Fix several bugs in model citations and add new safety checks so that…

… this won't happen again.
sybila · Oct 19, 2023 · 1a12ee1 · 1a12ee1
1 parent 1a10a7f
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diff --git a/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/README.md b/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/README.md
@@ -19,10 +19,12 @@ The following regulations were modified to ensure consistency of update function
 
 ```
 @article{bbm-024,
-  title={Ergodic sets as cell phenotype of budding yeast cell cycle},
-  author={Todd, Robert G and Helikar, Tom{\'a}{\v{s}}},
+  title={Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle},
+  author={Robert G. Todd and Tom{\'a}{\vs} Helikar},
+  journal={PLoS ONE},
   year={2012},
-  publisher={Public Library of Science San Francisco, USA}
+  volume={7},
+  url={https://api.semanticscholar.org/CorpusID:17537524}
 }
 ```
 
diff --git a/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/metadata.json b/models/[id-024]__[var-16]__[in-4]__[BUDDING-YEAST-CELL-CYCLE]/metadata.json
@@ -12,5 +12,5 @@
     "inputs": 4,
     "regulations": 42,
     "notes": "### Modifications\n\nThe following regulations were modified to ensure consistency of update functions with the regulatory graph:\n\n - Regulation `Cdc14 (S_12) -> Sic1 (S_3)` sign set to `unknown`.\n - Regulation `Start (S_9) -> Whi5 (S_14)` sign set to `unknown`.",
-    "bib": "@article{bbm-024,\n  title={Ergodic sets as cell phenotype of budding yeast cell cycle},\n  author={Todd, Robert G and Helikar, Tom{\\'a}{\\v{s}}},\n  year={2012},\n  publisher={Public Library of Science San Francisco, USA}\n}"
+    "bib": "@article{bbm-024,\n  title={Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle},\n  author={Robert G. Todd and Tom{\\'a}{\\vs} Helikar},\n  journal={PLoS ONE},\n  year={2012},\n  volume={7},\n  url={https://api.semanticscholar.org/CorpusID:17537524}\n}"
 }
diff --git a/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/README.md b/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/README.md
@@ -15,8 +15,16 @@ The model is provided without modifications.
 ### Model citation
 
 ```
-@article{bbm-999,
-  
+@article{bbm-170,
+  title={A logical analysis of the Drosophila gap-gene system},
+  author={S{\'a}nchez, Lucas and Thieffry, Denis},
+  journal={Journal of theoretical Biology},
+  volume={211},
+  number={2},
+  pages={115--141},
+  year={2001},
+  publisher={Elsevier}
 }
+
 ```
 
diff --git a/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/metadata.json b/models/[id-170]__[var-4]__[in-3]__[DROSOPHILA-GAP-B]/metadata.json
@@ -12,5 +12,5 @@
     "inputs": 3,
     "regulations": 15,
     "notes": "### Modifications\n\nThe model is provided without modifications.",
-    "bib": "@article{bbm-999,\n  \n}"
+    "bib": "@article{bbm-170,\n  title={A logical analysis of the Drosophila gap-gene system},\n  author={S{\\'a}nchez, Lucas and Thieffry, Denis},\n  journal={Journal of theoretical Biology},\n  volume={211},\n  number={2},\n  pages={115--141},\n  year={2001},\n  publisher={Elsevier}\n}\n"
 }
diff --git a/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/README.md b/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/README.md
@@ -15,8 +15,16 @@ The model is provided without modifications.
 ### Model citation
 
 ```
-@article{bbm-999,
-  
+@article{bbm-171,
+  title={A logical analysis of the Drosophila gap-gene system},
+  author={S{\'a}nchez, Lucas and Thieffry, Denis},
+  journal={Journal of theoretical Biology},
+  volume={211},
+  number={2},
+  pages={115--141},
+  year={2001},
+  publisher={Elsevier}
 }
+
 ```
 
diff --git a/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/metadata.json b/models/[id-171]__[var-5]__[in-2]__[DROSOPHILA-GAP-C]/metadata.json
@@ -12,5 +12,5 @@
     "inputs": 2,
     "regulations": 20,
     "notes": "### Modifications\n\nThe model is provided without modifications.",
-    "bib": "@article{bbm-999,\n  \n}"
+    "bib": "@article{bbm-171,\n  title={A logical analysis of the Drosophila gap-gene system},\n  author={S{\\'a}nchez, Lucas and Thieffry, Denis},\n  journal={Journal of theoretical Biology},\n  volume={211},\n  number={2},\n  pages={115--141},\n  year={2001},\n  publisher={Elsevier}\n}\n"
 }
diff --git a/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/README.md b/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/README.md
@@ -15,8 +15,16 @@ The model is provided without modifications.
