Table of Contents

Namespaces

Unused Namespaces 8

The source BEL script contained references to the following namespaces, but they were never used. It is suggested to delete their definitions from the BEL script to improve readability and parsing speed.

  • CHEBI
  • CHEMBLA
  • GOBP
  • GOCC
  • HGNC
  • MESHD
  • MGI
  • RGD

Annotations

This section lists all of the annotations that are defined in the original BEL script.

Keyword URL Stratify
Anatomy https://arty.scai.fraunhofer.de/artifactory/bel/annotation/anatomy/anatomy-20170511.belanno View Stratified Summary
Disease https://arty.scai.fraunhofer.de/artifactory/bel/annotation/disease/disease-20170511.belanno View Stratified Summary
MeSHAnatomy https://arty.scai.fraunhofer.de/artifactory/bel/annotation/mesh-anatomy/mesh-anatomy-20170511.belanno View Stratified Summary
Species https://arty.scai.fraunhofer.de/artifactory/bel/annotation/species-taxonomy-id/species-taxonomy-id-20170511.belanno View Stratified Summary

Unused Annotations 9

The source BEL script contained references to the following annotations, but they were never used. It is suggested to delete their definitions from the BEL script to improve readability and parsing speed.

Note: this may be due to errors occurring in all statements with these annotations.

  • Anatomy
  • Assay
  • CellLine
  • Disease
  • Dosage
  • MeSHAnatomy
  • MouseStrain
  • Species
  • TextLocation

Locally Defined Annotations 5

The source BEL script contained annotations defined as a list. Click each link to export the list definition as a BELANNO file that can hosted externally to promote re-usability and interoperability. After, you can replace the list definition in the source BEL with a SET ANNOTATION X AS URL "Y" definition.

Unused Locally Defined Annotations 5

The source BEL script contained the following list annotations, but no references to the following values. It is suggested to prune these values from the list definitions.

Note: this may be due to errors occurring in all statements with these annotations.

Annotation Values
Assay
  • ELISA
  • Reporter Gene Assays
  • IHC
  • Multiplex Assay
CellLine
  • HEK293A
Dosage
  • 10 µM
MouseStrain
  • 3xTG-AD
TextLocation
  • Abstract
  • Result

Warning Statistics

Syntax Errors 2

Line BEL Message
73 bp(GOBP:"non-canonical Wnt signaling pathway"))->a(CHEBI:"amyloid-beta") General Parser Failure on line 73 at pos 46: bp(GOBP:"non-canonical Wnt signaling pathway"))->a(CHEBI:"amyloid-beta")
74 bp(GOBP:"canonical Wnt signaling pathway"))-|a(CHEBI:"amyloid-beta") General Parser Failure on line 74 at pos 42: bp(GOBP:"canonical Wnt signaling pathway"))-|a(CHEBI:"amyloid-beta")

All Parser Warnings 147

A faceted table view of all parser warnings can be viewed and exported from here.

