From 47e112845ca3e5f73901340fe3a4882ef813b2d7 Mon Sep 17 00:00:00 2001 From: Samuel Pastva Date: Tue, 24 Sep 2024 10:48:31 +0200 Subject: [PATCH] Fix keywords in new models. --- .../README.md | 4 ++-- .../metadata.json | 8 +++----- .../README.md | 2 +- .../metadata.json | 6 ++---- .../README.md | 2 +- .../metadata.json | 6 ++---- .../README.md | 2 +- .../metadata.json | 6 ++---- .../README.md | 12 +----------- .../metadata.json | 8 +++----- .../README.md | 4 ++-- .../metadata.json | 8 +++----- .../metadata.json | 2 +- .../metadata.json | 2 +- .../metadata.json | 2 +- .../metadata.json | 2 +- .../metadata.json | 2 +- .../metadata.json | 2 +- 18 files changed, 29 insertions(+), 51 deletions(-) diff --git a/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/README.md b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/README.md index 354d8b4..fc56552 100644 --- a/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/README.md +++ b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/README.md @@ -5,12 +5,12 @@ - Regulations: 268 - Publication: https://doi.org/10.1371/journal.pone.0298788 - Source: https://github.com/Ktaoma/BoolSyn - - Keywords: source (?), curated (?), repaired (?), multi-valued (?) + - Keywords: curated, repaired ### Modifications -Rows deleted from the model: +Rows deleted from the source file: DLL_i, DLL_i IGF1, IGF1 diff --git a/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/metadata.json b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/metadata.json index c2f0b0a..9ac837f 100644 --- a/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/metadata.json +++ b/models/[id-231]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS]/metadata.json @@ -4,14 +4,12 @@ "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", "keywords": [ - "source (?)", - "curated (?)", - "repaired (?)", - "multi-valued (?)" + "curated", + "repaired" ], "variables": 110, "inputs": 7, "regulations": 268, - "notes": "### Modifications\n\nRows deleted from the model:\n\nDLL_i, DLL_i\nIGF1, IGF1\nNRG1, NRG1\nPG, PG\nES, ES\nEGF, EGF\nINS, INS\n", + "notes": "### Modifications\n\nRows deleted from the source file:\n\nDLL_i, DLL_i\nIGF1, IGF1\nNRG1, NRG1\nPG, PG\nES, ES\nEGF, EGF\nINS, INS\n", "bib": "@article{bbm-231,\n\tauthor = {Taoma, Kittisak and Ruengjitchatchawalya, Marasri and Liangruksa, Monrudee and Laomettachit, Teeraphan},\n\tyear = {2024},\n\tdoi = {https://doi.org/10.1371/journal.pone.0298788},\n\ttitle = {Boolean modeling of breast cancer signaling pathways uncovers mechanisms of drug synergy},\n\tpublisher = {PLOS ONE}\n}\n\n" } \ No newline at end of file diff --git a/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/README.md b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/README.md index f3200aa..c3d8833 100644 --- a/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/README.md +++ b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/README.md @@ -5,7 +5,7 @@ - Regulations: 275 - Publication: https://doi.org/10.1371/journal.pone.0298788 - Source: https://github.com/Ktaoma/BoolSyn - - Keywords: source (?), curated (?), repaired (?), multi-valued (?) + - Keywords: curated, repaired ### Modifications diff --git a/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/metadata.json b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/metadata.json index dfd8fb5..80afb1b 100644 --- a/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/metadata.json +++ b/models/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/metadata.json @@ -4,10 +4,8 @@ "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", "keywords": [ - "source (?)", - "curated (?)", - "repaired (?)", - "multi-valued (?)" + "curated", + "repaired" ], "variables": 109, "inputs": 8, diff --git a/models/[id-233]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE]/README.md b/models/[id-233]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE]/README.md index e00efe3..ca8b3a0 100644 --- a/models/[id-233]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE]/README.md +++ b/models/[id-233]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE]/README.md @@ -5,7 +5,7 @@ - Regulations: 260 - Publication: https://doi.org/10.1371/journal.pone.0298788 - Source: https://github.com/Ktaoma/BoolSyn - - Keywords: source (?), curated (?), repaired (?), multi-valued (?) + - Keywords: curated, repaired ### Modifications diff --git a/models/[id-233]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE]/metadata.json b/models/[id-233]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE]/metadata.json index d50915c..4f7a34a 100644 --- a/models/[id-233]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE]/metadata.json +++ b/models/[id-233]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE]/metadata.json @@ -4,10 +4,8 @@ "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", "keywords": [ - "source (?)", - "curated (?)", - "repaired (?)", - "multi-valued (?)" + "curated", + "repaired" ], "variables": 109, "inputs": 8, diff --git a/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/README.md b/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/README.md index c4beb2f..55e49bd 100644 --- a/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/README.md +++ b/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/README.md @@ -5,7 +5,7 @@ - Regulations: 271 - Publication: https://doi.org/10.1371/journal.pone.0298788 - Source: https://github.com/Ktaoma/BoolSyn - - Keywords: source (?), curated (?), repaired (?), multi-valued (?) + - Keywords: curated, repaired ### Modifications diff --git a/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/metadata.json b/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/metadata.json index 619ec1a..2f9b718 100644 --- a/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/metadata.json +++ b/models/[id-234]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/metadata.json @@ -4,10 +4,8 @@ "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", "keywords": [ - "source (?)", - "curated (?)", - "repaired (?)", - "multi-valued (?)" + "curated", + "repaired" ], "variables": 111, "inputs": 6, diff --git a/models/[id-235]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE]/README.md b/models/[id-235]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE]/README.md index df179f7..b084cb7 100644 --- a/models/[id-235]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE]/README.md +++ b/models/[id-235]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE]/README.md @@ -5,7 +5,7 @@ - Regulations: 270 - Publication: https://doi.org/10.1371/journal.pone.0298788 - Source: https://github.com/Ktaoma/BoolSyn - - Keywords: source (?), curated (?), repaired (?), multi-valued (?) + - Keywords: curated, repaired ### Modifications @@ -19,16 +19,6 @@ EGF, EGF DLL_i, DLL_i IGF1, IGF1 -Regulation: - -CYCLIN_D_c, (((TEAD1 | TCF4 | STAT3) & !(GSK3B & (CDKN2A & P21)))) & (EIF4E & MYC & STAT3) - -was updated to: - -CYCLIN_D_c, (((STAT3) & !(GSK3B & (CDKN2A & P21)))) & (EIF4E & MYC & STAT3) - -as the analysis stated that TEAD1 and TCF4 have no effect on CYCLIN_D_c. - ### Model citation diff --git a/models/[id-235]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE]/metadata.json b/models/[id-235]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE]/metadata.json index b11bf95..eb6a70e 100644 --- a/models/[id-235]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE]/metadata.json +++ b/models/[id-235]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE]/metadata.json @@ -4,14 +4,12 @@ "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", "keywords": [ - "source (?)", - "curated (?)", - "repaired (?)", - "multi-valued (?)" + "curated", + "repaired" ], "variables": 110, "inputs": 7, "regulations": 270, - "notes": "### Modifications\n\nRemoved regulations:\nPG, PG\nNRG1, NRG1\nINS, INS\nES, ES\nEGF, EGF\nDLL_i, DLL_i\nIGF1, IGF1\n\nRegulation:\n\nCYCLIN_D_c, (((TEAD1 | TCF4 | STAT3) & !(GSK3B & (CDKN2A & P21)))) & (EIF4E & MYC & STAT3)\n\nwas updated to:\n\nCYCLIN_D_c, (((STAT3) & !(GSK3B & (CDKN2A & P21)))) & (EIF4E & MYC & STAT3)\n\nas the analysis stated that TEAD1 and TCF4 have no effect on CYCLIN_D_c.\n", + "notes": "### Modifications\n\nRemoved regulations:\nPG, PG\nNRG1, NRG1\nINS, INS\nES, ES\nEGF, EGF\nDLL_i, DLL_i\nIGF1, IGF1\n", "bib": "@article{bbm-235,\n\tauthor = {Taoma, Kittisak and Ruengjitchatchawalya, Marasri and Liangruksa, Monrudee and Laomettachit, Teeraphan},\n\tyear = {2024},\n\tdoi = {https://doi.org/10.1371/journal.pone.0298788},\n\ttitle = {Boolean modeling of breast cancer signaling pathways uncovers mechanisms of drug synergy},\n\tpublisher = {PLOS ONE}\n}\n\n" } \ No newline at end of file diff --git a/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/README.md b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/README.md index a654dc2..7e23d3a 100644 --- a/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/README.md +++ b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/README.md @@ -5,13 +5,13 @@ - Regulations: 263 - Publication: https://doi.org/10.1371/journal.pone.0298788 - Source: https://github.com/Ktaoma/BoolSyn - - Keywords: source (?), curated (?), repaired (?), multi-valued (?) + - Keywords: curated, repaired ### Modifications Removed regulations: -INS +INS, INS PG, PG NRG1, NRG1 FASLG, FASLG diff --git a/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/metadata.json b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/metadata.json index b5b5886..a42d083 100644 --- a/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/metadata.json +++ b/models/[id-236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/metadata.json @@ -4,14 +4,12 @@ "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", "keywords": [ - "source (?)", - "curated (?)", - "repaired (?)", - "multi-valued (?)" + "curated", + "repaired" ], "variables": 109, "inputs": 8, "regulations": 263, - "notes": "### Modifications\n\nRemoved regulations:\nINS\nPG, PG\nNRG1, NRG1\nFASLG, FASLG\nES, ES\nEGF, EGF\nDLL_i, DLL_i\nIGF1, IGF1\n", + "notes": "### Modifications\n\nRemoved regulations:\nINS, INS\nPG, PG\nNRG1, NRG1\nFASLG, FASLG\nES, ES\nEGF, EGF\nDLL_i, DLL_i\nIGF1, IGF1\n", "bib": "@article{bbm-236,\n\tauthor = {Taoma, Kittisak and Ruengjitchatchawalya, Marasri and Liangruksa, Monrudee and Laomettachit, Teeraphan},\n\tyear = {2024},\n\tdoi = {https://doi.org/10.1371/journal.pone.0298788},\n\ttitle = {Boolean modeling of breast cancer signaling pathways uncovers mechanisms of drug synergy},\n\tpublisher = {PLOS ONE}\n}\n\n" } \ No newline at end of file diff --git a/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/metadata.json b/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/metadata.json index 64f4414..c9fc1d0 100644 --- a/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/metadata.json +++ b/sources/231_BREAST-CANCER-SIGNALLING-PATHWAYS/metadata.json @@ -3,5 +3,5 @@ "name": "BREAST-CANCER-SIGNALLING-PATHWAYS", "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", - "keywords": ["source (?)","curated (?)","repaired (?)", "multi-valued (?)"] + "keywords": ["curated","repaired"] } diff --git a/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/metadata.json b/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/metadata.json index 73a1729..fa1027c 100644 --- a/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/metadata.json +++ b/sources/232_BREAST-CANCER-PATHWAYS-MCF7-COMPLETE/metadata.json @@ -3,5 +3,5 @@ "name": "BREAST-CANCER-PATHWAYS-MCF7-COMPLETE", "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", - "keywords": ["source (?)","curated (?)","repaired (?)", "multi-valued (?)"] + "keywords": ["curated","repaired"] } diff --git a/sources/233_BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE/metadata.json b/sources/233_BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE/metadata.json index 04aab91..04ef18b 100644 --- a/sources/233_BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE/metadata.json +++ b/sources/233_BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE/metadata.json @@ -3,5 +3,5 @@ "name": "BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE", "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", - "keywords": ["source (?)","curated (?)","repaired (?)", "multi-valued (?)"] + "keywords": ["curated","repaired"] } diff --git a/sources/234_BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE/metadata.json b/sources/234_BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE/metadata.json index 8815b9f..5611eb8 100644 --- a/sources/234_BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE/metadata.json +++ b/sources/234_BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE/metadata.json @@ -3,5 +3,5 @@ "name": "BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE", "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", - "keywords": ["source (?)","curated (?)","repaired (?)", "multi-valued (?)"] + "keywords": ["curated","repaired"] } diff --git a/sources/235_BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE/metadata.json b/sources/235_BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE/metadata.json index cc42f7d..e1fbef4 100644 --- a/sources/235_BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE/metadata.json +++ b/sources/235_BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE/metadata.json @@ -3,5 +3,5 @@ "name": "BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE", "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", - "keywords": ["source (?)","curated (?)","repaired (?)", "multi-valued (?)"] + "keywords": ["curated","repaired"] } diff --git a/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/metadata.json b/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/metadata.json index d18c9c3..956882c 100644 --- a/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/metadata.json +++ b/sources/236_BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE/metadata.json @@ -3,5 +3,5 @@ "name": "BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE", "url-publication": "https://doi.org/10.1371/journal.pone.0298788", "url-model": "https://github.com/Ktaoma/BoolSyn", - "keywords": ["source (?)","curated (?)","repaired (?)", "multi-valued (?)"] + "keywords": ["curated","repaired"] }