 ### Model citation
 
 ```
-@article{bbm-999,
-  
+@article{bbm-172,
+  title={A logical analysis of the Drosophila gap-gene system},
+  author={S{\'a}nchez, Lucas and Thieffry, Denis},
+  journal={Journal of theoretical Biology},
+  volume={211},
+  number={2},
+  pages={115--141},
+  year={2001},
+  publisher={Elsevier}
 }
+
 ```
 
diff --git a/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/metadata.json b/models/[id-172]__[var-5]__[in-2]__[DROSOPHILA-GAP-D]/metadata.json
@@ -12,5 +12,5 @@
     "inputs": 2,
     "regulations": 12,
     "notes": "### Modifications\n\nThe model is provided without modifications.",
-    "bib": "@article{bbm-999,\n  \n}"
+    "bib": "@article{bbm-172,\n  title={A logical analysis of the Drosophila gap-gene system},\n  author={S{\\'a}nchez, Lucas and Thieffry, Denis},\n  journal={Journal of theoretical Biology},\n  volume={211},\n  number={2},\n  pages={115--141},\n  year={2001},\n  publisher={Elsevier}\n}\n"
 }
diff --git a/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/README.md b/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/README.md
@@ -15,16 +15,14 @@ The model is reproduced based on the table and figure within the paper.
 ### Model citation
 
 ```
-@article {bbm-208,
-	author = {H{\'e}rault, L{\'e}onard and Poplineau, Mathilde and Duprez, Estelle and Remy, {\'E}lisabeth},
-	title = {A novel Boolean network inference strategy to model early hematopoiesis aging},
-	year = {2022},
-	doi = {10.1101/2022.02.08.479548},
-	publisher = {Cold Spring Harbor Laboratory},
-	URL = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548},
-	eprint = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548.full.pdf},
-	journal = {bioRxiv}
+@article{bbm-208,
+  title={A novel Boolean network inference strategy to model early hematopoiesis aging},
+  author={L{\'e}onard H{\'e}rault and Mathilde Poplineau and Estelle Duprez and {\'E}lisabeth Remy},
+  journal={Computational and Structural Biotechnology Journal},
+  year={2022},
+  volume={21},
+  pages={21 - 33},
+  url={https://api.semanticscholar.org/CorpusID:248672123}
 }
-
 ```
 
diff --git a/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/metadata.json b/models/[id-208]__[var-15]__[in-0]__[HEMATOPOIESIS-AGING]/metadata.json
@@ -10,5 +10,5 @@
     "inputs": 0,
     "regulations": 36,
     "notes": "### Modifications\n\nThe model is reproduced based on the table and figure within the paper.",
-    "bib": "@article {bbm-208,\n\tauthor = {H{\\'e}rault, L{\\'e}onard and Poplineau, Mathilde and Duprez, Estelle and Remy, {\\'E}lisabeth},\n\ttitle = {A novel Boolean network inference strategy to model early hematopoiesis aging},\n\tyear = {2022},\n\tdoi = {10.1101/2022.02.08.479548},\n\tpublisher = {Cold Spring Harbor Laboratory},\n\tURL = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548},\n\teprint = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548.full.pdf},\n\tjournal = {bioRxiv}\n}\n"
+    "bib": "@article{bbm-208,\n  title={A novel Boolean network inference strategy to model early hematopoiesis aging},\n  author={L{\\'e}onard H{\\'e}rault and Mathilde Poplineau and Estelle Duprez and {\\'E}lisabeth Remy},\n  journal={Computational and Structural Biotechnology Journal},\n  year={2022},\n  volume={21},\n  pages={21 - 33},\n  url={https://api.semanticscholar.org/CorpusID:248672123}\n}"
 }
diff --git a/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/README.md b/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/README.md
@@ -52,8 +52,14 @@ The following regulations were updated to fix logical inconsistencies:
 ### Model citation
 
 ```
-@article{bbm-999,
-  
+@article{bbm-222,
+  title={Temporal protein expression pattern in intracellular signalling cascade during T-cell activation: A computational study},
+  author={Ganguli, Piyali and Chowdhury, Saikat and Bhowmick, Rupa and Sarkar, Ram Rup},
+  journal={Journal of biosciences},
+  volume={40},
+  pages={769--789},
+  year={2015},
+  publisher={Springer}
 }
 ```
 
diff --git a/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/metadata.json b/models/[id-222]__[var-167]__[in-39]__[TEMPORAL-PROTEIN-EXPRESSION]/metadata.json
@@ -12,5 +12,5 @@
     "inputs": 39,
