Licenses in OmniPath databases

Licenses in OmniPath databases#

Most prior knowledge databases make their information accessible to all entities, including academic, commercial, and nonprofit organizations. However, some databases impose usage restrictions.

To simplify this, OmniPath allows filtering of results based on the selected license. By default, the academic license is used, as it grants access to all available entries, though this can be modified using the license parameter.

import decoupler as dc

dc.op.collectri(license="academic")
source target weight resources references sign_decision
0 MYC TERT 1.0 DoRothEA-A;ExTRI;HTRI;NTNU.Curated;Pavlidis202... 10022128;10491298;10606235;10637317;10723141;1... PMID
1 SPI1 BGLAP 1.0 ExTRI 10022617 default activation
2 SMAD3 JUN 1.0 ExTRI;NTNU.Curated;TFactS;TRRUST 10022869;12374795 PMID
3 SMAD4 JUN 1.0 ExTRI;NTNU.Curated;TFactS;TRRUST 10022869;12374795 PMID
4 STAT5A IL2 1.0 ExTRI 10022878;11435608;17182565;17911616;22854263;2... default activation
... ... ... ... ... ... ...
42985 NFKB hsa-miR-143-3p 1.0 ExTRI 19472311 default activation
42986 AP1 hsa-miR-206 1.0 ExTRI;GEREDB;NTNU.Curated 19721712 PMID
42987 NFKB hsa-miR-21 1.0 ExTRI 20813833;22387281 default activation
42988 NFKB hsa-miR-224-5p 1.0 ExTRI 23474441;23988648 default activation
42989 AP1 hsa-miR-144-3p 1.0 ExTRI 23546882 default activation

42990 rows × 6 columns

Changing the license to non-profit or commercial may result in the loss of certain entries.

dc.op.collectri(license="nonprofit")
source target weight resources references sign_decision
0 MYC TERT 1.0 DoRothEA-A;ExTRI;HTRI;NTNU.Curated;Pavlidis202... 10022128;10491298;10606235;10637317;10723141;1... PMID
1 SPI1 BGLAP 1.0 ExTRI 10022617 default activation
2 SMAD3 JUN 1.0 ExTRI;NTNU.Curated;TFactS;TRRUST 10022869;12374795 PMID
3 SMAD4 JUN 1.0 ExTRI;NTNU.Curated;TFactS;TRRUST 10022869;12374795 PMID
4 STAT5A IL2 1.0 ExTRI 10022878;11435608;17182565;17911616;22854263;2... default activation
... ... ... ... ... ... ...
42985 NFKB hsa-miR-143-3p 1.0 ExTRI 19472311 default activation
42986 AP1 hsa-miR-206 1.0 ExTRI;GEREDB;NTNU.Curated 19721712 PMID
42987 NFKB hsa-miR-21 1.0 ExTRI 20813833;22387281 default activation
42988 NFKB hsa-miR-224-5p 1.0 ExTRI 23474441;23988648 default activation
42989 AP1 hsa-miR-144-3p 1.0 ExTRI 23546882 default activation

42990 rows × 6 columns

dc.op.collectri(license="commercial")
source target weight resources references sign_decision
0 MYC TERT 1.0 DoRothEA-A;ExTRI;HTRI;NTNU.Curated;Pavlidis202... 10022128;10491298;10606235;10637317;10723141;1... PMID
1 SPI1 BGLAP 1.0 ExTRI 10022617 default activation
2 SMAD3 JUN 1.0 ExTRI;NTNU.Curated;TFactS;TRRUST 10022869;12374795 PMID
3 SMAD4 JUN 1.0 ExTRI;NTNU.Curated;TFactS;TRRUST 10022869;12374795 PMID
4 STAT5A IL2 1.0 ExTRI 10022878;11435608;17182565;17911616;22854263;2... default activation
... ... ... ... ... ... ...
42985 NFKB hsa-miR-143-3p 1.0 ExTRI 19472311 default activation
42986 AP1 hsa-miR-206 1.0 ExTRI;GEREDB;NTNU.Curated 19721712 PMID
42987 NFKB hsa-miR-21 1.0 ExTRI 20813833;22387281 default activation
42988 NFKB hsa-miR-224-5p 1.0 ExTRI 23474441;23988648 default activation
42989 AP1 hsa-miR-144-3p 1.0 ExTRI 23546882 default activation

42990 rows × 6 columns

For some resources, entries may not be available at all.

dc.op.resource("HPMR", license="commercial")
genesymbol

The removal of entries is required to comply with licensing regulations, and users are expected to be aware of and adhere to these guidelines.