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Removed the no longer open DisGeNET and added a reference for Wikidata
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Marvin Martens&nbsp;<a href="https://orcid.org/0000-0003-2230-0840"><img alt="ORCID icon" src="./images/orcid.png" height="20px">&nbsp;0000-0003-2230-0840</a>,
Egon L. Willighagen&nbsp;<a href="https://orcid.org/0000-0001-7542-0286"><img alt="ORCID icon" src="./images/orcid.png" height="20px">&nbsp;0000-0001-7542-0286</a>**

© 2021-2023 The Authors
© 2021-2024 The Authors

License: CC-BY-SA 4.0 International

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36 changes: 18 additions & 18 deletions docs/list.md
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# List of Databases

Various projects collect <a name="tp1">SPARQL endpoint</a>s, like <a name="tp2">YummyData</a> at [yummydata.org](https://yummydata.org/) [<a href="#citeref1">1</a>].
Various projects collect <a name="tp1">SPARQL endpoint</a>s, like <a name="tp2">YummyData</a> at [yummydata.org](https://yummydata.org/) [<a href="#citeref1">1</a>]
and [RDF Portal](https://rdfportal.org/datasets).
Here is an alphabetically sorted list of graphical interfaces to various SPARQL endpoints:

* AOP-Wiki: [https://aopwiki.rdf.bigcat-bioinformatics.org/](https://aopwiki.rdf.bigcat-bioinformatics.org/) [<a href="#citeref2">2</a>] (see also [this chapter](aopwiki.md))
* Bgee: [https://www.bgee.org/sparql/](https://www.bgee.org/sparql/) [<a href="#citeref3">3</a>]
* Bio2RDF: [https://bio2rdf.org/sparql](https://bio2rdf.org/sparql) [<a href="#citeref4">4</a>]
* Cellosaurus: via Wikidata (see below) [<a href="#citeref3">3</a>]
* ChEMBL: [https://chemblmirror.rdf.bigcat-bioinformatics.org/](https://chemblmirror.rdf.bigcat-bioinformatics.org/) [<a href="#citeref5">5</a>,<a href="#citeref6">6</a>] (see also [this chapter](chembl.md))
* DisGeNET: [http://rdf.disgenet.org/](http://rdf.disgenet.org/) [<a href="#citeref7">7</a>]
* GlyConnect: [https://glyconnect.expasy.org/sparql](https://glyconnect.expasy.org/sparql) [<a href="#citeref3">3</a>]
* HAMAP: [https://hamap.expasy.org/sparql](https://hamap.expasy.org/sparql) [<a href="#citeref8">8</a>]
* LIPID MAPS: [https://lipidmaps.org/sparql](https://lipidmaps.org/sparql) [<a href="#citeref9">9</a>]
* MetaNetX: [https://rdf.metanetx.org/](https://rdf.metanetx.org/) [<a href="#citeref10">10</a>]
* OMA: [https://sparql.omabrowser.org/](https://sparql.omabrowser.org/) [<a href="#citeref8">8</a>]
* OrthoDB: [https://sparql.orthodb.org/](https://sparql.orthodb.org/) [<a href="#citeref8">8</a>]
* neXtProt: [https://aopwiki.rdf.bigcat-bioinformatics.org/](https://aopwiki.rdf.bigcat-bioinformatics.org/) [<a href="#citeref11">11</a>]
* HAMAP: [https://hamap.expasy.org/sparql](https://hamap.expasy.org/sparql) [<a href="#citeref7">7</a>]
* LIPID MAPS: [https://lipidmaps.org/sparql](https://lipidmaps.org/sparql) [<a href="#citeref8">8</a>]
* MetaNetX: [https://rdf.metanetx.org/](https://rdf.metanetx.org/) [<a href="#citeref9">9</a>]
* OMA: [https://sparql.omabrowser.org/](https://sparql.omabrowser.org/) [<a href="#citeref7">7</a>]
* OrthoDB: [https://sparql.orthodb.org/](https://sparql.orthodb.org/) [<a href="#citeref7">7</a>]
* neXtProt: [https://aopwiki.rdf.bigcat-bioinformatics.org/](https://aopwiki.rdf.bigcat-bioinformatics.org/) [<a href="#citeref10">10</a>]
* Rhea: [https://sparql.rhea-db.org/sparql](https://sparql.rhea-db.org/sparql) [<a href="#citeref3">3</a>]
* STRING: [https://sparql.string-db.org/](https://sparql.string-db.org/) [<a href="#citeref8">8</a>]
* SwissLipids: [https://beta.sparql.swisslipids.org/](https://beta.sparql.swisslipids.org/) [<a href="#citeref8">8</a>]
* UniProt: [https://sparql.uniprot.org/](https://sparql.uniprot.org/) [<a href="#citeref12">12</a>]
* Wikidata: [https://query.wikidata.org/](https://query.wikidata.org/) (see also [this chapter](wikidata.md))
* STRING: [https://sparql.string-db.org/](https://sparql.string-db.org/) [<a href="#citeref7">7</a>]
* SwissLipids: [https://beta.sparql.swisslipids.org/](https://beta.sparql.swisslipids.org/) [<a href="#citeref7">7</a>]
* UniProt: [https://sparql.uniprot.org/](https://sparql.uniprot.org/) [<a href="#citeref11">11</a>]
* Wikidata: [https://query.wikidata.org/](https://query.wikidata.org/) [<a href="#citeref12">12</a>] (see also [this chapter](wikidata.md))
* WikiPathways: [https://sparql.wikipathways.org/](https://sparql.wikipathways.org/) [<a href="#citeref13">13</a>,<a href="#citeref14">14</a>] (see also [this chapter](wikipathways.md))

