PRA3006-SPARQL

List of Databases

Various projects collect SPARQL endpoints, like YummyData at yummydata.org [1] and RDF Portal. Here is an alphabetically sorted list of graphical interfaces to various SPARQL endpoints:

• AOP-Wiki: https://aopwiki.rdf.bigcat-bioinformatics.org/ [2] (see also this chapter)
• Bgee: https://www.bgee.org/sparql/ [3]
• Bio2RDF: https://bio2rdf.org/sparql [4]
• Cellosaurus: via Wikidata (see below) [3]
• ChEMBL: https://chemblmirror.rdf.bigcat-bioinformatics.org/ [5,6] (see also this chapter)
• GlyConnect: https://glyconnect.expasy.org/sparql [3]
• HAMAP: https://hamap.expasy.org/sparql [7]
• LIPID MAPS: https://lipidmaps.org/sparql [8]
• MetaNetX: https://rdf.metanetx.org/ [9]
• OMA: https://sparql.omabrowser.org/ [7]
• OrthoDB: https://sparql.orthodb.org/ [7]
• neXtProt: https://aopwiki.rdf.bigcat-bioinformatics.org/ [10]
• Rhea: https://sparql.rhea-db.org/sparql [3]
• STRING: https://sparql.string-db.org/ [7]
• SwissLipids: https://beta.sparql.swisslipids.org/ [7]
• UniProt: https://sparql.uniprot.org/ [11] (see also this chapter)
• Wikidata: https://query.wikidata.org/ [12] (see also this chapter)
• WikiPathways: https://sparql.wikipathways.org/ [13,14] (see also this chapter)

Other useful resources

There are also the following ontology SPARQL endpoints:

• Ontobee: https://ontobee.org/sparql [15]
• Ubergraph: https://github.com/INCATools/ubergraph [16]

References

1. Yamamoto Y, Yamaguchi A, Splendiani A. YummyData: providing high-quality open life science data. Database. 2018 Jan 1;2018. doi:10.1093/DATABASE/BAY022 (Scholia)
2. Martens M, Evelo CT, Willighagen EL. Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. Applied In Vitro Toxicology. 2022 Feb 25; doi:10.1089/AIVT.2021.0010 (Scholia)
3. Lombardot T, Morgat A, Axelsen KB, Aimo L, Hyka-Nouspikel N, Niknejad A, et al. Updates in Rhea: SPARQLing biochemical reaction data. NAR. 2019 Jan 1;47(D1):D596–600. doi:10.1093/NAR/GKY876 (Scholia)
4. Belleau F, Nolin M-A, Tourigny N, Rigault P, Morissette J. Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. J Biomed Inform. 2008 Oct;41(5):706–16. doi:10.1016/J.JBI.2008.03.004 (Scholia)
5. Bento AP, Gaulton A, Hersey A, Bellis L, Chambers J, Davies M, et al. The ChEMBL bioactivity database: an update. NAR. 2014 Jan;42(Database issue):D1083-90. doi:10.1093/NAR/GKT1031 (Scholia)
6. Willighagen E, Waagmeester A, Spjuth O, Ansell P, Williams AJ, Tkachenko V, et al. The ChEMBL database as linked open data. J Cheminform. 2013;5(1):23. doi:10.1186/1758-2946-5-23 (Scholia)
7. Altenhoff A, Bairoch A, Bansal P, Baratin D, Bastian F, Bolleman* J, et al. The SIB Swiss Institute of Bioinformatics Semantic Web of data. NAR. 2023 Oct 25; doi:10.1093/NAR/GKAD902 (Scholia)
8. Conroy MJ, Andrews RM, Andrews S, Cockayne L, Dennis EA, Fahy E, et al. LIPID MAPS: update to databases and tools for the lipidomics community. NAR. 2023 Oct 19; doi:10.1093/NAR/GKAD896 (Scholia)
9. Ganter M, Bernard T, Moretti S, Stelling J, Pagni M. MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. Bioinformatics. 2013 Jan 28;29(6):815–6. doi:10.1093/BIOINFORMATICS/BTT036 (Scholia)
10. Zahn-Zabal M, Michel P-A, Gateau A, Nikitin F, Schaeffer M, Audot E, et al. The neXtProt knowledgebase in 2020: data, tools and usability improvements. NAR. 2020 Jan 1;48(D1):D328–34. doi:10.1093/NAR/GKZ995 (Scholia)
11. Morgat A, Lombardot T, Coudert E, Axelsen K, Neto TB, Gehant S, et al. Enzyme annotation in UniProtKB using Rhea. Bioinformatics. 2020 Mar 1;36(6):1896–901. doi:10.1093/BIOINFORMATICS/BTZ817 (Scholia)
12. Vrandečić D, Pintscher L, Krötzsch M. Wikidata: The Making Of. WWW ’23 Companion: Companion Proceedings of the ACM Web Conference 2023 [Internet]. 2023 Apr 30; Available from: https://dl.acm.org/doi/10.1145/3543873.3585579 doi:10.1145/3543873.3585579 (Scholia)
13. Waagmeester A, Summer-Kutmon M, Riutta A, Miller R, Willighagen E, Evelo CT, et al. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PLoS Comput Biol. 2016 Jun;12(6):e1004989. doi:10.1371/JOURNAL.PCBI.1004989 (Scholia)
14. Miller RA, Woollard P, Willighagen EL, Digles D, Kutmon M, Loizou A, et al. Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform. F1000Research. 2018 Oct 12;7:75. doi:10.12688/F1000RESEARCH.13197.2 (Scholia)
15. Ong E, Xiang Z, Zhao B, Liu Y, Lin Y, Zheng J, et al. Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration. NAR. 2016 Oct 12;45(D1):gkw918. doi:10.1093/NAR/GKW918 (Scholia)
16. Balhoff JP, Bayindir U, Caron AR, Matentzoglu N, Osumi-Sutherland D, Mungall CJ. Ubergraph: integrating OBO ontologies into a unified semantic graph. zenodo. Geneva, Confoederatio Helvetica: zenodo; 2022. doi:10.5281/ZENODO.7249759 (Scholia)

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