Line BEL Message
39 SET Citation = {"Transl Psychiatry. 2018 Sep 20;8(1):179. doi: 10.1038/s41398-018-0231-6","30232325"} [pos:4] "Transl Psychiatry. 2018 Sep 20;8(1):179. doi: 10.1038/s41398-018-0231-6" is not a valid citation type
41 SET TextLocation = "Abstract" Missing citation; can't add: SET TextLocation = "Abstract"
47 SET Disease: "Alzheimer's disease" Missing citation; can't add: SET Disease: "Alzheimer's disease"
49 p(HGNC:DKK1)-| bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:DKK1)-| bp(GOBP:"canonical Wnt signaling pathway")
50 a(CHEBI:"amyloid-beta")->p(MGI:Dkk1) Missing citation; can't add: a(CHEBI:"amyloid-beta")->p(MGI:Dkk1)
51 p(HGNC:DKK1)->bp(GOBP:"non-canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:DKK1)->bp(GOBP:"non-canonical Wnt signaling pathway")
52 a(CHEBI:"amyloid-beta")->bp(GOBP:"non-canonical Wnt signaling pathway") Missing citation; can't add: a(CHEBI:"amyloid-beta")->bp(GOBP:"non-canonical Wnt signaling pathway")
54 UNSET Disease Missing citation; can't add: UNSET Disease
60 bp(GOBP:"canonical Wnt signaling pathway")-> bp("synapse stability") [pos:48] "synapse stability" should be qualified with a valid namespace
61 bp(GOBP:"non-canonical Wnt signaling pathway")->bp(GOBP:"synapse pruning") "synapse pruning" is not in the GOBP namespace
62 p(HGNC:DKK1)->bp(GOBP:"synapse pruning") "synapse pruning" is not in the GOBP namespace
63 complex(p(HGNC:APP),p(HGNC:LRP6))-> bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: complex(p(HGNC:APP),p(HGNC:LRP6))-> bp(GOBP:"canonical Wnt signaling pathway")
64 complex(p(HGNC:APP),p(HGNC:LRP6))-> bp(GOBP:"non-canonical Wnt signaling pathway") Missing citation; can't add: complex(p(HGNC:APP),p(HGNC:LRP6))-> bp(GOBP:"non-canonical Wnt signaling pathway")
65 complex(p(HGNC:APP),p(HGNC:VANGl2))-> bp(GOBP:"canonical Wnt signaling pathway") "VANGl2" is not in the HGNC namespace
66 complex(p(HGNC:APP),p(HGNC:VANGl2))-> bp(GOBP:"non-canonical Wnt signaling pathway") "VANGl2" is not in the HGNC namespace
73 bp(GOBP:"non-canonical Wnt signaling pathway"))->a(CHEBI:"amyloid-beta") General Parser Failure on line 73 at pos 46: bp(GOBP:"non-canonical Wnt signaling pathway"))->a(CHEBI:"amyloid-beta")
74 bp(GOBP:"canonical Wnt signaling pathway"))-|a(CHEBI:"amyloid-beta") General Parser Failure on line 74 at pos 42: bp(GOBP:"canonical Wnt signaling pathway"))-|a(CHEBI:"amyloid-beta")
75 a(CHEBI:"amyloid-beta")->p(HGNC:DKK1) Missing citation; can't add: a(CHEBI:"amyloid-beta")->p(HGNC:DKK1)
76 a(CHEBI:"amyloid-beta")->bp(GOBP:"non-canonical Wnt signaling pathway") Missing citation; can't add: a(CHEBI:"amyloid-beta")->bp(GOBP:"non-canonical Wnt signaling pathway")
77 a(CHEBI:"amyloid-beta") pos bp(GOBP:"synapse pruning") "synapse pruning" is not in the GOBP namespace
78 bp(GOBP:"non-canonical Wnt signaling pathway") pos bp(GOBP:"synapse pruning") "synapse pruning" is not in the GOBP namespace
79 bp(GOBP:"synapse pruning")->a(CHEBI:"amyloid-beta") "synapse pruning" is not in the GOBP namespace
80 bp(GOBP:"non-canonical Wnt signaling pathway")->a(CHEBI:"amyloid-beta") Missing citation; can't add: bp(GOBP:"non-canonical Wnt signaling pathway")->a(CHEBI:"amyloid-beta")
87 p(HGNC:APP,var("?"))-> bp(GOBP:"non-canonical Wnt signaling pathway")) Missing citation; can't add: p(HGNC:APP,var("?"))-> bp(GOBP:"non-canonical Wnt signaling pathway"))
88 p(HGNC:APP,var("?")) neg bp(GOBP:"canonical Wnt signaling pathway")) Missing citation; can't add: p(HGNC:APP,var("?")) neg bp(GOBP:"canonical Wnt signaling pathway"))
89 p(HGNC:APP,var("?")) pos a(GOCC:synapse) Missing citation; can't add: p(HGNC:APP,var("?")) pos a(GOCC:synapse)
90 p(HGNC:APP,var("?"))->a(CHEBI:"amyloid-beta") Missing citation; can't add: p(HGNC:APP,var("?"))->a(CHEBI:"amyloid-beta")
97 SET Species = "Mus musculus" Missing citation; can't add: SET Species = "Mus musculus"
