Versions 3

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
  • MESHD
  • MGI
  • RGD

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

Warning Statistics

Syntax Errors 1

Line BEL Message
50 p(MGI:Gsk3b)->(MGI:Mapt, pmod(P)) General Parser Failure on line 50 at pos 15: p(MGI:Gsk3b)->(MGI:Mapt, pmod(P))

All Parser Warnings 28

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

Line BEL Message
40 SET Citation={"PubMed"," Cell Physiol. 2018 Dec 3. doi: 10.1002/jcp.27709."} [pos:4] " Cell Physiol. 2018 Dec 3. doi: 10.1002/jcp.27709." is not a valid PubMed identifier
44 SET Species:"Mus musculus" Missing citation; can't add: SET Species:"Mus musculus"
45 SET MeSHAnatomy="Hippocampus" Missing citation; can't add: SET MeSHAnatomy="Hippocampus"
46 p(MGI:Grk5)negativeCorrelation path(MESHD:"Cognitive Dysfunction") Missing citation; can't add: p(MGI:Grk5)negativeCorrelation path(MESHD:"Cognitive Dysfunction")
47 p(MGI:Grk5)negativeCorrelation path("Alzheimer-like pathology") [pos:36] "Alzheimer-like pathology" should be qualified with a valid namespace
48 p(MGI:Grk5)negativeCorrelation p(MGI:Mapt, pmod(P)) Missing citation; can't add: p(MGI:Grk5)negativeCorrelation p(MGI:Mapt, pmod(P))
49 p(MGI:Grk5)->p(MGI:Gsk3b)(MGI:Mapt, pmod(P)) Missing citation; can't add: p(MGI:Grk5)->p(MGI:Gsk3b)(MGI:Mapt, pmod(P))
50 p(MGI:Gsk3b)->(MGI:Mapt, pmod(P)) General Parser Failure on line 50 at pos 15: p(MGI:Gsk3b)->(MGI:Mapt, pmod(P))
51 p(MGI:Grk5)-|p(MGI:Gsk3b) Missing citation; can't add: p(MGI:Grk5)-|p(MGI:Gsk3b)
52 p(MGI:Grk5)-| p(MGI:Gsk3b) Missing citation; can't add: p(MGI:Grk5)-| p(MGI:Gsk3b)
53 p(MGI:Grk5)-|path(MESHD:"Alzheimer Disease") Missing citation; can't add: p(MGI:Grk5)-|path(MESHD:"Alzheimer Disease")
55 SET Citation={"PubMed","Int J Mol Sci. 2018 Nov 22;19(12). pii: ijms19123716. doi: 10.3390/ijms19123716."} [pos:4] "Int J Mol Sci. 2018 Nov 22;19(12). pii: ijms19123716. doi: 10.3390/ijms19123716." is not a valid PubMed identifier
60 p(RGD:Arc)->bp(GOBP:"long-term memory") Missing citation; can't add: p(RGD:Arc)->bp(GOBP:"long-term memory")
61 p(RGD:Egr1)->bp(GOBP:"long-term memory") Missing citation; can't add: p(RGD:Egr1)->bp(GOBP:"long-term memory")
62 bp(GOBP:"chemical synaptic transmission")positiveCorrelation p(RGD:Arc) Missing citation; can't add: bp(GOBP:"chemical synaptic transmission")positiveCorrelation p(RGD:Arc)
63 bp(GOBP:"chemical synaptic transmission")positiveCorrelation p(RGD:Egr1) Missing citation; can't add: bp(GOBP:"chemical synaptic transmission")positiveCorrelation p(RGD:Egr1)
64 bp(GOBP:"cAMP-dependent protein kinase activity")-- p(RGD:Arc) "cAMP-dependent protein kinase activity" is not in the GOBP namespace
65 bp(GOBP:"cAMP-dependent protein kinase activity")--p(RGD:Egr1) "cAMP-dependent protein kinase activity" is not in the GOBP namespace
66 bp(GOBP:"response to cAMP")--p (RGD:Arc) Missing citation; can't add: bp(GOBP:"response to cAMP")--p (RGD:Arc)
67 bp(GOBP:"response to cAMP")--p(RGD:Egr1) Missing citation; can't add: bp(GOBP:"response to cAMP")--p(RGD:Egr1)
68 p(RGD:Arc)->p(RGD:Prkaa1) Missing citation; can't add: p(RGD:Arc)->p(RGD:Prkaa1)
69 p(RGD:Egr1)->p(RGD:Prkaa1) Missing citation; can't add: p(RGD:Egr1)->p(RGD:Prkaa1)
70 p(RGD:Prkaa1)->bp(GOBP:"chemical synaptic transmission") Missing citation; can't add: p(RGD:Prkaa1)->bp(GOBP:"chemical synaptic transmission")
71 p(RGD:Prkaa1)->p(RGD:Arc),p(RGD:Egr1) Missing citation; can't add: p(RGD:Prkaa1)->p(RGD:Arc),p(RGD:Egr1)
72 p(RGD:Arc)->bp(GOBP:"learning") Missing citation; can't add: p(RGD:Arc)->bp(GOBP:"learning")
73 p(RGD:Egr1)->bp(GOBP:"learning") Missing citation; can't add: p(RGD:Egr1)->bp(GOBP:"learning")
74 p(RGD:Arc)->bp(GOBP:"memory") Missing citation; can't add: p(RGD:Arc)->bp(GOBP:"memory")
75 p(RGD:Egr1)->bp(GOBP:"memory") Missing citation; can't add: p(RGD:Egr1)->bp(GOBP:"memory")

Top Warnings

Error Frequency
"cAMP-dependent protein kinase activity" is not in the GOBP namespace 2

Naked Names 1

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 1

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.