Versions 3

Table of Contents

Namespaces

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 2

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.

  • Disease
  • 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.

Warning Statistics

Syntax Errors 1

Line BEL Message
47 SET Disease: "Alzheimer's disease" General Parser Failure on line 47 at pos 11: SET Disease: "Alzheimer's disease"

All Parser Warnings 24

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

Line BEL Message
47 SET Disease: "Alzheimer's disease" General Parser Failure on line 47 at pos 11: SET Disease: "Alzheimer's disease"
54 UNSET Disease "Disease" is not set, so it can't be unset
60 bp(GOBP:"canonical Wnt signaling pathway")-> bp(FIXME:"synapse stability") "FIXME" is not a defined 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
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
97 SET Species = "Mus musculus" "Mus musculus" is not defined in the Species annotation
102 a(CHEBI:"amyloid-beta")--bp(GOBP:"synapse pruning") "synapse pruning" is not in the GOBP namespace
104 UNSET Species "Species" is not set, so it can't be unset
217 p(HGNC:DKK1) positiveCorrelation bp(FIXME:"Aβ synaptotoxicity") "FIXME" is not a defined namespace
232 p(HGNC:DKK1) -- bp(FIXME:"Aβ synaptotoxicity") "FIXME" is not a defined namespace
233 p(HGNC:APP)-- bp(FIXME:"Aβ synaptotoxicity") "FIXME" is not a defined namespace
268 SET Species = "Rattus norvegicus" "Rattus norvegicus" is not defined in the Species annotation
275 UNSET Species "Species" is not set, so it can't be unset
281 SET Species = "Rattus norvegicus" "Rattus norvegicus" is not defined in the Species annotation
287 UNSET Species "Species" is not set, so it can't be unset
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
300 a(CHEMBLA:CHEMBL38380) negativeCorrelation bp(GOBP:"synapse pruning") "synapse pruning" is not in the GOBP namespace
309 SET Species = "Mus musculus" "Mus musculus" is not defined in the Species annotation
313 bp("Aβ-immunoreactive deposits") -- path (MESHD:"Alzheimer Disease") [pos:3] "Aβ-immunoreactive deposits" should be qualified with a valid namespace
316 UNSET Species "Species" is not set, so it can't be unset

Top Warnings

Error Frequency
"synapse pruning" is not in the GOBP namespace 9
"FIXME" is not a defined namespace 4
"Species" is not set, so it can't be unset 4
"Rattus norvegicus" is not defined in the Species annotation 2
"Mus musculus" is not defined in the Species annotation 2

Naked Names 1

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.

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.

Namespaces with Incorrect Names 1

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.