99 a(CHEMBLA:CHEMBL38380)-|a(CHEBI:"amyloid-beta") Missing citation; can't add: a(CHEMBLA:CHEMBL38380)-|a(CHEBI:"amyloid-beta")
100 a(CHEMBLA:CHEMBL38380)--bp(GOBP:"non-canonical Wnt signaling pathway") Missing citation; can't add: a(CHEMBLA:CHEMBL38380)--bp(GOBP:"non-canonical Wnt signaling pathway")
101 a(CHEMBLA:CHEMBL38380)--bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: a(CHEMBLA:CHEMBL38380)--bp(GOBP:"canonical Wnt signaling pathway")
102 a(CHEBI:"amyloid-beta")--bp(GOBP:"synapse pruning") "synapse pruning" is not in the GOBP namespace
104 UNSET Species Missing citation; can't add: UNSET Species
106 UNSET TextLocation Missing citation; can't add: UNSET TextLocation
108 SET TextLocation = "Result" Missing citation; can't add: SET TextLocation = "Result"
114 SET CellLine = "HEK293A" Missing citation; can't add: SET CellLine = "HEK293A"
115 SET Assay = "Reporter Gene Assays" Missing citation; can't add: SET Assay = "Reporter Gene Assays"
117 p(HGNC:APP)-- bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: p(HGNC:APP)-- bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
119 UNSET CellLine Missing citation; can't add: UNSET CellLine
120 UNSET Assay Missing citation; can't add: UNSET Assay
125 composite(p(HGNC:APP), p(HGNC:WNT3A))->bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: composite(p(HGNC:APP), p(HGNC:WNT3A))->bp(GOBP:"canonical Wnt signaling pathway")
126 composite(p(HGNC:APP), p(HGNC:WNT5A))->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: composite(p(HGNC:APP), p(HGNC:WNT5A))->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
131 complex(p(HGNC:APP),p(HGNC:VANGL2))--bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: complex(p(HGNC:APP),p(HGNC:VANGL2))--bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
132 composite(p(HGNC:APP),p(HGNC:LRP6))--bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: composite(p(HGNC:APP),p(HGNC:LRP6))--bp(GOBP:"canonical Wnt signaling pathway")
138 composite(p(HGNC:APP), p(HGNC:WNT3A))->bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: composite(p(HGNC:APP), p(HGNC:WNT3A))->bp(GOBP:"canonical Wnt signaling pathway")
139 p(HGNC:LRP6) positiveCorrelation bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:LRP6) positiveCorrelation bp(GOBP:"canonical Wnt signaling pathway")
140 p(HGNC:VANGL2) negativeCorrelation bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:VANGL2) negativeCorrelation bp(GOBP:"canonical Wnt signaling pathway")
141 composite(p(HGNC:APP), p(HGNC:WNT5A))->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: composite(p(HGNC:APP), p(HGNC:WNT5A))->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
142 p(HGNC:VANGL2) positiveCorrelation bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: p(HGNC:VANGL2) positiveCorrelation bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
143 p(HGNC:LRP6)negativeCorrelation bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: p(HGNC:LRP6)negativeCorrelation bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
149 p(HGNC:APP)--bp(GOBP:"Wnt signaling pathway") Missing citation; can't add: p(HGNC:APP)--bp(GOBP:"Wnt signaling pathway")
150 bp(GOBP:"Wnt signaling pathway")--bp(GOBP:"synapse organization") Missing citation; can't add: bp(GOBP:"Wnt signaling pathway")--bp(GOBP:"synapse organization")
157 SET CellLine = "HEK293A" Missing citation; can't add: SET CellLine = "HEK293A"
158 SET Assay = "Reporter Gene Assays" Missing citation; can't add: SET Assay = "Reporter Gene Assays"
160 p(HGNC:APP)->bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:APP)->bp(GOBP:"canonical Wnt signaling pathway")
161 p(HGNC:APP)->bp(GOBP:"non-canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:APP)->bp(GOBP:"non-canonical Wnt signaling pathway")
