Versions 7

Table of Contents

Namespaces

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

AFFX
http://resources.openbel.org/belframework/20150611/namespace/affy-probeset-ids.belns
CHEBI
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/chebi/chebi-20170511.belns
CHEBIID
http://resources.openbel.org/belframework/20150611/namespace/chebi-ids.belns
CHEMBL
http://belief.scai.fraunhofer.de/openbel/repository/namespaces/chembl-names.belns
CHEMBLID
http://belief.scai.fraunhofer.de/openbel/repository/namespaces/chembl-ids.belns
DO
http://resources.openbel.org/belframework/20150611/namespace/disease-ontology.belns
DOID
http://resources.openbel.org/belframework/20150611/namespace/disease-ontology-ids.belns
EGID
http://resources.openbel.org/belframework/20150611/namespace/entrez-gene-ids.belns
GFAM
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/hgnc-gene-families/hgnc-gene-families-20170430.belns
GOBP
http://resources.openbel.org/belframework/20150611/namespace/go-biological-process.belns
GOBPID
http://resources.openbel.org/belframework/20150611/namespace/go-biological-process-ids.belns
GOCC
http://resources.openbel.org/belframework/20150611/namespace/go-cellular-component.belns
GOCCID
http://resources.openbel.org/belframework/20150611/namespace/go-cellular-component-ids.belns
HGNC
http://resources.openbel.org/belframework/20150611/namespace/hgnc-human-genes.belns
LMSD
http://belief.scai.fraunhofer.de/openbel/repository/namespaces/LMSD.belns
MESHC
http://resources.openbel.org/belframework/20150611/namespace/mesh-chemicals.belns
MESHCID
http://resources.openbel.org/belframework/20150611/namespace/mesh-chemicals-ids.belns
MESHCS
http://resources.openbel.org/belframework/20150611/namespace/mesh-cellular-structures.belns
MESHCSID
http://resources.openbel.org/belframework/20150611/namespace/mesh-cellular-structures-ids.belns
MESHD
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh-diseases/mesh-diseases-20170511.belns
MESHDID
http://resources.openbel.org/belframework/20150611/namespace/mesh-diseases-ids.belns
MESHPP
http://resources.openbel.org/belframework/20150611/namespace/mesh-processes.belns
MESHPPID
http://resources.openbel.org/belframework/20150611/namespace/mesh-processes-ids.belns
MGI
http://resources.openbel.org/belframework/20150611/namespace/mgi-mouse-genes.belns
MeSH
https://raw.githubusercontent.com/pharmacome/terminology/01c9daa61012b37dd0a1bc962521ba51a15b38f1/external/mesh-names.belns
PH
http://belief.scai.fraunhofer.de/openbel/repository/namespaces/Placeholder.belns
PMIBP
http://belief.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/pmibp.belns
PMICHEM
http://belief.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/pmichem.belns
PMICOMP
http://belief.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/pmicomp.belns
PMIDIS
http://belief.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/pmidis.belns
PMIPFAM
http://belief.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/pmipfam.belns
RGD
http://resources.openbel.org/belframework/20150611/namespace/rgd-rat-genes.belns
SCHEM
http://resources.openbel.org/belframework/20150611/namespace/selventa-legacy-chemicals.belns
SCOMP
http://resources.openbel.org/belframework/20150611/namespace/selventa-named-complexes.belns
SDIS
http://resources.openbel.org/belframework/20150611/namespace/selventa-legacy-diseases.belns
SFAM
http://resources.openbel.org/belframework/20150611/namespace/selventa-protein-families.belns
SP
http://resources.openbel.org/belframework/20150611/namespace/swissprot.belns
SPID
http://resources.openbel.org/belframework/20150611/namespace/swissprot-ids.belns
ZFIN
http://belief.scai.fraunhofer.de/openbel/repository/namespaces/zfin-zebrafish-genes.belns

Unused Namespaces 20

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.

