Table of Contents

Namespaces

Unused Namespaces 6

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.

  • CHEMBLA
  • GOBP
  • GOCC
  • HGNC
  • MESHD
  • 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 8

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

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

Warning Statistics

All Parser Warnings 64

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

Line BEL Message
60 SET SpeciesNames = "Mus musculus" "SpeciesNames" is not defined
64 SET Confidence = "very high" "Confidence" is not defined
68 UNSET Confidence "Confidence" is not defined
71 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i3)) "CHEMBLID" is not a defined namespace
77 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i3)) "CHEMBLID" is not a defined namespace
79 SET Confidence = "very high" "Confidence" is not defined
83 UNSET Confidence "Confidence" is not defined
92 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i2)) "CHEMBLID" is not a defined namespace
98 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i3)) "CHEMBLID" is not a defined namespace
100 SET Confidence = "very high" "Confidence" is not defined
104 UNSET Confidence "Confidence" is not defined
113 UNSET Confidence "Confidence" is not defined
116 SET Confidence = "very high" "Confidence" is not defined
118 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i3)) "CHEMBLID" is not a defined namespace
121 UNSET Confidence "Confidence" is not defined
126 SET Confidence = "very high" "Confidence" is not defined
130 UNSET Confidence "Confidence" is not defined
137 SET Confidence = "very high" "Confidence" is not defined
138 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i3)) "CHEMBLID" is not a defined namespace
140 UNSET Confidence "Confidence" is not defined
150 SET SpeciesNames = "Homo sapiens" "SpeciesNames" is not defined
151 SET Cell = "hepatocyte" "Cell" is not defined
157 SET Confidence = "very high" "Confidence" is not defined
164 UNSET Confidence "Confidence" is not defined
173 SET MeSHDisease = "no disease" "MeSHDisease" is not defined
202 SET Confidence = "very high" "Confidence" is not defined
208 UNSET Confidence "Confidence" is not defined
214 SET Confidence = "very high" "Confidence" is not defined
219 UNSET Confidence "Confidence" is not defined
226 SET Confidence = "very high" "Confidence" is not defined
232 UNSET Confidence "Confidence" is not defined
234 UNSET STATEMENT_GROUP "STATEMENT_GROUP" is not set, so it can't be unset
235 SET SpeciesNames = "Mus musculus" "SpeciesNames" is not defined
239 SET Confidence = "very high" "Confidence" is not defined
243 UNSET Confidence "Confidence" is not defined
246 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i3)) "CHEMBLID" is not a defined namespace
252 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i3)) "CHEMBLID" is not a defined namespace
254 SET Confidence = "very high" "Confidence" is not defined
258 UNSET Confidence "Confidence" is not defined
267 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i2)) "CHEMBLID" is not a defined namespace
273 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i3)) "CHEMBLID" is not a defined namespace
275 SET Confidence = "very high" "Confidence" is not defined
279 UNSET Confidence "Confidence" is not defined
288 UNSET Confidence "Confidence" is not defined
291 SET Confidence = "very high" "Confidence" is not defined
293 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i3)) "CHEMBLID" is not a defined namespace
296 UNSET Confidence "Confidence" is not defined
301 SET Confidence = "very high" "Confidence" is not defined
305 UNSET Confidence "Confidence" is not defined
312 SET Confidence = "very high" "Confidence" is not defined
313 a(CHEMBLID:CHEMBL488803) => act(p(MGI:Nr1i3)) "CHEMBLID" is not a defined namespace
315 UNSET Confidence "Confidence" is not defined
325 SET SpeciesNames = "Homo sapiens" "SpeciesNames" is not defined
326 SET Cell = "hepatocyte" "Cell" is not defined
332 SET Confidence = "very high" "Confidence" is not defined
339 UNSET Confidence "Confidence" is not defined
348 SET MeSHDisease = "no disease" "MeSHDisease" is not defined
377 SET Confidence = "very high" "Confidence" is not defined
383 UNSET Confidence "Confidence" is not defined
389 SET Confidence = "very high" "Confidence" is not defined
394 UNSET Confidence "Confidence" is not defined
401 SET Confidence = "very high" "Confidence" is not defined
407 UNSET Confidence "Confidence" is not defined
409 UNSET STATEMENT_GROUP "STATEMENT_GROUP" is not set, so it can't be unset

Top Warnings

Error Frequency
"Confidence" is not defined 42
"CHEMBLID" is not a defined namespace 12
"SpeciesNames" is not defined 4
"Cell" is not defined 2
"MeSHDisease" is not defined 2
"STATEMENT_GROUP" is not set, so it can't be unset 2

Undefined Namespaces 1

The source BEL script contained references to the following namespaces, but they were never defined. Click the links to download them as enumerated namespaces, and update the BEL script accordingly.

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.