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
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 |
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 |
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 |
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 |