Fix keywords in new models.

sybila · Sep 24, 2024 · 47e1128 · 47e1128
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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
@@ -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
@@ -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"
 }
diff --git a/...s/[id-232]__[var-109]__[in-8]__[BREAST-CANCER-PATHWAYS-MCF7-COMPLETE]/README.md b/...s/[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
@@ -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/..._[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE]/README.md b/..._[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/...-233]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-T47D-COMPLETE]/metadata.json b/...-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/...r-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/README.md b/...r-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/...]__[var-111]__[in-6]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB468-COMPLETE]/metadata.json b/...]__[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/...r-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE]/README.md b/...r-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/...]__[var-110]__[in-7]__[BREAST-CANCER-SIGNALLING-PATHWAYS-MDAMB231-COMPLETE]/metadata.json b/...]__[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"
 }
diff --git a/...[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/README.md b/...[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/...236]__[var-109]__[in-8]__[BREAST-CANCER-SIGNALLING-PATHWAYS-BT549-COMPLETE]/metadata.json b/...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"
 }
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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"]
 }