## Other useful resources
Expand All @@ -38,12 +38,12 @@ There are also the following <a name="tp3">ontology</a> SPARQL endpoints:
4. <a name="citeref4"></a>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](https://doi.org/10.1016/J.JBI.2008.03.004) ([Scholia](https://scholia.toolforge.org/doi/10.1016/J.JBI.2008.03.004))
5. <a name="citeref5"></a>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](https://doi.org/10.1093/NAR/GKT1031) ([Scholia](https://scholia.toolforge.org/doi/10.1093/NAR/GKT1031))
6. <a name="citeref6"></a>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](https://doi.org/10.1186/1758-2946-5-23) ([Scholia](https://scholia.toolforge.org/doi/10.1186/1758-2946-5-23))
7. <a name="citeref7"></a>Rosinach NQ, Piñero J, Bravo À, Sanz F, Furlong LI. DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases. Bioinformatics. 2016 Jul 15;32(14):2236–8. doi:[10.1093/BIOINFORMATICS/BTW214](https://doi.org/10.1093/BIOINFORMATICS/BTW214) ([Scholia](https://scholia.toolforge.org/doi/10.1093/BIOINFORMATICS/BTW214))
8. <a name="citeref8"></a>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](https://doi.org/10.1093/NAR/GKAD902) ([Scholia](https://scholia.toolforge.org/doi/10.1093/NAR/GKAD902))
9. <a name="citeref9"></a>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](https://doi.org/10.1093/NAR/GKAD896) ([Scholia](https://scholia.toolforge.org/doi/10.1093/NAR/GKAD896))
10. <a name="citeref10"></a>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](https://doi.org/10.1093/BIOINFORMATICS/BTT036) ([Scholia](https://scholia.toolforge.org/doi/10.1093/BIOINFORMATICS/BTT036))
11. <a name="citeref11"></a>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](https://doi.org/10.1093/NAR/GKZ995) ([Scholia](https://scholia.toolforge.org/doi/10.1093/NAR/GKZ995))
12. <a name="citeref12"></a>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](https://doi.org/10.1093/BIOINFORMATICS/BTZ817) ([Scholia](https://scholia.toolforge.org/doi/10.1093/BIOINFORMATICS/BTZ817))
7. <a name="citeref7"></a>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](https://doi.org/10.1093/NAR/GKAD902) ([Scholia](https://scholia.toolforge.org/doi/10.1093/NAR/GKAD902))
8. <a name="citeref8"></a>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](https://doi.org/10.1093/NAR/GKAD896) ([Scholia](https://scholia.toolforge.org/doi/10.1093/NAR/GKAD896))
9. <a name="citeref9"></a>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](https://doi.org/10.1093/BIOINFORMATICS/BTT036) ([Scholia](https://scholia.toolforge.org/doi/10.1093/BIOINFORMATICS/BTT036))
10. <a name="citeref10"></a>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](https://doi.org/10.1093/NAR/GKZ995) ([Scholia](https://scholia.toolforge.org/doi/10.1093/NAR/GKZ995))