  • AFFX
  • CHEBIID
  • CHEMBL
  • DOID
  • GOBPID
  • GOCCID
  • LMSD
  • MESHCID
  • MESHCS
  • MESHCSID
  • MESHDID
  • MESHPPID
  • PMIBP
  • PMICHEM
  • PMICOMP
  • PMIDIS
  • PMIPFAM
  • SP
  • SPID
  • ZFIN

Annotations

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

Keyword URL Stratify
Anatomy http://resources.openbel.org/belframework/20150611/annotation/anatomy.belanno View Stratified Summary
Cell http://resources.openbel.org/belframework/20150611/annotation/cell.belanno View Stratified Summary
CellLine https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell-line/cell-line-20170511.belanno View Stratified Summary
CellStructure http://resources.openbel.org/belframework/20150611/annotation/cell-structure.belanno View Stratified Summary
Disease http://resources.openbel.org/belframework/20150611/annotation/disease.belanno View Stratified Summary
Eco http://belief.scai.fraunhofer.de/openbel/repository/annotation/evidence.belanno View Stratified Summary
MeSHAnatomy http://resources.openbel.org/belframework/20150611/annotation/mesh-anatomy.belanno View Stratified Summary
MeSHDisease http://resources.openbel.org/belframework/20150611/annotation/mesh-diseases.belanno View Stratified Summary
Species http://belief.scai.fraunhofer.de/openbel/repository/annotation/ncbi-taxonomy-id.belanno View Stratified Summary
SpeciesNames http://belief.scai.fraunhofer.de/openbel/repository/annotation/ncbi-taxonomy-names.belanno View Stratified Summary

Unused Annotations 14

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.

  • BRCO
  • Condition
  • Developmental_Phase__of_patient
  • DiseaseState
  • Duration_of_Chemical_Exposure
  • Encode_Feature_Types
  • Experimental_Group
  • FDASTATUS
  • KnockoutMice
  • NIFT
  • Patient
  • Transcriptionally_active_region
  • UserdefinedCell
  • UserdefinedCellLine

Locally Defined Annotations 40

Unused Locally Defined Annotations 18

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
BRCO
  • Parietal_Lobe
  • Striatum
  • Frontal_cortex
  • Hippocampus
  • Temporal_Lobe
  • Occipital_cortex
  • Cerebellum
Condition
  • Normal Healthy State
Confidence
  • high
  • medium
  • low
  • very low
Developmental_Phase__of_patient
  • Developmental stage
  • Old
  • Young
  • Adolescence
  • Adult
DiseaseState
  • Early-onset AD
  • Mild AD
  • Moderate AD
  • Pre-dementia
  • Late-onset AD
Duration_of_Chemical_Exposure
  • Chronic
  • Subchronic
Encode_Feature_Types
  • Promoter
  • Enhancer
  • CTCF
  • TF binding site
  • Open chromatin
  • Promoter Flanking Region
Experimental_Group
  • Sedentary group
  • Physical exercised group
FDASTATUS
  • Phase 2
  • Phase 3
  • Phase 1
  • Phase 2/3
  • Approved
  • Inactive
  • Phase 4
  • Discontinued
KnockoutMice
  • IDE KO mice
  • INSR knockout mice
  • LID mice
  • GLP1 KO mice
  • IRS1 KO mice
  • KO Mapk8ip1
  • IGF1 KO mice
  • NIRKO mice
  • App transgenic
  • IRS2 KO mice
NIFT
  • Volumetric MRI
  • Positron Emission Tomography
Pathway
  • MEK-ERK pathway
  • Colorectal cancer pathway
  • Wnt/beta-catenin pathway
  • EGFR pathway
  • PI3K/AKT signaling
  • Wnt signaling pathway
Patient
  • APOE e4 -ve
  • AD T2DM -ve
  • AD T2DM +ve
  • APOE e4 +ve
Race
  • Swedish
  • Colombian
  • silhouettes women
  • Chinese
  • White
  • non-Hispanic black
  • Black
  • Taiwanese
  • non-Hispanic white
  • Han Chinese in Taiwan
  • Han Chinese in Singapore
  • Hispanic
  • US women
  • Caucasian
  • Japanese
  • Italian
TisueType
  • cancerous
Transcriptionally_active_region
  • intron 1
  • 5 prime UTR
  • 3 prime UTR
  • exon 3
  • exon 41
UserdefinedCell
  • Beta cell
  • Astrocyte
  • Islets
UserdefinedCellLine
  • primary neuron
  • IDE APP transgenic
  • N2a695 cell
  • Neuroblastoma cell
  • 293APPwt
  • App transgenic
  • CHOAPPsw
  • INS-1 cells
  • primary cortical neuron
  • NT2N cells

