Table of Contents

Namespaces

Unused Namespaces 1

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.

  • GOCC

Annotations

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

Keyword URL Stratify
Cell https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell/cell-20170511.belanno View Stratified Summary
MeSHAnatomy https://arty.scai.fraunhofer.de/artifactory/bel/annotation/mesh-anatomy/mesh-anatomy-20170511.belanno View Stratified Summary
MeSHDisease https://arty.scai.fraunhofer.de/artifactory/bel/annotation/mesh-diseases/mesh-diseases-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 3

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.

  • MeSHAnatomy
  • MeSHDisease
  • Species

Locally Defined Annotations 1

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

All Parser Warnings 8

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

Line BEL Message
48 complex(a(I2CTF),p(HGNC:PPP2CA)) -| phos(p(HGNC:PPP2CA) [pos:10] "I2CTF" should be qualified with a valid namespace
102 complex(p(HGNC:YTHDF1),a(CHEBI:"N6-methyladenosine")) -> bp(GOBP:learning) "N6-methyladenosine" is not in the CHEBI namespace
103 complex(p(HGNC:YTHDF1),a(CHEBI:"N6-methyladenosine")) -> bp(GOBP:memory) "N6-methyladenosine" is not in the CHEBI namespace
111 SET MeSHDisease = "Esophageal Squamous Cell Carcinoma" "Esophageal Squamous Cell Carcinoma" is not defined in the MeSHDisease annotation
113 path(MESHD:"Esophageal Squamous Cell Carcinoma")negativeCorrelation m(HGNC:MIR133B) "Esophageal Squamous Cell Carcinoma" is not in the MESHD namespace
114 path(MESHD:"Esophageal Squamous Cell Carcinoma, malignant") negativeCorrelation m(HGNC:MIR133B) "Esophageal Squamous Cell Carcinoma, malignant" is not in the MESHD namespace
121 SET MeSHDisease = "Esophageal Squamous Cell Carcinoma" "Esophageal Squamous Cell Carcinoma" is not defined in the MeSHDisease annotation
122 path(MESHD:"Esophageal Squamous Cell Carcinoma") neg m(HGNC:MIR133B) #Every disease do not affect miRNA levels "Esophageal Squamous Cell Carcinoma" is not in the MESHD namespace

Top Warnings

Error Frequency
"Esophageal Squamous Cell Carcinoma" is not in the MESHD namespace 2
"N6-methyladenosine" is not in the CHEBI namespace 2
"Esophageal Squamous Cell Carcinoma" is not defined in the MeSHDisease 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.

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.