162 p(HGNC:APP,var("p.Lys670Asn"))-|bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:APP,var("p.Lys670Asn"))-|bp(GOBP:"canonical Wnt signaling pathway")
163 p(HGNC:APP,var("p.Met671Leu"))-|bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:APP,var("p.Met671Leu"))-|bp(GOBP:"canonical Wnt signaling pathway")
164 p(HGNC:APP,var("p.Lys670Asn"))->bp(GOBP:"non-canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:APP,var("p.Lys670Asn"))->bp(GOBP:"non-canonical Wnt signaling pathway")
165 p(HGNC:APP,var("p.Met671Leu"))->bp(GOBP:"non-canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:APP,var("p.Met671Leu"))->bp(GOBP:"non-canonical Wnt signaling pathway")
167 UNSET CellLine Missing citation; can't add: UNSET CellLine
168 UNSET Assay Missing citation; can't add: UNSET Assay
174 composite(p(HGNC:LRP6),p(HGNC:APP,var("p.Lys670Asn")))-|bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: composite(p(HGNC:LRP6),p(HGNC:APP,var("p.Lys670Asn")))-|bp(GOBP:"canonical Wnt signaling pathway")
175 composite(p(HGNC:LRP6),p(HGNC:APP,var("p.Met671Leu")))-|bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: composite(p(HGNC:LRP6),p(HGNC:APP,var("p.Met671Leu")))-|bp(GOBP:"canonical Wnt signaling pathway")
176 composite(p(HGNC:LRP6),p(HGNC:APP,var("p.Lys670Asn")))->bp(GOBP:"non-canonical Wnt signaling pathway") Missing citation; can't add: composite(p(HGNC:LRP6),p(HGNC:APP,var("p.Lys670Asn")))->bp(GOBP:"non-canonical Wnt signaling pathway")
177 composite(p(HGNC:LRP6),p(HGNC:APP,var("p.Met671Leu")))->bp(GOBP:"non-canonical Wnt signaling pathway") Missing citation; can't add: composite(p(HGNC:LRP6),p(HGNC:APP,var("p.Met671Leu")))->bp(GOBP:"non-canonical Wnt signaling pathway")
182 p(HGNC:APP,var("p.Val717Leu"))->path (MESHD:"Alzheimer Disease") Missing citation; can't add: p(HGNC:APP,var("p.Val717Leu"))->path (MESHD:"Alzheimer Disease")
183 path(MESHD:"Alzheimer Disease")->a(CHEBI:"amyloid-beta") Missing citation; can't add: path(MESHD:"Alzheimer Disease")->a(CHEBI:"amyloid-beta")
184 p(HGNC:APP,var("p.Lys670Asn"))-|bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:APP,var("p.Lys670Asn"))-|bp(GOBP:"canonical Wnt signaling pathway")
185 p(HGNC:APP,var("p.Met671Leu"))-|bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:APP,var("p.Met671Leu"))-|bp(GOBP:"canonical Wnt signaling pathway")
186 p(HGNC:APP,var("p.Lys670Asn"))->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: p(HGNC:APP,var("p.Lys670Asn"))->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
187 p(HGNC:APP,var("p.Met671Leu"))->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: p(HGNC:APP,var("p.Met671Leu"))->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
194 p(HGNC:WNT3A)-|p(HGNC:APP) Missing citation; can't add: p(HGNC:WNT3A)-|p(HGNC:APP)
195 p(HGNC:WNT3A)->bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:WNT3A)->bp(GOBP:"canonical Wnt signaling pathway")
196 p(HGNC:WNT5A)->p(HGNC:APP) Missing citation; can't add: p(HGNC:WNT5A)->p(HGNC:APP)
197 p(HGNC:WNT5A)->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: p(HGNC:WNT5A)->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
205 composite(r(HGNC:LRP6),r(HGNC:APP))-|a(CHEBI:"amyloid-beta") Missing citation; can't add: composite(r(HGNC:LRP6),r(HGNC:APP))-|a(CHEBI:"amyloid-beta")
206 composite(r(HGNC:VANGL2),r(HGNC:APP))->a(CHEBI:"amyloid-beta") Missing citation; can't add: composite(r(HGNC:VANGL2),r(HGNC:APP))->a(CHEBI:"amyloid-beta")
207 bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") positiveCorrelation a(CHEBI:"amyloid-beta") Missing citation; can't add: bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") positiveCorrelation a(CHEBI:"amyloid-beta")
208 bp(GOBP:"canonical Wnt signaling pathway") negativeCorrelation a(CHEBI:"amyloid-beta") Missing citation; can't add: bp(GOBP:"canonical Wnt signaling pathway") negativeCorrelation a(CHEBI:"amyloid-beta")
