RuleWorld · akutuva21 · May 11, 2026 · May 11, 2026 · May 11, 2026 · May 16, 2026
diff --git a/Published/An2009/metadata.yaml b/Published/An2009/metadata.yaml
@@ -1,7 +1,7 @@
-id: "An_2009"
-name: "An 2009"
+id: An_TLR4_2009
+name: "An et al. 2009: TLR4 Signaling Model"
 description: "TLR4 signaling"
-tags: ["published", "immunology", "an", "2009", "cd14", "md2", "tlr4", "tram", "trif", "sarm", "traf4", "irak1"]
+tags: ["tlr4", "immune-signaling", "innate-immunity", "2009", "an"]
 category: "immunology"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Barua2007/metadata.yaml b/Published/Barua2007/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Barua_2007"
-name: "Barua 2007"
+id: Barua_EGFR_2007
+name: "Barua et al. 2007: EGFR Signaling Model"
 description: "Model from Haugh (2006)"
-tags: ["published", "barua", "2007", "version", "r", "s"]
+tags: ["egfr", "signaling", "2007", "barua"]
 category: "signaling"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Barua2009/metadata.yaml b/Published/Barua2009/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Barua_2009"
-name: "Barua 2009"
+id: Barua_JAK2_2009
+name: "Barua et al. 2009: JAK2-STAT5 Signaling Model"
 description: "JAK2-SH2B signaling"
-tags: ["published", "barua", "2009", "s", "j"]
+tags: ["jak2", "stat5", "signaling", "2009", "barua"]
 category: "signaling"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Barua2013/metadata.yaml b/Published/Barua2013/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Barua_2013"
-name: "Barua 2013"
+id: Barua_bcat_2013
+name: "Barua et al. 2013: Beta-Catenin Regulation Model"
 description: "Beta-catenin destruction"
-tags: ["published", "barua", "2013", "axin", "gsk3b", "apc", "bcat", "ck1a"]
+tags: ["beta-catenin", "regulation", "wnt-signaling", "2013", "barua"]
 category: "regulation"
 compatibility:
   bng2_compatible: false

diff --git a/Published/BaruaBCR2012/metadata.yaml b/Published/BaruaBCR2012/metadata.yaml
@@ -1,7 +1,7 @@
-id: "BaruaBCR_2012"
-name: "Barua 2012"
+id: Barua_BCR_2012
+name: "Barua et al. 2012: BCR Signaling Model"
 description: "BCR signaling"
-tags: ["published", "immunology", "baruabcr", "2012", "bcr", "lyn", "fyn", "csk", "pag", "syk"]
+tags: ["bcr", "immune-signaling", "b-cell", "2012", "barua"]
 category: "immunology"
 compatibility:
   bng2_compatible: true

diff --git a/Published/BaruaFceRI2012/metadata.yaml b/Published/BaruaFceRI2012/metadata.yaml
@@ -1,7 +1,7 @@
-id: "BaruaFceRI_2012"
-name: "BaruaFceRI 2012"
+id: Barua_FceRI_2012
+name: "Barua et al. 2012: FceRI Signaling Model"
 description: "FcÃƒÅ½Ã‚ÂµRI signaling"
-tags: ["published", "immunology", "baruafceri", "2012", "r_o", "rdimer_o", "l_o", "t_o", "l", "fcr", "lyn", "syk"]
+tags: ["fceri", "immune-signaling", "mast-cell", "2012", "barua"]
 category: "immunology"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Blinov2006/metadata.yaml b/Published/Blinov2006/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Blinov_2006"
-name: "Blinov 2006"
+id: Blinov_egfr_2006
+name: "Blinov et al. 2006: EGFR Signaling Pathway (ODE)"
 description: "Phosphotyrosine signaling"
-tags: ["published", "blinov", "2006", "egf", "egfr", "shc", "grb2", "sos"]
+tags: ["egfr", "signaling", "ode", "receptor-activation", "2006", "blinov"]
 category: "signaling"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Blinovegfr/metadata.yaml b/Published/Blinovegfr/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Blinov_egfr"
-name: "Blinov egfr"
+id: Blinov_egfr_NF_2006
+name: "Blinov et al. 2006: EGFR Signaling Pathway (NFsim)"
 description: "EGFR signaling model"
-tags: ["published", "nfsim", "blinov", "egfr", "egf", "grb2", "shc", "simulate_nf"]
+tags: ["egfr", "signaling", "nfsim", "receptor-activation", "2006", "blinov"]
 category: "signaling"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Blinovran/metadata.yaml b/Published/Blinovran/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Blinov_ran"
-name: "Blinov ran"
+id: Blinov_ran_2006
+name: "Blinov et al. 2006: Ran-Mediated Nuclear Transport (NFsim)"
 description: "Ran GTPase cycle"
-tags: ["published", "nfsim", "blinov", "ran", "c", "rcc1", "simulate_nf"]
+tags: ["ran-gtpase", "nuclear-transport", "nfsim", "2006", "blinov"]
 category: "regulation"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Chattaraj2021/metadata.yaml b/Published/Chattaraj2021/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Chattaraj_2021"
-name: "Chattaraj 2021"
+id: Chattaraj_nephrin_2021
+name: "Chattaraj et al. 2021: Nephrin-Nck-NWASP Clustering Model"
 description: "NFkB oscillations"
-tags: ["published", "chattaraj", "2021", "nephrin", "nck", "nwasp", "writexml"]
+tags: ["nephrin", "nck", "nwasp", "clustering", "2021", "chattaraj"]
 category: "signaling"
 compatibility:
   bng2_compatible: false

