Licenses in OmniPath databases
Most prior knowledge databases make their information available to all entities, whether academic, commercial, or nonprofit. However, some databases impose usage restrictions. To simplify this, OmniPath allows you to filter results based on the specified license. By default, the academic license is used, as it provides access to all available entries, but it can be changed with the license parameter.
[1]:
import decoupler as dc
dc.get_collectri(license='academic')
[1]:
| source | target | weight | pmid | |
|---|---|---|---|---|
| 0 | MYC | TERT | 1 | 10022128;10491298;10606235;10637317;10723141;1... |
| 1 | SPI1 | BGLAP | 1 | 10022617 |
| 2 | AP1 | JUN | 1 | 10022869;10037172;10208431;10366004;11281649;1... |
| 3 | AP1 | JUN | 1 | 10022869;10037172;10208431;10366004;11281649;1... |
| 4 | AP1 | JUN | 1 | 10022869;10037172;10208431;10366004;11281649;1... |
| ... | ... | ... | ... | ... |
| 64490 | RUNX1 | LCP2 | 1 | <NA> |
| 64491 | RUNX1 | PRR5L | 1 | <NA> |
| 64492 | TWIST1 | GLI1 | 1 | <NA> |
| 64493 | USF1 | NUP188 | 1 | 22951020 |
| 64494 | ZNF148 | RNLS | 1 | 25295465 |
64495 rows × 4 columns
If we change it to non-profit or commercial we lose some entries:
[2]:
dc.get_collectri(license='nonprofit')
[2]:
| source | target | weight | pmid | |
|---|---|---|---|---|
| 0 | MYC | TERT | 1 | 10022128;10491298;10606235;10637317;10723141;1... |
| 1 | SPI1 | BGLAP | 1 | 10022617 |
| 2 | AP1 | JUN | 1 | 10022869;10037172;10208431;10366004;11281649;1... |
| 3 | AP1 | JUN | 1 | 10022869;10037172;10208431;10366004;11281649;1... |
| 4 | AP1 | JUN | 1 | 10022869;10037172;10208431;10366004;11281649;1... |
| ... | ... | ... | ... | ... |
| 61572 | RUNX1 | LCP2 | 1 | <NA> |
| 61573 | RUNX1 | PRR5L | 1 | <NA> |
| 61574 | TWIST1 | GLI1 | 1 | <NA> |
| 61575 | USF1 | NUP188 | 1 | 22951020 |
| 61576 | ZNF148 | RNLS | 1 | 25295465 |
61577 rows × 4 columns
[3]:
dc.get_collectri(license='commercial')
[3]:
| source | target | weight | pmid | |
|---|---|---|---|---|
| 0 | MYC | TERT | 1 | 10022128;10491298;10606235;10637317;10723141;1... |
| 1 | SPI1 | BGLAP | 1 | 10022617 |
| 2 | AP1 | JUN | 1 | 10022869;10037172;10208431;10366004;11281649;1... |
| 3 | AP1 | JUN | 1 | 10022869;10037172;10208431;10366004;11281649;1... |
| 4 | AP1 | JUN | 1 | 10022869;10037172;10208431;10366004;11281649;1... |
| ... | ... | ... | ... | ... |
| 61572 | RUNX1 | LCP2 | 1 | <NA> |
| 61573 | RUNX1 | PRR5L | 1 | <NA> |
| 61574 | TWIST1 | GLI1 | 1 | <NA> |
| 61575 | USF1 | NUP188 | 1 | 22951020 |
| 61576 | ZNF148 | RNLS | 1 | 25295465 |
61577 rows × 4 columns
For some resources, entries may not be available at all:
[4]:
dc.get_resource('HPMR', license='commercial')
[4]:
| genesymbol | |
|---|---|
This removal is necessary to comply with licensing regulations, and we expect users to be aware of and adhere to them