216 p(HGNC:DKK1)--bp(GOBP:"Wnt signaling pathway") Missing citation; can't add: p(HGNC:DKK1)--bp(GOBP:"Wnt signaling pathway")
217 p(HGNC:DKK1) positiveCorrelation bp("Aβ synaptotoxicity") [pos:36] "Aβ synaptotoxicity" should be qualified with a valid namespace
218 r(HGNC:APP) negativeCorrelation act(p(HGNC:DKK1)) Missing citation; can't add: r(HGNC:APP) negativeCorrelation act(p(HGNC:DKK1))
219 composite(p(HGNC:DKK1),p(HGNC:WNT3A))-|bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: composite(p(HGNC:DKK1),p(HGNC:WNT3A))-|bp(GOBP:"canonical Wnt signaling pathway")
224 r(HGNC:APP) positiveCorrelation act(p(HGNC:DKK1)) Missing citation; can't add: r(HGNC:APP) positiveCorrelation act(p(HGNC:DKK1))
225 composite(p(HGNC:DKK1),p(HGNC:WNT5A)) ->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: composite(p(HGNC:DKK1),p(HGNC:WNT5A)) ->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
226 composite (p(HGNC:APP),p(HGNC:DKK1))--bp(GOBP:"Wnt signaling pathway") Missing citation; can't add: composite (p(HGNC:APP),p(HGNC:DKK1))--bp(GOBP:"Wnt signaling pathway")
232 p(HGNC:DKK1) -- bp("Aβ synaptotoxicity") [pos:19] "Aβ synaptotoxicity" should be qualified with a valid namespace
233 p(HGNC:APP)-- bp("Aβ synaptotoxicity") [pos:17] "Aβ synaptotoxicity" should be qualified with a valid namespace
234 p(HGNC:APP) -> p(MGI:Dkk1) Missing citation; can't add: p(HGNC:APP) -> p(MGI:Dkk1)
235 p(HGNC:APP) negativeCorrelation bp(GOBP:"canonical Wnt signaling pathway") Missing citation; can't add: p(HGNC:APP) negativeCorrelation bp(GOBP:"canonical Wnt signaling pathway")
236 p(HGNC:APP) positiveCorrelation bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: p(HGNC:APP) positiveCorrelation bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
244 SET CellLine = "HEK293A" Missing citation; can't add: SET CellLine = "HEK293A"
245 SET Dosage = "10 µM" Missing citation; can't add: SET Dosage = "10 µM"
246 SET Assay = "ELISA" Missing citation; can't add: SET Assay = "ELISA"
248 p(HGNC:RHOA)-- bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: p(HGNC:RHOA)-- bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
249 p(HGNC:ROCK1)--bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: p(HGNC:ROCK1)--bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
250 a(CHEMBLA:CHEMBL38380)-|p(HGNC:ROCK1) Missing citation; can't add: a(CHEMBLA:CHEMBL38380)-|p(HGNC:ROCK1)
251 a(CHEMBLA:CHEMBL38380)-|bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") Missing citation; can't add: a(CHEMBLA:CHEMBL38380)-|bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway")
252 a(CHEMBLA:CHEMBL38380) negativeCorrelation path(MESHD:"Vasospasm, Intracranial") Missing citation; can't add: a(CHEMBLA:CHEMBL38380) negativeCorrelation path(MESHD:"Vasospasm, Intracranial")
253 a(CHEMBLA:CHEMBL38380) negativeCorrelation p(HGNC:DKK1) Missing citation; can't add: a(CHEMBLA:CHEMBL38380) negativeCorrelation p(HGNC:DKK1)
254 a(CHEMBLA:CHEMBL38380) negativeCorrelation p(HGNC:VANGL2) Missing citation; can't add: a(CHEMBLA:CHEMBL38380) negativeCorrelation p(HGNC:VANGL2)
256 UNSET CellLine Missing citation; can't add: UNSET CellLine
257 UNSET Dosage Missing citation; can't add: UNSET Dosage
258 UNSET Assay Missing citation; can't add: UNSET Assay
268 SET Species = "Rattus norvegicus" Missing citation; can't add: SET Species = "Rattus norvegicus"
269 SET MeSHAnatomy = "Neurons" Missing citation; can't add: SET MeSHAnatomy = "Neurons"
270 SET Assay = "Multiplex Assay" Missing citation; can't add: SET Assay = "Multiplex Assay"
272 p(RGD:Dkk1)-| a(GOCC:"dendritic spine") Missing citation; can't add: p(RGD:Dkk1)-| a(GOCC:"dendritic spine")
273 p(RGD:Dkk1)->a(CHEBI:"amyloid-beta") Missing citation; can't add: p(RGD:Dkk1)->a(CHEBI:"amyloid-beta")
275 UNSET Species Missing citation; can't add: UNSET Species