diff --git a/Published/CheemalavaguJAKSTAT/metadata.yaml b/Published/CheemalavaguJAKSTAT/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Cheemalavagu_JAK_STAT"
-name: "Cheemalavagu 2024"
+id: Cheemalavagu_JAKSTAT_2024
+name: "Cheemalavagu et al. 2024: JAK-STAT Signaling Model"
 description: "JAK-STAT signaling"
-tags: ["published", "literature", "signaling", "cheemalavagu", "jak", "stat", "l1", "il6r", "gp130", "l2", "il10r1", "il10r2", "jak1", "jak2"]
+tags: ["jak-stat", "signaling", "2024", "cheemalavagu"]
 category: "other"
 compatibility:
   bng2_compatible: true

diff --git a/Published/ChylekFceRI2014/metadata.yaml b/Published/ChylekFceRI2014/metadata.yaml
@@ -1,7 +1,7 @@
-id: "ChylekFceRI_2014"
-name: "Chylek 2014 (FceRI)"
+id: Chylek_FceRI_2014
+name: "Chylek et al. 2014: FceRI Signaling Model"
 description: "FceRI signaling"
-tags: ["published", "immunology", "chylekfceri", "2014", "lig", "rec", "lyn", "fyn", "syk", "pag1", "csk", "lat"]
+tags: ["fceri", "immune-signaling", "mast-cell", "2014", "chylek"]
 category: "immunology"
 compatibility:
   bng2_compatible: false

