Versions 4

Table of Contents

Namespaces

Unused Namespaces 2

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.

  • GOBP
  • GOCC

Annotations

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

Keyword URL Stratify
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

Syntax Errors 7

Line BEL Message
102 p(HGNC:NOS3),pmod(P,S,1177)->a(CHEBI: "Nitric oxide") General Parser Failure on line 102 at pos 12: p(HGNC:NOS3),pmod(P,S,1177)->a(CHEBI: "Nitric oxide")
112 p(HGNC:STK11)->(p(HGNC:PRKAA2, pmod(P))) General Parser Failure on line 112 at pos 39: p(HGNC:STK11)->(p(HGNC:PRKAA2, pmod(P)))
146 m(HGNC:MIR133B)))negativeCorrelation path(MESHD:"esophageal squamous cell carcinoma" General Parser Failure on line 146 at pos 15: m(HGNC:MIR133B)))negativeCorrelation path(MESHD:"esophageal squamous cell carcinoma"
147 m(HGNC:MIR133B))negativeCorrelation p(HGNC:EGFR) General Parser Failure on line 147 at pos 15: m(HGNC:MIR133B))negativeCorrelation p(HGNC:EGFR)
148 m(HGNC:MIR133B))negativeCorrelation p(HGNC:ITGB4) General Parser Failure on line 148 at pos 15: m(HGNC:MIR133B))negativeCorrelation p(HGNC:ITGB4)
149 m(HGNC:MIR133B))negativeCorrelation pmod(HGNC:PTK2) General Parser Failure on line 149 at pos 15: m(HGNC:MIR133B))negativeCorrelation pmod(HGNC:PTK2)
150 m(HGNC:MIR133B))-| r(HGNC:EGFR) General Parser Failure on line 150 at pos 15: m(HGNC:MIR133B))-| r(HGNC:EGFR)

All Parser Warnings 19

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

Line BEL Message
56 p(HGNC:CREB1)-> bp(GOBP:"type B pancreatic proliferation") "type B pancreatic proliferation" is not in the GOBP namespace
57 p(HGNC:CREBBP)->bp (GOBP:"type B pancreatic proliferation") "type B pancreatic proliferation" is not in the GOBP namespace
69 complex(p(HGNC:I2NTF), p(HGNC: PPP2CA)) -| phos(p(HGNC:PPP2CA)) "I2NTF" is not in the HGNC namespace
70 complex (p(HGNC:I2CTF), p(HGNC: PPP2CA))-| phos(p(HGNC:PPP2CA)) "I2CTF" is not in the HGNC namespace
94 cat(p(HGNC:NOS3))-> a(CHEBI: "Nitric Oxide") "Nitric Oxide" is not in the CHEBI namespace
101 p(HGNC:PRKAA2)->a(CHEBI:"Nitric Oxide") "Nitric Oxide" is not in the CHEBI namespace
102 p(HGNC:NOS3),pmod(P,S,1177)->a(CHEBI: "Nitric oxide") General Parser Failure on line 102 at pos 12: p(HGNC:NOS3),pmod(P,S,1177)->a(CHEBI: "Nitric oxide")
103 a(CHEBI:"dorsomorphin")-|a(CHEBI:"Nitric oxide") "Nitric oxide" is not in the CHEBI namespace
112 p(HGNC:STK11)->(p(HGNC:PRKAA2, pmod(P))) General Parser Failure on line 112 at pos 39: p(HGNC:STK11)->(p(HGNC:PRKAA2, pmod(P)))
127 complex (p(HGNC:YTHDF1), a(CHEBI:"N6-Methyladenosine"))->bp(GOBP:"learning") "N6-Methyladenosine" is not in the CHEBI namespace
128 complex (p(HGNC:YTHDF1), a(CHEBI:"N6-Methyladenosine"))->bp(GOBP:"memory") "N6-Methyladenosine" is not in the CHEBI namespace
136 path(MESHD:"Neoplasm")negativeCorrelation m(HGNC:MIR133B) "Neoplasm" is not in the MESHD namespace
137 m(HGNC:MIR133B)negativeCorrelation path(MESHD:"Esophageal Squamous Cell Carcinoma") "Esophageal Squamous Cell Carcinoma" is not in the MESHD namespace
145 SET MESHD= "esophageal squamous cell carcinoma" "MESHD" is not defined
146 m(HGNC:MIR133B)))negativeCorrelation path(MESHD:"esophageal squamous cell carcinoma" General Parser Failure on line 146 at pos 15: m(HGNC:MIR133B)))negativeCorrelation path(MESHD:"esophageal squamous cell carcinoma"
147 m(HGNC:MIR133B))negativeCorrelation p(HGNC:EGFR) General Parser Failure on line 147 at pos 15: m(HGNC:MIR133B))negativeCorrelation p(HGNC:EGFR)
148 m(HGNC:MIR133B))negativeCorrelation p(HGNC:ITGB4) General Parser Failure on line 148 at pos 15: m(HGNC:MIR133B))negativeCorrelation p(HGNC:ITGB4)
149 m(HGNC:MIR133B))negativeCorrelation pmod(HGNC:PTK2) General Parser Failure on line 149 at pos 15: m(HGNC:MIR133B))negativeCorrelation pmod(HGNC:PTK2)
150 m(HGNC:MIR133B))-| r(HGNC:EGFR) General Parser Failure on line 150 at pos 15: m(HGNC:MIR133B))-| r(HGNC:EGFR)

Top Warnings

Error Frequency
"Nitric Oxide" is not in the CHEBI namespace 2
"type B pancreatic proliferation" is not in the GOBP namespace 2
"N6-Methyladenosine" is not in the CHEBI namespace 2

Namespaces with Incorrect Names 4

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.