Versions 2

Table of Contents

Namespaces

Unused Namespaces 5

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
  • GOBP
  • HGNC
  • MESHD
  • RGD

Annotations

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

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

Unused Annotations 1

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.

  • Species

Warning Statistics

Syntax Errors 2

Line BEL Message
41 p(HGNC:BDNF, sub(V,66,M)))--path(MESHD:"Stress Disorders") General Parser Failure on line 41 at pos 25: p(HGNC:BDNF, sub(V,66,M)))--path(MESHD:"Stress Disorders")
67 a(CHEBI:malonaldehyde)-|(GOBP:"neuron apoptotic process") General Parser Failure on line 67 at pos 25: a(CHEBI:malonaldehyde)-|(GOBP:"neuron apoptotic process")

All Parser Warnings 15

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

Line BEL Message
34 complex(p(HGNC:MAG),p(HGNC:RTN4RL2))=> act(p(HGNC:RTN4RL2)) Missing citation; can't add: complex(p(HGNC:MAG),p(HGNC:RTN4RL2))=> act(p(HGNC:RTN4RL2))
35 p(HGNC:MAG)->act(p("NGR1")) [pos:19] "NGR1" should be qualified with a valid namespace
41 p(HGNC:BDNF, sub(V,66,M)))--path(MESHD:"Stress Disorders") General Parser Failure on line 41 at pos 25: p(HGNC:BDNF, sub(V,66,M)))--path(MESHD:"Stress Disorders")
48 path(MESHD:"Brain Injuries , Traumatic")causesNOChange a(p(HGNC:ADAM10),a(p(HGNC:PSEN1))) "Brain Injuries , Traumatic" is not in the MESHD namespace
57 SET Species="Rattus norvegicus" Missing citation; can't add: SET Species="Rattus norvegicus"
58 m(HGNC:MIR200A)positiveCorrelation p(HGNC:BAX) Missing citation; can't add: m(HGNC:MIR200A)positiveCorrelation p(HGNC:BAX)
59 m(HGNC:MIR200A)positiveCorrelation p(RGD:Gpx1) Missing citation; can't add: m(HGNC:MIR200A)positiveCorrelation p(RGD:Gpx1)
60 m(HGNC:MIR200A)positiveCorrelation p(RGD:Sod1) Missing citation; can't add: m(HGNC:MIR200A)positiveCorrelation p(RGD:Sod1)
61 m(HGNC:MIR200A)positiveCorrelation a(CHEBI:dopamine) Missing citation; can't add: m(HGNC:MIR200A)positiveCorrelation a(CHEBI:dopamine)
62 m(HGNC:MIR200A)positiveCorrelation a(CHEBI:"3,4-dihydroxyphenylacetic acid") "3,4-dihydroxyphenylacetic acid" is not in the CHEBI namespace
63 m(HGNC:MIR200A)positiveCorrelation a(CHEBI:"homovanillic acid") Missing citation; can't add: m(HGNC:MIR200A)positiveCorrelation a(CHEBI:"homovanillic acid")
65 m(HGNC:MIR200A)-> a(CHEBI:malonaldehyde) Missing citation; can't add: m(HGNC:MIR200A)-> a(CHEBI:malonaldehyde)
66 m(HGNC:MIR200A)-> p(HGNC:BCL2) Missing citation; can't add: m(HGNC:MIR200A)-> p(HGNC:BCL2)
67 a(CHEBI:malonaldehyde)-|(GOBP:"neuron apoptotic process") General Parser Failure on line 67 at pos 25: a(CHEBI:malonaldehyde)-|(GOBP:"neuron apoptotic process")
68 p(HGNC:BCL2)->bp("TH-positive cell number") [pos:17] "TH-positive cell number" should be qualified with a valid namespace

Top Warnings

Error Frequency

Naked Names 2

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.