     "regulations": 435,
     "notes": "### Availability\n\nHonestly, I'm not quite sure where they found the rules, but they are available in the `grn-principles` dataset\nand converted using `rules_to_bnet.py`. In order to be able to properly annotate the logical errors, we then \ncovert the model to `.aeon`.\n\n### Modifications\n\nThe following regulations were updated to fix logical inconsistencies:\n \n - Regulation `ATF2 -> AP1` set as non-essential.\n - Regulation `CRE -> AP1` set as non-essential.\n - Regulation `NUC_ERK1_2 -> AP1` set as non-essential.\n - Regulation `NUC_P38 -> AP1` set as non-essential.\n - Regulation `JNK -> BAD` set as non-essential.\n - Regulation `CALCIPRESSIN -> CALCINEURIN` set as non-essential.\n - Regulation `VAV -> CAM` set as non-essential.\n - Regulation `CBL -> FYN` set as non-essential.\n - Regulation `CD45 -> FYN` set as non-essential.\n - Regulation `AP1 -> GM_CSF` set as non-essential.\n - Regulation `IKK_GAMMA -> IKB_BETA` set as non-essential.\n - Regulation `TAK1_TAB -> IKK_GAMMA` set as non-essential.\n - Regulation `ETS -> IL2` set as non-essential.\n - Regulation `GSK3_BETA -> IL2` set as non-essential.\n - Regulation `GSK3_BETA -> IL4` set as non-essential.\n - Regulation `CBL -> LCK` set as non-essential.\n - Regulation `CD28 -> LCK` set as non-essential.\n - Regulation `CD45 -> LCK` set as non-essential.\n - Regulation `CABIN1 -> MEF2` set as non-essential.\n - Regulation `HDAC -> MEF2` set as non-essential.\n - Regulation `PKC -> NCK` set as non-essential.\n - Regulation `GSK3_BETA -> NUC_NFAT` set as non-essential.\n - Regulation `IL1 -> NUC_NFKB` set as non-essential.\n - Regulation `GRB7 -> RAS` set as non-essential.\n - Regulation `NCK_SOS -> RAS` set as non-essential.\n - Regulation `SHC_GRB2_SOS -> RAS` set as non-essential.\n - Regulation `SHP1_GRB2_SOS -> RAS` set as non-essential.\n - Regulation `SHP2_GRB2_GAB1_SOS -> RAS` set as non-essential.\n - Regulation `LYP -> ZAP70` set as non-essential.\n - Regulation `VAV -> ZAP70` set as non-essential.",
-    "bib": "@article{bbm-999,\n  \n}"
+    "bib": "@article{bbm-222,\n  title={Temporal protein expression pattern in intracellular signalling cascade during T-cell activation: A computational study},\n  author={Ganguli, Piyali and Chowdhury, Saikat and Bhowmick, Rupa and Sarkar, Ram Rup},\n  journal={Journal of biosciences},\n  volume={40},\n  pages={769--789},\n  year={2015},\n  publisher={Springer}\n}"
 }
diff --git a/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/README.md b/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/README.md
@@ -21,8 +21,13 @@ The model is provided without modifications.
 ### Model citation
 
 ```
-@article{bbm-999,
-  
+@article{bbm-223,
+  title={A Network Model to Explore the Effect of the Micro-environment on Endothelial Cell Behavior during Angiogenesis},
+  author={Nathan Weinstein and Luis Mendoza and Isidoro Gitler and Jaime Klapp},
+  journal={Frontiers in Physiology},
+  year={2017},
+  volume={8},
+  url={https://api.semanticscholar.org/CorpusID:12294741}
 }
 ```
 
diff --git a/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/metadata.json b/models/[id-223]__[var-114]__[in-27]__[ANGIOGENESIS-MICROENVIRONMENT]/metadata.json
@@ -11,5 +11,5 @@
     "inputs": 27,
     "regulations": 254,
     "notes": "### Availability\n\nThe models is given as a list of functions in the supplementary material, but these\nare already translated in the `grn-principles` dataset, hence we use those and convert\nto `.bnet`.\n\n### Modifications\n\nThe model is provided without modifications.",
-    "bib": "@article{bbm-999,\n  \n}"
+    "bib": "@article{bbm-223,\n  title={A Network Model to Explore the Effect of the Micro-environment on Endothelial Cell Behavior during Angiogenesis},\n  author={Nathan Weinstein and Luis Mendoza and Isidoro Gitler and Jaime Klapp},\n  journal={Frontiers in Physiology},\n  year={2017},\n  volume={8},\n  url={https://api.semanticscholar.org/CorpusID:12294741}\n}"
 }
diff --git a/...228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/README.md b/...228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/README.md
@@ -19,7 +19,7 @@ The model is provided without modifications.
