds [377]PheKnowLator Human Disease Knowledge Graph Benchmarks Archive [378]pheknowlator – Bucket-Details – Cloud Storage – Google Cloud Console
|
2021
|
Computational Bioscience Program, University of Colorado [379]Computational Bioscience Home - School of Medicine , Individuals from various research institutes
|
| 65 |
PrimeKG
|
[380]Precision Medicine Oriented Knowledge Graph
|
[381]Building a knowledge graph to enable precision medicine
|
GitHub [382]PrimeKG
|
.csv / .tab [383]PrimeKG
|
2022
|
Zitnik Lab, Harvard University [384]Artificial Intelligence for Medicine and Science
|
| 66 |
PubChemRDF
|
[385]PubChemRDF
|
[386]PubChemRDF: towards the semantic annotation of PubChem compound and substance databases [387]PubChem 2023 update
|
-
|
.ttl [388]FTP Download [389]Loading PubChemRDF , REST API [390]RESTful Interface
|
2023
|
PubChem, NCBI [391]PubChem
|
| 67 |
PyKEEN
|
[392]PyKEEN
|
[393]The KEEN Universe [394]BioKEEN: a library for learning and evaluating biological knowledge graph embeddings [395]PyKEEN 1.0: a Python library for training and evaluating knowledge graph embeddings
|
GitHub [396]PyKEEN , PyPI [397]pykeen · PyPI
|
.csv [398]Datasets — pykeen 1.10.2-dev documentation [399]pykeen/src/pykeen/datasets at master · pykeen/pykeen · GitHub
|
2023
|
Smart Data Analytics Group, University of Bonn [400]Smart Data Analytics , Individuals from various research institutes
|
| 68 |
RDKG-115
|
-
|
[401]RDKG-115: Assisting drug repurposing and discovery for rare diseases by trimodal knowledge graph embedding
|
GitHub [402]RDKG-115
|
.csv [403]RDKG-115/Model/KG at main · ZhuChaoY/RDKG-115 · GitHub [404]RDKG-115/RDKG-115 at main · ZhuChaoY/RDKG-115 · GitHub
|
2023
|
Intelligent Medicine Institute, Fudan University [405]Intelligent Medicine Institute, Fudan University , Individuals from various research institutes
|
| 69 |
RNA-KG
|
-
|
[406]RNA-KG: An ontology-based knowledge graph for representing interactions involving RNA molecules [407]A Meta-Graph for the Construction of an RNA-Centered Knowledge Graph
|
GitHub [408]RNA-KG
|
.nt / .txt [409]RNA-KG , SPARQL endpoint [410]Blazegraph Workbench
|
2023
|
AnacletoLAB, University of Milan [411]AnacletoLAB - Computational Biology and Bioinformatics , Individuals from various research institutes
|
| 70 |
ROBOKOP
|
[412]ROBOKOP [413]ROBOKOP U24 · GitHub
|
[414]ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering [415]ROBOKOP KG and KGB: Integrated Knowledge Graphs from Federated Sources
|
GitHub [416]robokop
|
.dump (Neo4j) / .json / .jsonl [417]Index of /var/plater/bl-3.5.4/RobokopKG/929354295ba7d43c/ , Neo4j Browser [418]Neo4j Browser , REST API [419]ROBOKOP KG
|
2023
|
Renaissance Computing Institute (RENCI), University of North Carolina [420]RENCI - Renaissance Computing Institute at UNC
|
| 71 |
RPath KGs
|
-
|
[421]Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery
|
GitHub [422]RPath
|
.tsv [423]RPath/data/kg at master · enveda/RPath · GitHub [424]Causal reasoning over knowledge graphs leveraging drug-perturbed and disease-specific transcriptomic signatures for drug discovery
|
2022
|
Company: Enveda Biosciences [425]Enveda Biosciences - Plant-Powered Drug Discovery
|
| 72 |
RTX-KG2
|
-
|
[426]RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine
|
GitHub [427]KG2: the second-generation RTX knowledge graph
|
.json [428]RTX KG2 [429]translator-lfs-artifacts/files at main · ncats/translator-lfs-artifacts
|
2023
|
Development team for the RTX biomedical reasoning tool [430]Development team for the RTX biomedical reasoning tool · GitHub , Individuals from various research institutes
|
| 73 |
Rare diseases integrative KG
|
-
|
[431]An integrative knowledge graph for rare diseases, derived from the Genetic and Rare Diseases Information Center (GARD)
|
GitHub [432]Stitcher
|
Neo4j Browser [433]Neo4j Browser
|
2020
|
Division of Pre-Clinical Innovation, NCATS, NIH [434]Divisions and Offices - National Center for Advancing Translational Sciences
|
| 74 |
Reactome Graph Database
|
[435]Graph Database - Reactome Pathway Database
|
[436]Reactome: a knowledgebase of biological pathways [437]Reactome graph database: Efficient access to complex pathway data
