WikiPathways linksets

WikiPathways: connecting communities.
Martens M, Ammar A, Riutta A, Waagmeester A, Slenter DN, Hanspers K, Miller RA, Digles D, Lopes EN, Ehrhart F, Dupuis LJ, Winckers LA, Coort SL, Willighagen EL, Evelo CT, Pico AR, Kutmon M.
Nucleic Acids Res. 2021 Jan 8;49(D1):D613-D621.
doi: 10.1093/nar/gkaa1024

WikiPathways website: www.wikipathways.org
WikiPathways license: license

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WikiPathways release 2024-04-10

The database content was retrieved through the WikiPathways SPARQL endpoint using the relevant SPARQL query. The Linkset can be downloaded from Figshare.

Linkset	Species	Interactions	Pathways	Genes	Supported gene identifiers
wikipathways_hsa_20240410.xgmml	Homo sapiens (hsa) - curated collection	39,804	1032	10,386	Ensembl, NCBI Gene, HGNC

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WikiPathways release 2022-05-10

The database content was retrieved through the WikiPathways SPARQL endpoint using the relevant queries. Both linksets can be downloaded from Figshare.

Linkset	Species	Interactions	Pathways	Genes	Supported gene identifiers
wikipathways-20220511-hsa-WP.xgmml	Homo sapiens (hsa) - curated collection	31,871	751	8,254	Ensembl, NCBI Gene, HGNC
wikipathways-20220511-hsa-REACTOME.xgmml	Homo sapiens (hsa) - Reactome collection	37,300	511	10,311	Ensembl, NCBI Gene, HGNC

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WikiPathways release 2021-01-10

The database content was retrieved through the WikiPathways SPARQL endpoint using the relevant queries.

Linkset	Species	Interactions	Pathways	Genes	Supported gene identifiers
wikipathways-hsa-curated-20210110.xgmml	Homo sapiens (hsa) - curated collection	29,706	882	8,724	Ensembl, NCBI Gene, HGNC
wikipathways-hsa-Reactome-20210110.xgmml	Homo sapiens (hsa) - Reactome collection	37,760	523	10,366	Ensembl, NCBI Gene, HGNC

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WikiPathways release 2019-06-10

The database content was retrieved from here. Don’t forget to first unzip all linkset files that you want to use and put them in the same folder.

Linkset	Species	Interactions	Pathways	Genes	Supported gene identifiers
wikipathways-hsa-20190610.zip	Homo sapiens (hsa)	22,622	526	6,599	Ensembl, NCBI Gene, HGNC

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WikiPathways release 2018-05-10

The database content was retrieved from here. Don’t forget to first unzip all linkset files that you want to use and put them in the same folder.

Linkset	Species	Interactions	Pathways	Genes	Supported gene identifiers
wikipathways-hsa-20180510.zip	Homo sapiens (hsa)	18,716	431	5,942	Ensembl, NCBI Gene, HGNC
wikipathways-mmu-20180510.zip	Mus musculus (mmu)	9,343	173	4,519	Ensembl, NCBI Gene, HGNC
wikipathways-rno-20180510.zip	Rattus norvegicus (rno)	6,601	152	3,259	Ensembl, NCBI Gene, HGNC