 ### Model citation
 
 ```
-@article{ryll2014model,
+@article{bbm-228,
   title={A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models},
   author={Ryll, Anke and Bucher, Joachim and Bonin, Anne and Bongard, Sophia and Gon{\c{c}}alves, E and Saez-Rodriguez, Julio and Niklas, Jens and Klamt, Steffen},
   journal={Biosystems},

diff --git a/...s/[id-228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/metadata.json b/...s/[id-228]__[var-47]__[in-9]__[INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS]/metadata.json
@@ -11,5 +11,5 @@
     "inputs": 9,
     "regulations": 107,
     "notes": "The original model is available in the supplement of the document, but our source is \nfrom `grn-principles` dataset. There seem to be four variants of the model. Here,\nwe consider the `AND_OR` version.\n\n### Modifications\n\nThe model is provided without modifications.",
-    "bib": "@article{ryll2014model,\n  title={A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models},\n  author={Ryll, Anke and Bucher, Joachim and Bonin, Anne and Bongard, Sophia and Gon{\\c{c}}alves, E and Saez-Rodriguez, Julio and Niklas, Jens and Klamt, Steffen},\n  journal={Biosystems},\n  volume={124},\n  pages={26--38},\n  year={2014},\n  publisher={Elsevier}\n}"
+    "bib": "@article{bbm-228,\n  title={A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models},\n  author={Ryll, Anke and Bucher, Joachim and Bonin, Anne and Bongard, Sophia and Gon{\\c{c}}alves, E and Saez-Rodriguez, Julio and Niklas, Jens and Klamt, Steffen},\n  journal={Biosystems},\n  volume={124},\n  pages={26--38},\n  year={2014},\n  publisher={Elsevier}\n}"
 }
diff --git a/sources/024_BUDDING-YEAST-CELL-CYCLE/citation.bib b/sources/024_BUDDING-YEAST-CELL-CYCLE/citation.bib
@@ -1,6 +1,8 @@
 @article{bbm-024,
-  title={Ergodic sets as cell phenotype of budding yeast cell cycle},
-  author={Todd, Robert G and Helikar, Tom{\'a}{\v{s}}},
+  title={Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle},
+  author={Robert G. Todd and Tom{\'a}{\vs} Helikar},
+  journal={PLoS ONE},
   year={2012},
-  publisher={Public Library of Science San Francisco, USA}
+  volume={7},
+  url={https://api.semanticscholar.org/CorpusID:17537524}
 }
diff --git a/sources/170_DROSOPHILA-GAP-B/citation.bib b/sources/170_DROSOPHILA-GAP-B/citation.bib
@@ -1,3 +1,10 @@
-@article{bbm-999,
-
-}
+@article{bbm-170,
+  title={A logical analysis of the Drosophila gap-gene system},
+  author={S{\'a}nchez, Lucas and Thieffry, Denis},
+  journal={Journal of theoretical Biology},
+  volume={211},
+  number={2},
+  pages={115--141},
+  year={2001},
+  publisher={Elsevier}
+}
diff --git a/sources/171_DROSOPHILA-GAP-C/citation.bib b/sources/171_DROSOPHILA-GAP-C/citation.bib
@@ -1,3 +1,10 @@
-@article{bbm-999,
-
-}
+@article{bbm-171,
+  title={A logical analysis of the Drosophila gap-gene system},
+  author={S{\'a}nchez, Lucas and Thieffry, Denis},
+  journal={Journal of theoretical Biology},
+  volume={211},
+  number={2},
+  pages={115--141},
+  year={2001},
+  publisher={Elsevier}
+}
diff --git a/sources/172_DROSOPHILA-GAP-D/citation.bib b/sources/172_DROSOPHILA-GAP-D/citation.bib
@@ -1,3 +1,10 @@
-@article{bbm-999,
-
-}
+@article{bbm-172,
+  title={A logical analysis of the Drosophila gap-gene system},
+  author={S{\'a}nchez, Lucas and Thieffry, Denis},
+  journal={Journal of theoretical Biology},
+  volume={211},
+  number={2},
+  pages={115--141},
+  year={2001},
+  publisher={Elsevier}
+}
