Rebuilt CONIB

pharmacome · Apr 26, 2021 · 3898cd0 · 3898cd0
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commit 3898cd0
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Showing 6 changed files with 139,757 additions and 57,847 deletions.
diff --git a/conib/_cache.bel.nodelink.json b/conib/_cache.bel.nodelink.json
@@ -352,7 +352,7 @@
       "description": "Mechanistic knowledge surrounding several neurodegenerative diseases, with specific focus on protein aggregation, nicotinic receptor signalling, proteostasis, and other mechanisms.",
       "licenses": "CC BY 4.0",
       "name": "Curation of Neurodegeneration in BEL (CONIB)",
-      "version": "0.0.8-dev"
+      "version": "0.0.8"
     },
     "namespace_pattern": {
       "BTO": "^\\d{7}$",

diff --git a/conib/_cache.bel.summary.json b/conib/_cache.bel.summary.json
@@ -1,6 +1,6 @@
 {
   "Name": "Curation of Neurodegeneration in BEL (CONIB)",
-  "Version": "0.0.8-dev",
+  "Version": "0.0.8",
   "Authors": "Charles Tapley Hoyt, Daniel Domingo-Fern\u00e1ndez, Esther Wollert, Sandra Spalek, Rana Al Disi, Lingling Xu, Kristian Kolpeja, Yojana Gadiya, Trusha Adeshara, Stephan Gebel, Sepehr Golriz",
   "Number of Nodes": 8976,
   "Number of Namespaces": 37,

diff --git a/conib/_cache.bel.summary.tsv b/conib/_cache.bel.summary.tsv
@@ -1,5 +1,5 @@
 	Name	Version	Authors	Number of Nodes	Number of Namespaces	Number of Edges	Number of Annotations	Number of Citations	Number of Authors	Network Density	Number of Components	Number of Warnings	Author
-misc/damesquita2018.bel	Curation of Neurodegeneration in BEL (CONIB)	0.0.8-dev	Charles Tapley Hoyt, Daniel Domingo-Fernández, Esther Wollert, Sandra Spalek, Rana Al Disi, Lingling Xu, Kristian Kolpeja, Yojana Gadiya, Trusha Adeshara, Stephan Gebel, Sepehr Golriz	51	6	120	5	1	23	4.71E-02	1	0	
+misc/damesquita2018.bel	Curation of Neurodegeneration in BEL (CONIB)	0.0.8	Charles Tapley Hoyt, Daniel Domingo-Fernández, Esther Wollert, Sandra Spalek, Rana Al Disi, Lingling Xu, Kristian Kolpeja, Yojana Gadiya, Trusha Adeshara, Stephan Gebel, Sepehr Golriz	51	6	120	5	1	23	4.71E-02	1	0	
 misc/gant2018.bel	FK506-Binding Protein 12.6/1b, a Negative Regulator of [Ca2], Rescues Memory and Restores Genomic Regulation in the Hippocampus of Aging Rats	1.0.0		30	5	51	3	1	7	5.86E-02	1	0	Lingling Xu
 misc/maniati2019.bel	New insights into the role of microRNAs and long noncoding RNAs in most common neurodegenerative diseases	1.0.0		94	9	181	5	1	5	2.07E-02	2	0	Sandra Spalek
 misc/neurotransmitter_insulin_neurommsig_enrichment.bel	Neurotransmitter and Insulin NeuroMMSig enrichments	0.0.1	Kristian Kolpeja, Daniel Domingo-Fernandez	121	13	234	6	16	90	1.61E-02	5	0	

diff --git a/conib/_cache.bel.warnings.tsv b/conib/_cache.bel.warnings.tsv
@@ -4,7 +4,7 @@ Line Number	Position	Line	Error	Message
 159	32	"bp(GO:aging) negativeCorrelation r(CONSO:""alpha-7-containing nAChR"")"	InvalidFunctionSemantic	"RNA CONSO:""alpha-7-containing nAChR"" should be encoded as one of: Complex"
 218	66	"p(MESH:""Receptors, Nicotinic"",loc(MESH:""GABAergic Neurons"")) -- a(CONSO:neurotransmitters)"	MissingNamespaceNameWarning	"""neurotransmitters"" is not in the CONSO namespace"
 219	41	"p(MESH:""Receptors, Nicotinic"") reg sec(a(CONSO:neurotransmitters))"	MissingNamespaceNameWarning	"""neurotransmitters"" is not in the CONSO namespace"
-117	17	"p(CONSO:DC8E8) -- path(CONSO:""Braak_Stage I"")"	InvalidFunctionSemantic	"Pathology CONSO:""Braak_Stage I"" should be encoded as one of: miRNA, Abundance, Gene, Complex, Protein, RNA"
+117	17	"p(CONSO:DC8E8) -- path(CONSO:""Braak_Stage I"")"	InvalidFunctionSemantic	"Pathology CONSO:""Braak_Stage I"" should be encoded as one of: miRNA, Gene, Complex, RNA, Abundance, Protein"
 551	4	"SET MeSHDisease = ""Hypoxia"""	UndefinedAnnotationWarning	"""MeSHDisease"" is not defined"
 568	6	UNSET MeSHDisease	UndefinedAnnotationWarning	"""MeSHDisease"" is not defined"
 157	56	"p(CONSO:""Tau isoform F (441 aa)"", var(""p.Lys280del"")) -- a(CONSO:""Tau epitope, 12E8"")"	InvalidFunctionSemantic	"Abundance CONSO:""Tau epitope, 12E8"" should be encoded as one of: Protein"

diff --git a/conib/immunotherapy/kontsekova2014.bel.warnings.tsv b/conib/immunotherapy/kontsekova2014.bel.warnings.tsv
@@ -1,2 +1,2 @@
 Line Number	Position	Line	Error	Message
-117	17	"p(CONSO:DC8E8) -- path(CONSO:""Braak_Stage I"")"	InvalidFunctionSemantic	"Pathology CONSO:""Braak_Stage I"" should be encoded as one of: miRNA, Abundance, Gene, Complex, Protein, RNA"
+117	17	"p(CONSO:DC8E8) -- path(CONSO:""Braak_Stage I"")"	InvalidFunctionSemantic	"Pathology CONSO:""Braak_Stage I"" should be encoded as one of: miRNA, Gene, Complex, RNA, Abundance, Protein"