276 UNSET MeSHAnatomy Missing citation; can't add: UNSET MeSHAnatomy
277 UNSET Assay Missing citation; can't add: UNSET Assay
281 SET Species = "Rattus norvegicus" Missing citation; can't add: SET Species = "Rattus norvegicus"
282 SET MeSHAnatomy = "Synapses" Missing citation; can't add: SET MeSHAnatomy = "Synapses"
284 p(RGD:Dkk1)->a(CHEBI:"amyloid-beta") Missing citation; can't add: p(RGD:Dkk1)->a(CHEBI:"amyloid-beta")
285 a(CHEMBLA:CHEMBL38380) negativeCorrelation p(RGD:Dkk1) Missing citation; can't add: a(CHEMBLA:CHEMBL38380) negativeCorrelation p(RGD:Dkk1)
287 UNSET Species Missing citation; can't add: UNSET Species
288 UNSET MeSHAnatomy Missing citation; can't add: UNSET MeSHAnatomy
296 a(CHEBI:"amyloid-beta") positiveCorrelation bp(GOBP:"synapse pruning") "synapse pruning" is not in the GOBP namespace
297 p(HGNC:DKK1) positiveCorrelation bp(GOBP:"synapse pruning") "synapse pruning" is not in the GOBP namespace
298 a(CHEBI:"amyloid-beta") positiveCorrelation path(MESHD:"Cognitive Dysfunction") Missing citation; can't add: a(CHEBI:"amyloid-beta") positiveCorrelation path(MESHD:"Cognitive Dysfunction")
299 p(HGNC:DKK1) positiveCorrelation path(MESHD:"Cognitive Dysfunction") Missing citation; can't add: p(HGNC:DKK1) positiveCorrelation path(MESHD:"Cognitive Dysfunction")
300 a(CHEMBLA:CHEMBL38380) negativeCorrelation bp(GOBP:"synapse pruning") "synapse pruning" is not in the GOBP namespace
301 a(CHEMBLA:CHEMBL38380) negativeCorrelation path(MESHD:"Cognitive Dysfunction") Missing citation; can't add: a(CHEMBLA:CHEMBL38380) negativeCorrelation path(MESHD:"Cognitive Dysfunction")
302 a(CHEMBLA:CHEMBL38380) negativeCorrelation act(a(CHEBI:"amyloid-beta")) Missing citation; can't add: a(CHEMBLA:CHEMBL38380) negativeCorrelation act(a(CHEBI:"amyloid-beta"))
303 a(CHEMBLA:CHEMBL38380) negativeCorrelation act(p(HGNC:DKK1)) Missing citation; can't add: a(CHEMBLA:CHEMBL38380) negativeCorrelation act(p(HGNC:DKK1))
305 SET MeSHAnatomy = "Neurons" Missing citation; can't add: SET MeSHAnatomy = "Neurons"
307 composite (a(CHEMBLA:CHEMBL38380),p(MGI:Dkk1)) -| a(CHEBI:"amyloid-beta") Missing citation; can't add: composite (a(CHEMBLA:CHEMBL38380),p(MGI:Dkk1)) -| a(CHEBI:"amyloid-beta")
309 SET Species = "Mus musculus" Missing citation; can't add: SET Species = "Mus musculus"
310 SET MouseStrain = "3xTG-AD" Missing citation; can't add: SET MouseStrain = "3xTG-AD"
312 path(MESHD:"Plaque, Amyloid") -- path (MESHD:"Alzheimer Disease") Missing citation; can't add: path(MESHD:"Plaque, Amyloid") -- path (MESHD:"Alzheimer Disease")
313 bp("Aβ-immunoreactive deposits") -- path (MESHD:"Alzheimer Disease") [pos:3] "Aβ-immunoreactive deposits" should be qualified with a valid namespace
315 UNSET MeSHAnatomy Missing citation; can't add: UNSET MeSHAnatomy
316 UNSET Species Missing citation; can't add: UNSET Species
317 UNSET MouseStrain Missing citation; can't add: UNSET MouseStrain
322 SET Assay = "ELISA" Missing citation; can't add: SET Assay = "ELISA"
324 a(CHEMBLA:CHEMBL38380) negativeCorrelation a(CHEBI:"amyloid-beta") Missing citation; can't add: a(CHEMBLA:CHEMBL38380) negativeCorrelation a(CHEBI:"amyloid-beta")
326 UNSET Assay Missing citation; can't add: UNSET Assay
331 SET Anatomy = "subiculum" Missing citation; can't add: SET Anatomy = "subiculum"
332 SET MeSHAnatomy = "CA1,hippocampal" Missing citation; can't add: SET MeSHAnatomy = "CA1,hippocampal"
333 SET Assay = "IHC" Missing citation; can't add: SET Assay = "IHC"
335 a(CHEMBLA:CHEMBL38380)-| a(CHEBI:"amyloid-beta") Missing citation; can't add: a(CHEMBLA:CHEMBL38380)-| a(CHEBI:"amyloid-beta")
337 UNSET Anatomy Missing citation; can't add: UNSET Anatomy
338 UNSET MeSHAnatomy Missing citation; can't add: UNSET MeSHAnatomy
339 UNSET Assay Missing citation; can't add: UNSET Assay
342 UNSET TextLocation Missing citation; can't add: UNSET TextLocation