11. <a name="citeref11"></a>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](https://doi.org/10.1093/BIOINFORMATICS/BTZ817) ([Scholia](https://scholia.toolforge.org/doi/10.1093/BIOINFORMATICS/BTZ817))
12. <a name="citeref12"></a>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](https://doi.org/10.1145/3543873.3585579) ([Scholia](https://scholia.toolforge.org/doi/10.1145/3543873.3585579))
13. <a name="citeref13"></a>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](https://doi.org/10.1371/JOURNAL.PCBI.1004989) ([Scholia](https://scholia.toolforge.org/doi/10.1371/JOURNAL.PCBI.1004989))
14. <a name="citeref14"></a>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](https://doi.org/10.12688/F1000RESEARCH.13197.2) ([Scholia](https://scholia.toolforge.org/doi/10.12688/F1000RESEARCH.13197.2))
15. <a name="citeref15"></a>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](https://doi.org/10.1093/NAR/GKW918) ([Scholia](https://scholia.toolforge.org/doi/10.1093/NAR/GKW918))
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Expand Up @@ -9,7 +9,6 @@ Here is an alphabetically sorted list of graphical interfaces to various SPARQL
* Bio2RDF: [https://bio2rdf.org/sparql](https://bio2rdf.org/sparql) [<cite>Q27921271</cite>]
* Cellosaurus: via Wikidata (see below) [<cite>Q57060627</cite>]
* ChEMBL: [https://chemblmirror.rdf.bigcat-bioinformatics.org/](https://chemblmirror.rdf.bigcat-bioinformatics.org/) [<cite>Q27144224</cite>,<cite>Q27062334</cite>] (see also [this chapter](chembl.i.md))
* DisGeNET: [http://rdf.disgenet.org/](http://rdf.disgenet.org/) [<cite>Q28596617</cite>]
* GlyConnect: [https://glyconnect.expasy.org/sparql](https://glyconnect.expasy.org/sparql) [<cite>Q57060627</cite>]
* HAMAP: [https://hamap.expasy.org/sparql](https://hamap.expasy.org/sparql) [<cite>Q123285784</cite>]
* LIPID MAPS: [https://lipidmaps.org/sparql](https://lipidmaps.org/sparql) [<cite>Q123135804</cite>]
Expand All @@ -21,7 +20,7 @@ Here is an alphabetically sorted list of graphical interfaces to various SPARQL
* STRING: [https://sparql.string-db.org/](https://sparql.string-db.org/) [<cite>Q123285784</cite>]
* SwissLipids: [https://beta.sparql.swisslipids.org/](https://beta.sparql.swisslipids.org/) [<cite>Q123285784</cite>]
* UniProt: [https://sparql.uniprot.org/](https://sparql.uniprot.org/) [<cite>Q91121270</cite>]
* Wikidata: [https://query.wikidata.org/](https://query.wikidata.org/) (see also [this chapter](wikidata.i.md))
* Wikidata: [https://query.wikidata.org/](https://query.wikidata.org/) [<cite>Q118130164</cite>] (see also [this chapter](wikidata.i.md))
* WikiPathways: [https://sparql.wikipathways.org/](https://sparql.wikipathways.org/) [<cite>Q26261238</cite>,<cite>Q57337377</cite>] (see also [this chapter](wikipathways.i.md))

## Other useful resources
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