diff --git a/Published/ChylekTCR2014/metadata.yaml b/Published/ChylekTCR2014/metadata.yaml
@@ -1,7 +1,7 @@
-id: "ChylekTCR_2014"
-name: "Chylek 2014 (TCR)"
+id: Chylek_TCR_2014
+name: "Chylek et al. 2014: T Cell Receptor (TCR) Signaling Model"
 description: "TCR signaling"
-tags: ["published", "immunology", "chylektcr", "2014", "lig1", "lig2", "lig3", "tcr", "cd28", "lck", "itk", "zap70"]
+tags: ["tcr", "immune-signaling", "t-cell", "2014", "chylek"]
 category: "immunology"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Dembo1978/metadata.yaml b/Published/Dembo1978/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Dembo_1978"
-name: "Dembo 1978"
+id: Dembo_blbr_1978
+name: "Dembo et al. 1978: Bivalent Ligand Bivalent Receptor (BLBR) Model"
 description: "BLBR dembo 1978"
-tags: ["published", "physics", "dembo", "1978"]
+tags: ["blbr", "ligand-receptor", "binding", "1978", "dembo"]
 category: "physics"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Dolan2015/metadata.yaml b/Published/Dolan2015/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Dolan_2015"
-name: "Dolan 2015"
+id: Dolan_Insulin_2015
+name: "Dolan et al. 2015: Insulin Receptor Signaling Model"
 description: "Insulin signaling"
-tags: ["published", "literature", "signaling", "dolan", "2015", "time", "t", "p", "e", "ir", "d", "p53_mrna", "p53"]
+tags: ["insulin", "metabolism", "2015", "dolan"]
 category: "other"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Dreisigmeyer2008/metadata.yaml b/Published/Dreisigmeyer2008/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Dreisigmeyer_2008"
-name: "Dreisigmeyer 2008"
+id: Dreisigmeyer_LacOperon_2008
+name: "Dreisigmeyer et al. 2008: Lac Operon Regulation Model"
 description: "Lac operon"
-tags: ["published", "gene-expression", "dreisigmeyer", "2008"]
+tags: ["lac-operon", "gene-expression", "bacterial-regulation", "2008", "dreisigmeyer"]
 category: "gene-expression"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Dushek2011/metadata.yaml b/Published/Dushek2011/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Dushek_2011"
-name: "Dushek 2011"
+id: Dushek_TCR_2011
+name: "Dushek et al. 2011: T Cell Receptor Kinase Kinase Cascade"
 description: "TCR signaling"
-tags: ["published", "dushek", "2011", "s"]
+tags: ["tcr", "phosphorylation", "immune-signaling", "2011", "dushek"]
 category: "signaling"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Dushek2014/metadata.yaml b/Published/Dushek2014/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Dushek_2014"
-name: "Dushek 2014"
+id: Dushek_TCR_2014
+name: "Dushek et al. 2014: T Cell Receptor Phosphorylation Feedback"
 description: "TCR signaling dynamics"
-tags: ["published", "dushek", "2014", "e", "f", "b"]
+tags: ["tcr", "feedback-loop", "immune-signaling", "2014", "dushek"]
 category: "signaling"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Erdem2021/metadata.yaml b/Published/Erdem2021/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Erdem_2021"
-name: "Erdem 2021"
+id: Erdem_InsR_2021
+name: "Erdem et al. 2021: Insulin Receptor Internalization Model"
 description: "InsR/IGF1R signaling"
-tags: ["published", "erdem", "2021", "igf1", "ins", "igf1r", "insr", "irs", "sos", "ras", "raf"]
+tags: ["insulin", "receptor-internalization", "2021", "erdem"]
 category: "signaling"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Faeder2003/metadata.yaml b/Published/Faeder2003/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Faeder_2003"
-name: "Faeder 2003"
+id: Faeder_FceRI_2003
+name: "Faeder et al. 2003: FceRI Signaling Model"
 description: "FceRI signaling"
-tags: ["published", "immunology", "faeder", "2003", "lig", "lyn", "syk", "rec"]
+tags: ["fceri", "immune-signaling", "mast-cell", "2003", "faeder"]
 category: "immunology"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Gardner2000/metadata.yaml b/Published/Gardner2000/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Gardner_2000"
-name: "Gardner 2000"
+id: Gardner_Toggle_2000
+name: "Gardner et al. 2000: Synthetic Gene Toggle Switch"
 description: "Genetic toggle switch"
-tags: ["published", "synthetic-biology", "gardner", "2000"]
+tags: ["toggle-switch", "synthetic-biology", "gene-regulation", "2000", "gardner"]
 category: "synthetic-biology"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Goldstein1980/metadata.yaml b/Published/Goldstein1980/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Goldstein_1980"
-name: "Goldstein 1980"
+id: Goldstein_blbr_1980
+name: "Goldstein et al. 1980: Bivalent Ligand Bivalent Receptor (BLBR) Model"
 description: "BLBR heterogeneity"
-tags: ["published", "physics", "goldstein", "1980"]
+tags: ["blbr", "ligand-receptor", "binding", "1980", "goldstein"]
 category: "physics"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Harmon2017/metadata.yaml b/Published/Harmon2017/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Harmon_2017"
-name: "Harmon 2017"
+id: Harmon_Antigen_2017
+name: "Harmon et al. 2017: Antigen Recognition Feedback Model"
 description: "Antigen pulses"
-tags: ["published", "immunology", "harmon", "2017"]
+tags: ["antigen-recognition", "immune-signaling", "2017", "harmon"]
 category: "immunology"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Hat2016/metadata.yaml b/Published/Hat2016/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Hat_2016"
-name: "Hat 2016"
+id: Hat_wip1_2016
+name: "Hat et al. 2016: Wip1-Mediated Feedback Oscillator"
 description: "Nuclear transport"
-tags: ["published", "hat", "2016", "dna_dsb", "atm", "siah1", "hipk2", "wip1", "gene_wip1", "mrna_wip1", "p53"]
+tags: ["wip1", "feedback-loop", "p53-pathway", "2016", "hat"]
 category: "regulation"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Hlavacek1999/metadata.yaml b/Published/Hlavacek1999/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Hlavacek_1999"
-name: "Hlavacek 1999"
+id: Hlavacek_Steric_1999
+name: "Hlavacek et al. 1999: Steric Hindrance in Ligand Binding"
 description: "Steric effects"
-tags: ["published", "physics", "hlavacek", "1999"]
+tags: ["steric-hindrance", "ligand-binding", "1999", "hlavacek"]
 category: "physics"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Hlavacek2001/metadata.yaml b/Published/Hlavacek2001/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Hlavacek_2001"
-name: "Hlavacek 2001"
+id: Hlavacek_Proofreading_2001
+name: "Hlavacek et al. 2001: Kinetic Proofreading Model"
 description: "Kinetic proofreading"
-tags: ["published", "physics", "hlavacek", "2001"]
+tags: ["kinetic-proofreading", "ligand-discrimination", "2001", "hlavacek"]
 category: "physics"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Hlavacek2018Egg/metadata.yaml b/Published/Hlavacek2018Egg/metadata.yaml
@@ -1,7 +1,7 @@
-id: Hlavacek2018Egg_egg
-name: Hlavacek2018Egg
+id: Hlavacek_Egg_2018
+name: "Hlavacek et al. 2018: Calcium Oscillations in Egg Activation"
 description: End of permute change log
-tags: ["a0__free", "a1__free", "a2__free", "b1__free", "b2__free", "c0__free", "c1__free", "c2__free", "d1__free", "d2__free", "a0", "a1", "a2", "b1", "b2", "c0", "c1", "c2", "d1", "d2", "period", "t", "species"]
+tags: ["calcium-oscillations", "egg-activation", "2018", "hlavacek"]
 category: other
 compatibility:
   bng2_compatible: true