diff --git a/sources/208_HEMATOPOIESIS-AGING/citation.bib b/sources/208_HEMATOPOIESIS-AGING/citation.bib
@@ -1,10 +1,9 @@
-@article {bbm-208,
-	author = {H{\'e}rault, L{\'e}onard and Poplineau, Mathilde and Duprez, Estelle and Remy, {\'E}lisabeth},
-	title = {A novel Boolean network inference strategy to model early hematopoiesis aging},
-	year = {2022},
-	doi = {10.1101/2022.02.08.479548},
-	publisher = {Cold Spring Harbor Laboratory},
-	URL = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548},
-	eprint = {https://www.biorxiv.org/content/early/2022/05/08/2022.02.08.479548.full.pdf},
-	journal = {bioRxiv}
-}
+@article{bbm-208,
+  title={A novel Boolean network inference strategy to model early hematopoiesis aging},
+  author={L{\'e}onard H{\'e}rault and Mathilde Poplineau and Estelle Duprez and {\'E}lisabeth Remy},
+  journal={Computational and Structural Biotechnology Journal},
+  year={2022},
+  volume={21},
+  pages={21 - 33},
+  url={https://api.semanticscholar.org/CorpusID:248672123}
+}
diff --git a/sources/222_TEMPORAL-PROTEIN-EXPRESSION/citation.bib b/sources/222_TEMPORAL-PROTEIN-EXPRESSION/citation.bib
@@ -1,3 +1,9 @@
-@article{bbm-999,
-
+@article{bbm-222,
+  title={Temporal protein expression pattern in intracellular signalling cascade during T-cell activation: A computational study},
+  author={Ganguli, Piyali and Chowdhury, Saikat and Bhowmick, Rupa and Sarkar, Ram Rup},
+  journal={Journal of biosciences},
+  volume={40},
+  pages={769--789},
+  year={2015},
+  publisher={Springer}
 }
diff --git a/sources/223_ANGIOGENESIS-MICROENVIRONMENT/citation.bib b/sources/223_ANGIOGENESIS-MICROENVIRONMENT/citation.bib
@@ -1,3 +1,8 @@
-@article{bbm-999,
-
+@article{bbm-223,
+  title={A Network Model to Explore the Effect of the Micro-environment on Endothelial Cell Behavior during Angiogenesis},
+  author={Nathan Weinstein and Luis Mendoza and Isidoro Gitler and Jaime Klapp},
+  journal={Frontiers in Physiology},
+  year={2017},
+  volume={8},
+  url={https://api.semanticscholar.org/CorpusID:12294741}
 }
diff --git a/sources/228_INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS/citation.bib b/sources/228_INTEGRATION-OF-SIGNALING-AND-KINETIC-MODELS/citation.bib
@@ -1,4 +1,4 @@
-@article{ryll2014model,
+@article{bbm-228,
   title={A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models},
   author={Ryll, Anke and Bucher, Joachim and Bonin, Anne and Bongard, Sophia and Gon{\c{c}}alves, E and Saez-Rodriguez, Julio and Niklas, Jens and Klamt, Steffen},
   journal={Biosystems},

diff --git a/sync.py b/sync.py
@@ -26,7 +26,7 @@ def read_dir_name(dir_name):
 		print("ERROR: Invalid source directory:", dir_name)
 	return (int(result.group(1)), result.group(2))	
 
-def check_metadata(id, name, metadata):
+def check_metadata(id, name, metadata, bib):
 	if (not 'id' in metadata) or metadata['id'] != id:
 		print("ERROR: Invalid id in metadata of", name)
 		sys.exit(128)
@@ -47,6 +47,10 @@ def check_metadata(id, name, metadata):
 		print("ERROR: Missing keywords attribute in", name)
 		sys.exit(128)
 
+	if (not f'bbm-{int(id):03d}' in bib):
+		print(f"ERROR: Missing a `bbm-{int(id):03d}` key in the `citation.bib` file.")
+		sys.exit(128)
+
 def check_unused_variables(model):
 	graph = model.graph()
 	for var in graph.variables():
@@ -139,7 +143,7 @@ def fix_variable_names(model):
 	with open(metadata_file) as file:
 		metadata = json.load(file)
 
-	check_metadata(model_id, model_name, metadata)
+	check_metadata(model_id, model_name, metadata, bib)
 
 
 	# Load the model (including syntactic check)