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
Anatomy https://arty.scai.fraunhofer.de/artifactory/bel/annotation/anatomy/anatomy-20170511.belanno View Stratified Summary
CellLine https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell-line/cell-line-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
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 6

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.

  • Anatomy
  • CellLine
  • Disease
  • 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 9

Line BEL Message
74 g((HGNC:OPRK1),gmod(M)) -> r(HGNC:OPRK1) General Parser Failure on line 74 at pos 2: g((HGNC:OPRK1),gmod(M)) -> r(HGNC:OPRK1)
91 p(HGNC:PRKAA2)->(HGNC:TNF) General Parser Failure on line 91 at pos 17: p(HGNC:PRKAA2)->(HGNC:TNF)
103 p(HGNC:TNF) -> p((HGNC:STK11,pmod(P)) General Parser Failure on line 103 at pos 17: p(HGNC:TNF) -> p((HGNC:STK11,pmod(P))
104 p(HGNC:TNF) -> p((HGNC:CAMKK2,pmod(P)) General Parser Failure on line 104 at pos 17: p(HGNC:TNF) -> p((HGNC:CAMKK2,pmod(P))
105 p(HGNC:STK11,pmod(P)))->kin(p(HGNC:STK11)) General Parser Failure on line 105 at pos 21: p(HGNC:STK11,pmod(P)))->kin(p(HGNC:STK11))
106 p(HGNC:CAMKK2,pmod(P)))->kin(p(HGNC:CAMKK2)) General Parser Failure on line 106 at pos 22: p(HGNC:CAMKK2,pmod(P)))->kin(p(HGNC:CAMKK2))
150 m(HGNC:MIR133B)neg(p(HGNC:EGFR) General Parser Failure on line 150 at pos 18: m(HGNC:MIR133B)neg(p(HGNC:EGFR)
151 m(HGNC:MIR133B)neg(p(HGNC:IIGB4)) General Parser Failure on line 151 at pos 18: m(HGNC:MIR133B)neg(p(HGNC:IIGB4))
152 m(HGNC:MIR133B)neg p((HGNC:PTK2)pmod(p)) General Parser Failure on line 152 at pos 21: m(HGNC:MIR133B)neg p((HGNC:PTK2)pmod(p))

All Parser Warnings 28

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

Line BEL Message
41 p(HGNC:IRS1)-> p(HGNC:PI3K) "PI3K" is not in the HGNC namespace
42 p(HGNC:IRS2)-> p(HGNC:PI3K) "PI3K" is not in the HGNC namespace
43 p(HGNC:PI3K)->p(HGNC:AKT) "PI3K" is not in the HGNC namespace
44 p(HGNC:AKT)->p(HGNC:CREB1) "AKT" is not in the HGNC namespace
45 p(HGNC:AKT)->p(HGNC:CREBBP) "AKT" is not in the HGNC namespace
46 p(HGNC:CREB1)-> bp(GOBP:"type B pancreaic cell proliferation") "type B pancreaic cell proliferation" is not in the GOBP namespace
47 p(HGNC:CREBBP) -> bp(GOBP:"type B pancreaic cell proliferation") "type B pancreaic cell proliferation" is not in the GOBP namespace
58 SET Disease = "Alzheimer Disease" "Alzheimer Disease" is not defined in the Disease annotation
59 SET Anatomy = "Brain" "Brain" is not defined in the Anatomy annotation
61 complex(a(I2NTF),p(HGNC:PPP2CA))-|phos(p(HGNC:PPP2CA)) [pos:10] "I2NTF" should be qualified with a valid namespace
62 complex(a(I2CTF),p(HGNC:PPP2CA))-|phos(p(HGNC:PTPA)) [pos:10] "I2CTF" should be qualified with a valid namespace
74 g((HGNC:OPRK1),gmod(M)) -> r(HGNC:OPRK1) General Parser Failure on line 74 at pos 2: g((HGNC:OPRK1),gmod(M)) -> r(HGNC:OPRK1)
91 p(HGNC:PRKAA2)->(HGNC:TNF) General Parser Failure on line 91 at pos 17: p(HGNC:PRKAA2)->(HGNC:TNF)
103 p(HGNC:TNF) -> p((HGNC:STK11,pmod(P)) General Parser Failure on line 103 at pos 17: p(HGNC:TNF) -> p((HGNC:STK11,pmod(P))
104 p(HGNC:TNF) -> p((HGNC:CAMKK2,pmod(P)) General Parser Failure on line 104 at pos 17: p(HGNC:TNF) -> p((HGNC:CAMKK2,pmod(P))
105 p(HGNC:STK11,pmod(P)))->kin(p(HGNC:STK11)) General Parser Failure on line 105 at pos 21: p(HGNC:STK11,pmod(P)))->kin(p(HGNC:STK11))
106 p(HGNC:CAMKK2,pmod(P)))->kin(p(HGNC:CAMKK2)) General Parser Failure on line 106 at pos 22: p(HGNC:CAMKK2,pmod(P)))->kin(p(HGNC:CAMKK2))
118 SET Species="Mus musculus" "Mus musculus" is not defined in the Species annotation
121 complex(p(HGNC:YTHDF1,a(CHEBI:N6-methyladenosine)))-> bp(GOBP:learning) [pos:8] "p" should be qualified with a valid namespace
122 complex(p(HGNC:YTHDF1,a(CHEBI:N6-methyladenosine)))-> bp(GOBP:memory) [pos:8] "p" should be qualified with a valid namespace
134 SET MeSHDisease = "Esophageal Squamous Cell Carcinoma" "Esophageal Squamous Cell Carcinoma" is not defined in the MeSHDisease annotation
136 path(MESHD:"Esophageal Squamous Cell Carcinoma") neg m(HGNC:MIR133B) "Esophageal Squamous Cell Carcinoma" is not in the MESHD namespace
137 m(HGNC:MIR133B)neg path(MESHD:"Esophageal Squamous Cell Carcinoma,malignant") "Esophageal Squamous Cell Carcinoma,malignant" is not in the MESHD namespace
146 SET MeSHDisease = "Esophageal Squamous Cell Carcinoma" "Esophageal Squamous Cell Carcinoma" is not defined in the MeSHDisease annotation
149 path(MESHD:"Esophageal Squamous Cell Carcinoma")neg m(HGNC:MIR133B) "Esophageal Squamous Cell Carcinoma" is not in the MESHD namespace
150 m(HGNC:MIR133B)neg(p(HGNC:EGFR) General Parser Failure on line 150 at pos 18: m(HGNC:MIR133B)neg(p(HGNC:EGFR)
151 m(HGNC:MIR133B)neg(p(HGNC:IIGB4)) General Parser Failure on line 151 at pos 18: m(HGNC:MIR133B)neg(p(HGNC:IIGB4))
152 m(HGNC:MIR133B)neg p((HGNC:PTK2)pmod(p)) General Parser Failure on line 152 at pos 21: m(HGNC:MIR133B)neg p((HGNC:PTK2)pmod(p))

Top Warnings

Error Frequency
"PI3K" is not in the HGNC namespace 3
"AKT" is not in the HGNC namespace 2
"Esophageal Squamous Cell Carcinoma" is not defined in the MeSHDisease annotation 2
"Esophageal Squamous Cell Carcinoma" is not in the MESHD namespace 2
[pos:8] "p" should be qualified with a valid namespace 2
"type B pancreaic cell proliferation" is not in the GOBP namespace 2

Naked Names 3

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 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.