Top Warnings

Error Frequency
"synapse pruning" is not in the GOBP namespace 9
Missing citation; can't add: UNSET Assay 6
Missing citation; can't add: UNSET MeSHAnatomy 4
Missing citation; can't add: UNSET Species 4
Missing citation; can't add: UNSET CellLine 3
Missing citation; can't add: SET CellLine = "HEK293A" 3
Missing citation; can't add: p(HGNC:APP,var("p.Met671Leu"))-|bp(GOBP:"canonical Wnt signaling pathway") 2
Missing citation; can't add: UNSET TextLocation 2
Missing citation; can't add: composite(p(HGNC:APP), p(HGNC:WNT5A))->bp(GOBP:"Wnt signaling pathway, planar cell polarity pathway") 2
Missing citation; can't add: a(CHEBI:"amyloid-beta")->bp(GOBP:"non-canonical Wnt signaling pathway") 2
Missing citation; can't add: composite(p(HGNC:APP), p(HGNC:WNT3A))->bp(GOBP:"canonical Wnt signaling pathway") 2
"VANGl2" is not in the HGNC namespace 2
Missing citation; can't add: SET Assay = "ELISA" 2
Missing citation; can't add: p(HGNC:APP,var("p.Lys670Asn"))-|bp(GOBP:"canonical Wnt signaling pathway") 2
Missing citation; can't add: SET Assay = "Reporter Gene Assays" 2
Missing citation; can't add: SET MeSHAnatomy = "Neurons" 2
Missing citation; can't add: SET Species = "Rattus norvegicus" 2
Missing citation; can't add: SET Species = "Mus musculus" 2
Missing citation; can't add: p(RGD:Dkk1)->a(CHEBI:"amyloid-beta") 2

Naked Names 3

Names referenced without a namespace are antithetical to reproducible science and data integration practices. The list of "naked names" can be downloaded here for further use with tools to help find the appropriate names.

Namespaces with Incorrect Names 2

About

BEL Commons is developed and maintained in an academic capacity by Charles Tapley Hoyt and Daniel Domingo-Fernández at the Fraunhofer SCAI Department of Bioinformatics with support from the IMI project, AETIONOMY. It is built on top of the open source project, PyBEL. Please feel free to contact us here to give us feedback or report any issues.