Warning Statistics

Syntax Errors 1

Line BEL Message
3069 g(HGNC:PIK3CA, sub(E, 545, K)) -- path(MESHD:Neoplasms) General Parser Failure on line 3069 at pos 13: g(HGNC:PIK3CA, sub(E, 545, K)) -- path(MESHD:Neoplasms)

All Parser Warnings 49

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

Line BEL Message
3069 g(HGNC:PIK3CA, sub(E, 545, K)) -- path(MESHD:Neoplasms) General Parser Failure on line 3069 at pos 13: g(HGNC:PIK3CA, sub(E, 545, K)) -- path(MESHD:Neoplasms)
3650 a(XGFR) -| p(HGNC:EGFR,pmod(P)) [pos:2] "XGFR" should be qualified with a valid namespace
3651 a(XGFR) -| p(HGNC:IGF1R,pmod(P)) [pos:2] "XGFR" should be qualified with a valid namespace
3654 a(XGFR) -| bp(GOBP:"cell growth") [pos:2] "XGFR" should be qualified with a valid namespace
3663 a(XGFR) -| path(MESHD:"Pancreatic Neoplasms") [pos:2] "XGFR" should be qualified with a valid namespace
3723 a("MM-1151") -| path(MESHD:"Colorectal Neoplasms") [pos:2] "MM-1151" should be qualified with a valid namespace
4110 a("mAb198.3") -| p(HGNC:FAT1) [pos:2] "mAb198.3" should be qualified with a valid namespace
4114 a("mAb198.3") -| bp(GOBP:"cell growth") [pos:2] "mAb198.3" should be qualified with a valid namespace
4248 a("K-756") -| p(HGNC:TNKS) [pos:2] "K-756" should be qualified with a valid namespace
4261 a("K-756") -| bp(GOBP:"Wnt signaling pathway") [pos:2] "K-756" should be qualified with a valid namespace
5601 r(fus(HGNC:RET,"?",HGNC:KIF5B,"?")) -- path(DO:"lung adenocarcinoma") [pos:2] "fus" should be qualified with a valid namespace
7038 a("Mab#58") -- a("HER3/RH7777 cells") [pos:2] "Mab#58" should be qualified with a valid namespace
7048 a("Mab#58") biomarkerFor path(MESHD:"Colorectal Neoplasms") [pos:2] "Mab#58" should be qualified with a valid namespace
7182 a(AIIB2) =| p(HGNC:ITGB1) [pos:2] "AIIB2" should be qualified with a valid namespace
7192 complex(a(MeSH:Cetuximab),a(AIIB2)) -- bp(MESHPP:"MAP Kinase Signaling System") [pos:28] "AIIB2" should be qualified with a valid namespace
7193 complex(a(MeSH:Cetuximab),a(AIIB2)) -- kin(p(HGNC:MAPK8)) [pos:28] "AIIB2" should be qualified with a valid namespace
7194 complex(a(MeSH:Cetuximab),a(AIIB2)) -- kin(p(HGNC:AKT1)) [pos:28] "AIIB2" should be qualified with a valid namespace
7198 a(AIIB2) -- bp(MESHPP:"MAP Kinase Signaling System") [pos:2] "AIIB2" should be qualified with a valid namespace
7199 a(AIIB2) -- kin(p(HGNC:MAPK8)) [pos:2] "AIIB2" should be qualified with a valid namespace
7200 a(AIIB2) -- kin(p(HGNC:AKT1)) [pos:2] "AIIB2" should be qualified with a valid namespace
7208 a(AIIB2) -| path(MESHD:"Neoplasm Invasiveness") [pos:2] "AIIB2" should be qualified with a valid namespace
8990 a("ruthenacycles") -| bp(GOBP:"cell growth") [pos:2] "ruthenacycles" should be qualified with a valid namespace