|
GitHub [438]Reactome Graph Database [439]Reactome Graph Database Batch Importer
|
.graphdb (Neo4j) [440]Download - Reactome Pathway Database , REST API [441]Content Service - Reactome Pathway Database
|
2023
|
Reactome Team [442]Team - Reactome Pathway Database , Individuals from various research institutes
|
| 75 |
Rosalind knowledge graph
|
[443]Knowledge Graph & Search
|
[444]Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs
|
-
|
-
|
2020
|
Company: ROSALIND, Inc. [445]Discovery Platform & Data Hub for Scientists - ROSALIND , Company: BenevolentAI [446]BenevolentAI - AI Drug Discovery - AI Pharma
|
| 76 |
SDKG-11
|
-
|
[447]Multimodal reasoning based on knowledge graph embedding for specific diseases
|
GitHub [448]SDKG-11
|
.csv [449]SDKG-11/Dataset at main · ZhuChaoY/SDKG-11 · GitHub
|
2022
|
Institutes of Biomedical Sciences, Fudan University [450]Institute of Biomedical Sciences, Fudan University , Individuals from various research institutes
|
| 77 |
SLKG
|
[451]Synthetic Lethality Knowledge Graph
|
[452]The tumor therapy landscape of synthetic lethality
|
-
|
Web UI [453]Synthetic Lethality Knowledge Graph
|
2021
|
Individuals from various research institutes
|
| 78 |
SPOKE
|
[454]SPOKE [455]Neighborhood Explorer [456]SPOKE Nodes and Edges [457]Spoke
|
[458]The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information
|
GitHub [459]Envisioning SPOKE: Visualizing 3M Nodes and 30M Edges
|
REST API [460]Swagger UI
|
2023
|
SPOKE Team [461]People , Individuals from various research institutes
|
| 79 |
SemKG
|
-
|
[462]SemaTyP: a knowledge graph based literature mining method for drug discovery
|
GitHub [463]SemaTyP: a knowledge graph based literature mining method for drug discovery
|
.txt [464]SemaTyP/data at main · ShengtianSang/SemaTyP · GitHub
|
2021
|
College of Computer Science and Technology, Dalian University of Technology [465]Dalian University of Technology
|
| 80 |
SemNet / SemMedDB
|
[466]SemNet 2.0
|
[467]SemNet: Using Local Features to Navigate the Biomedical Concept Graph [468]Optimizations for Computing Relatedness in Biomedical Heterogeneous Information Networks: SemNet 2.0
|
GitHub [469]SemNet
|
.csv / .sql (MySQL) [470]Access to SemRep/SemMedDB/SKR Resources
|
2022
|
Laboratory for Pathology Dynamics, Emory University [471]Pathology Dynamics
|
| 81 |
StrokeKG
|
-
|
[472]Mining a stroke knowledge graph from literature
|
GitHub [473]Stroke
|
.csv / .txt [474]Stroke , Neo4j browser [475]Neo4j Browser
|
2020
|
College of Computer Science and Technology, National University of Defense Technology [476]Colleges & Institutes - National University of Defense Technology , Individuals from various research institutes
|
| 82 |
SynLethKG / KG4SL
|
[477]SynLethDB
|
[478]KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers [479]SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets
|
GitHub [480]KG4SL [481]SynLethDB
|
.csv / .npy / .txt [482]KG4SL/data at main · JieZheng-ShanghaiTech/KG4SL · GitHub , .csv / .json / .graphml [483]SynLethDB: Download
|
2023
|
Zheng Lab, ShanghaiTech University [484]Jie Zheng Lab at ShanghaiTech
|
| 83 |
TogoGenome
|
[485]TogoGenome
|
[486]TogoGenome/TogoStanza: modularized Semantic Web genome database
|
GitHub [487]togogenome
|
SPARQL endpoint [488]sparql-proxy
|
2019
|
Database Center for Life Science, University of Tokyo [489]DBCLS | Database Center for Life Science
|
| 84 |
TypeDB Bio
|
[490]TypeDB Blog: Accelerating drug discovery with applied knowledge engineering and TypeDB
|
-
|
GitHub [491]TypeDB Bio: Biomedical Knowledge Graph
|
.csv [492]typedb-bio/dataset at master · typedb-osi/typedb-bio · GitHub
|
2023
|
Company: Vaticle Ltd [493]TypeDB: The polymorphic database powered by types
|
| 85 |
Wikidata Biomedical Knowledge Graph
|
-
|
[494]Wikidata as a knowledge graph for the life sciences
|
GitHub [495]genewikiworld [496]WikidataIntegrator [497]scheduled-bots [498]WD-rephetio-analysis [499]Wikidata-phenomizer
|
.json / .ttl / .nt / .xml [500]Wikidata:Database download - Wikidata , SPARQL endpoint [501]Wikidata Query Service
|
2023
|
Su Lab, Scripps Research Institute [502]The Su Lab - Quantitative methods in biomedical discovery
|
