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
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

Syntax Errors 1

Line BEL Message
50 act(p(HGNC:LGMN)) -> loc(p(HGNC:SET), GOCC:nucleus, GOCC:cytoplasm) General Parser Failure on line 50 at pos 21: act(p(HGNC:LGMN)) -> loc(p(HGNC:SET), GOCC:nucleus, GOCC:cytoplasm)

All Parser Warnings 12

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

Line BEL Message
35 p(HNGC:CREB1) -> bp(GOBP:"type B pancreatic cell proliferation") "HNGC" is not a defined namespace
36 p(HNGC:CREBBP) -> bp(GOBP:"type B pancreatic cell proliferation") "HNGC" is not a defined namespace
48 complex(a(I2CTF),p(HGNC:PPP2CA)) -| phos(p(HGNC:PPP2CA) [pos:10] "I2CTF" should be qualified with a valid namespace
50 act(p(HGNC:LGMN)) -> loc(p(HGNC:SET), GOCC:nucleus, GOCC:cytoplasm) General Parser Failure on line 50 at pos 21: act(p(HGNC:LGMN)) -> loc(p(HGNC:SET), GOCC:nucleus, GOCC:cytoplasm)
74 cat(p(HGNC:NOS3)) -> a(CHEBI:"nitic oxide") "nitic oxide" is not in the CHEBI namespace
81 a(CHEBI:dorsomorphin) -| a(CHEBI:"nitic oxide") "nitic oxide" is not in the CHEBI namespace
102 complex(p(HGNC:YTHDFI),a(CHEBI:"N6-methyladenosine")) -> bp(GOBP:learning) "YTHDFI" is not in the HGNC namespace
103 complex(p(HGNC:YTHDFI),a(CHEBI:"N6-methyladenosine")) -> bp(GOBP:memory) "YTHDFI" is not in the HGNC namespace
112 path(MESHD:"Esophageal Squamous Cell Carcinoma")negativeCorrelation m(HGNC:MIR133B) "Esophageal Squamous Cell Carcinoma" is not in the MESHD namespace
113 path("Esophageal Squamous Cell Carcinoma, malignant") negativeCorrelation m(HGNC:MIR133B) [pos:5] "Esophageal Squamous Cell Carcinoma, malignant" should be qualified with a valid namespace
120 SET MeSHDisease = "Esophageal Squamous Cell Carcinoma" "Esophageal Squamous Cell Carcinoma" is not defined in the MeSHDisease annotation
121 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
"nitic oxide" is not in the CHEBI namespace 2
"HNGC" is not a defined namespace 2
"YTHDFI" is not in the HGNC namespace 2

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.

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 3

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.