diff --git a/Published/Hlavacek2018Elephant/metadata.yaml b/Published/Hlavacek2018Elephant/metadata.yaml
@@ -1,7 +1,7 @@
-id: Hlavacek2018Elephant_elephant_EFA
-name: Hlavacek2018Elephant
+id: Hlavacek_Elephant_2018
+name: "Hlavacek et al. 2018: Fitting an Elephant with Four Parameters"
 description: BNGL model: elephant_EFA
-tags: ["a0", "a1", "a2", "a3", "a4", "a5", "a6", "a7", "a8", "a9", "a10", "a11", "a12", "a13", "a14", "a15", "a16", "a17", "a18", "a19", "a20", "b0", "b1", "b2", "b3", "b4", "b5", "b6", "b7", "b8", "b9", "b10", "b11", "b12", "b13", "b14", "b15", "b16", "b17", "b18", "b19", "b20", "c0", "c1", "c2", "c3", "c4", "c5", "c6", "c7", "c8", "c9", "c10", "c11", "c12", "c13", "c14", "c15", "c16", "c17", "c18", "c19", "c20", "d0", "d1", "d2", "d3", "d4", "d5", "d6", "d7", "d8", "d9", "d10", "d11", "d12", "d13", "d14", "d15", "d16", "d17", "d18", "d19", "d20", "period", "t", "species"]
+tags: ["elephant-fitting", "mathematical-model", "2018", "hlavacek"]
 category: other
 compatibility:
   bng2_compatible: true

diff --git a/Published/Hlavacek2018Restructuration/metadata.yaml b/Published/Hlavacek2018Restructuration/metadata.yaml
@@ -1,7 +1,7 @@
-id: Hlavacek2018Restructuration_after_bunching
-name: Hlavacek2018Restructuration
+id: Hlavacek_Restructuration_2018
+name: "Hlavacek et al. 2018: Network Restructuration Analysis"
 description: BNGL model: after_bunching
-tags: ["na", "vecf", "egftot", "egfrtot", "kd", "kr", "kpx", "kmx", "kp", "kdp", "molecules"]
+tags: ["network-restructuration", "mathematical-model", "2018", "hlavacek"]
 category: other
 compatibility:
   bng2_compatible: true

