Versions 6

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 4

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.

  • Cell
  • CustomCellLine
  • MeSHAnatomy
  • 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.

Unused Locally Defined Annotations 1

The source BEL script contained the following list annotations, but no references to the following values. It is suggested to prune these values from the list definitions.

Note: this may be due to errors occurring in all statements with these annotations.

Annotation Values
CustomCellLine
  • EA.hy926 cells

Warning Statistics

Syntax Errors 7

Line BEL Message
50 p(HGNC:CREB1))->bp(GOBP:"type B pancreatic cell proliferation") General Parser Failure on line 50 at pos 13: p(HGNC:CREB1))->bp(GOBP:"type B pancreatic cell proliferation")
75 g(HGNC:OPRK1,gmod(M)))--r(HGNC:0PRK1) General Parser Failure on line 75 at pos 21: g(HGNC:OPRK1,gmod(M)))--r(HGNC:0PRK1)
102 p(HGNC:PRKAA2),pmod(P)->kin(p(HGNC:STK11)) General Parser Failure on line 102 at pos 14: p(HGNC:PRKAA2),pmod(P)->kin(p(HGNC:STK11))
104 p(HGNC:PRKAA2),pmod(P)->kin(p(HGNC:CAMKK2)) General Parser Failure on line 104 at pos 14: p(HGNC:PRKAA2),pmod(P)->kin(p(HGNC:CAMKK2))
117 complex(p(HGNC:YTHDF1)),a(CHEBI:"N6-methyladenosine" )->bp(GOBP:learning ) General Parser Failure on line 117 at pos 23: complex(p(HGNC:YTHDF1)),a(CHEBI:"N6-methyladenosine" )->bp(GOBP:learning )
118 complex(p(HGNC:YTHDF1)),a(CHEBI:"N6-methyladenosine" )->bp(GOBP:memory) General Parser Failure on line 118 at pos 23: complex(p(HGNC:YTHDF1)),a(CHEBI:"N6-methyladenosine" )->bp(GOBP:memory)
140 m(HGNC:MIR133B)negativeCorrelation P(HGNC:PTK2,pmod(P)) General Parser Failure on line 140 at pos 35: m(HGNC:MIR133B)negativeCorrelation P(HGNC:PTK2,pmod(P))

All Parser Warnings 17

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

Line BEL Message
50 p(HGNC:CREB1))->bp(GOBP:"type B pancreatic cell proliferation") General Parser Failure on line 50 at pos 13: p(HGNC:CREB1))->bp(GOBP:"type B pancreatic cell proliferation")
61 SET Cell="neurons" "neurons" is not defined in the Cell annotation
63 complex(a(I2NTF),p(HGNC:PTPA))-| phos(p(HGNC:PTPA)) [pos:10] "I2NTF" should be qualified with a valid namespace
64 complex(a(I2CTF),p(HGNC:PTPA))-| phos(p(HGNC:PTPA)) [pos:10] "I2CTF" should be qualified with a valid namespace
65 tloc(p(HGNC:LGMN),GOCC:lysosomes,GOCC:cytoplasm)--complex(p(HGNC:LGMN),p(HGNC:PPP2R1A)) "lysosomes" is not in the GOCC namespace
75 g(HGNC:OPRK1,gmod(M)))--r(HGNC:0PRK1) General Parser Failure on line 75 at pos 21: g(HGNC:OPRK1,gmod(M)))--r(HGNC:0PRK1)
76 r(HGNC:OPRK1)->path(MESHD:"Alzheimer's disease") "Alzheimer's disease" is not in the MESHD namespace
86 SET Custom cell line= "EA.hy926 cells" "Custom" is not defined
102 p(HGNC:PRKAA2),pmod(P)->kin(p(HGNC:STK11)) General Parser Failure on line 102 at pos 14: p(HGNC:PRKAA2),pmod(P)->kin(p(HGNC:STK11))
104 p(HGNC:PRKAA2),pmod(P)->kin(p(HGNC:CAMKK2)) General Parser Failure on line 104 at pos 14: p(HGNC:PRKAA2),pmod(P)->kin(p(HGNC:CAMKK2))
117 complex(p(HGNC:YTHDF1)),a(CHEBI:"N6-methyladenosine" )->bp(GOBP:learning ) General Parser Failure on line 117 at pos 23: complex(p(HGNC:YTHDF1)),a(CHEBI:"N6-methyladenosine" )->bp(GOBP:learning )
118 complex(p(HGNC:YTHDF1)),a(CHEBI:"N6-methyladenosine" )->bp(GOBP:memory) General Parser Failure on line 118 at pos 23: complex(p(HGNC:YTHDF1)),a(CHEBI:"N6-methyladenosine" )->bp(GOBP:memory)
128 path(MESHD:esophageal squamous cell carcinoma)negativeCorrelationm(HGNC:MIR133B) "esophageal" is not in the MESHD namespace
129 m(HGNC:MIR133B)negativeCorrelation path(" esophageal squamous cell carcinoma, malignant") [pos:40] " esophageal squamous cell carcinoma, malignant" should be qualified with a valid namespace
137 path(MESHD:"Esophageal Squamous Cell Carcinoma")-|m(HGNC:MIR133B) "Esophageal Squamous Cell Carcinoma" is not in the MESHD namespace
139 m(HGNC:MIR133B)negativeCorrelation p(HGNC:IGB4) "IGB4" is not in the HGNC namespace
140 m(HGNC:MIR133B)negativeCorrelation P(HGNC:PTK2,pmod(P)) General Parser Failure on line 140 at pos 35: m(HGNC:MIR133B)negativeCorrelation P(HGNC:PTK2,pmod(P))

Top Warnings

Error Frequency

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.