diff --git a/Published/JaruszewiczBlonska2023/metadata.yaml b/Published/JaruszewiczBlonska2023/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Jaruszewicz-Blonska_2023"
-name: "Jaruszewicz 2023"
+id: JaruszewiczBlonska_NFkB_2023
+name: "Jaruszewicz-Blonska et al. 2023: NF-kB Feedback Regulation"
 description: "T-cell discrimination"
-tags: ["published", "immunology", "jaruszewicz", "blonska", "2023", "ikk", "ikba", "ikba_mrna", "a20", "nfkb"]
+tags: ["nfkb", "feedback-regulation", "inflammatory-response", "2023", "jaruszewiczblonska"]
 category: "immunology"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Jung2017/metadata.yaml b/Published/Jung2017/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Jung_2017"
-name: "Jung 2017"
+id: Jung_CaMKII_2017
+name: "Jung et al. 2017: CaMKII Activation Kinetics"
 description: "M1 receptor signaling"
-tags: ["published", "jung", "2017", "m1r", "oxo", "arrestin", "mek", "erk", "perk", "oxo_ec", "pp2a"]
+tags: ["camkii", "neuroscience", "kinase-activation", "2017", "jung"]
 category: "signaling"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Kesseler2013/metadata.yaml b/Published/Kesseler2013/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Kesseler_2013"
-name: "Kesseler 2013"
+id: Kesseler_CellCycle_2013
+name: "Kesseler et al. 2013: Cell Cycle Regulation Model"
 description: "G2/Mitosis transition"
-tags: ["published", "kesseler", "2013", "mpf", "cdc25", "wee1", "myt1", "pin1", "pp2a", "prox", "e33"]
+tags: ["cell-cycle", "mitosis", "cdc25", "wee1", "2013", "kesseler"]
 category: "signaling"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Kocieniewski2012/metadata.yaml b/Published/Kocieniewski2012/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Kocieniewski_2012"
-name: "Kocieniewski 2012"
+id: Kocieniewski_published_2012
+name: "Kocieniewski et al. 2012: MAPK Signaling on Scaffolds"
 description: "Actin dynamics"
-tags: ["published", "kocieniewski", "2012", "map3k", "map2k", "mapk", "scaff"]
+tags: ["mapk", "scaffold-proteins", "signaling", "2012", "kocieniewski"]
 category: "regulation"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Korwek2023/metadata.yaml b/Published/Korwek2023/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Korwek_2023"
-name: "Korwek_2023"
+id: Korwek_ViralSensing_2023
+name: "Korwek et al. 2023: Viral Sensing and Innate Immune Activation"
 description: "This BioNetGen file features the article:"
-tags: ["validation", "korwek", "2023", "polyic", "rigi", "mavs", "pkr", "oas3", "rnasel", "eif2a", "rigi_mrna"]
+tags: ["innate-immunity", "rig-i-sensing", "pkr-activation", "rnase-l-cleavage", "viral-sensing", "2023", "korwek"]
 category: "validation"
 compatibility:
   bng2_compatible: true

diff --git a/Published/Kozer2013/metadata.yaml b/Published/Kozer2013/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Kozer_2013"
-name: "Kozer 2013"
+id: Kozer_egfr_2013
+name: "Kozer et al. 2013: EGFR Dimerization and Internalization"
 description: "EGFR oligomerization"
-tags: ["published", "kozer", "2013", "egf", "egfr"]
+tags: ["egfr", "dimerization", "internalization", "2013", "kozer"]
 category: "signaling"
 compatibility:
   bng2_compatible: false

diff --git a/Published/Kozer2014/metadata.yaml b/Published/Kozer2014/metadata.yaml
@@ -1,7 +1,7 @@
-id: "Kozer_2014"
-name: "Kozer 2014"
+id: Kozer_egfr_2014
+name: "Kozer et al. 2014: EGFR Oligomerization Dynamics"
 description: "Grb2-EGFR recruitment"
-tags: ["published", "kozer", "2014", "egf", "egfr", "grb2"]
+tags: ["egfr", "oligomerization", "internalization", "2014", "kozer"]
 category: "signaling"
 compatibility:
   bng2_compatible: false