8995 a("ruthenacycles") -> sec(p(HGNC:IFNG)) [pos:2] "ruthenacycles" should be qualified with a valid namespace
8996 a("ruthenacycles") -| sec(p(HGNC:CCL5)) [pos:2] "ruthenacycles" should be qualified with a valid namespace
8997 a("ruthenacycles") -| sec(p(HGNC:IGF1)) [pos:2] "ruthenacycles" should be qualified with a valid namespace
9002 a("ruthenacycles") -- p(RPS21) [pos:2] "ruthenacycles" should be qualified with a valid namespace
9003 a("ruthenacycles") -- bp(GOBP:"regulation of cytokine secretion") [pos:2] "ruthenacycles" should be qualified with a valid namespace
9032 a("VGX-100") =| p(HGNC:VEGFC)) [pos:2] "VGX-100" should be qualified with a valid namespace
9033 composite(a("VGX-100"),a(MeSH:Bevacizumab)) =| p(HGNC:KDR) [pos:12] "VGX-100" should be qualified with a valid namespace
9034 composite(a("VGX-100"),a(MeSH:Bevacizumab)) =| p(HGNC:FLT4) [pos:12] "VGX-100" should be qualified with a valid namespace
9056 a("MM-1151") -| bp(GOBP:"cell growth") [pos:2] "MM-1151" should be qualified with a valid namespace
9057 a("MM-1151") -| path(MESHD:"Colorectal Neoplasms") [pos:2] "MM-1151" should be qualified with a valid namespace
9058 a("MM-1151") -| path(MESHD:"Neoplasm Invasiveness") [pos:2] "MM-1151" should be qualified with a valid namespace
9059 a("MM-1151") -> a(MeSH:Cetuximab) [pos:2] "MM-1151" should be qualified with a valid namespace
9114 p(HGNC:TP53) -> a("p53 antibody") [pos:18] "p53 antibody" should be qualified with a valid namespace
9120 a("p53 antibody") biomarkerFor path(MESHD:"colorectal cancer") [pos:2] "p53 antibody" should be qualified with a valid namespace
9127 composite(a(MeSH:Bevacizumab),a(CHEBI:"5-formyltetrahydrofolic acid"),a(CHEBI:"5-fluorouracil"), a(CHEBI:oxaliplatin)) -| p("CA19-9") [pos:124] "CA19-9" should be qualified with a valid namespace
9133 composite(a(MeSH:Bevacizumab),a(CHEBI:"5-formyltetrahydrofolic acid"),a(CHEBI:"5-fluorouracil"), a(CHEBI:oxaliplatin)) -| a("p53 antibody") [pos:124] "p53 antibody" should be qualified with a valid namespace
9138 a("p53 antibody") biomarkerFor path("tumor recurrence") [pos:2] "p53 antibody" should be qualified with a valid namespace
9585 g(HGNC:FCGR1CP) -- bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity") "FCGR1CP" is not in the HGNC namespace
9837 a(CHEBI:"irinotecan") causesNoChange a("DEBIRI") [pos:39] "DEBIRI" should be qualified with a valid namespace
9838 a("DEBIRI") -| path(MESHD:"Drug-Related Side Effects and Adverse Reactions") [pos:2] "DEBIRI" should be qualified with a valid namespace
11202 a(CHEBI:sulindac) -| tloc(p(HGNC:CTNNB1)) [pos:25] Unqualified translocation: a(CHEBI:sulindac) -| tloc(p(HGNC:CTNNB1)) [['Protein', 'HGNC', 'CTNNB1']]
11894 a(EHT6706) -- bp(MESHPP:Polymerization) [pos:2] "EHT6706" should be qualified with a valid namespace
11895 a(EHT6706) -| complex(GOCC:microtubule) [pos:2] "EHT6706" should be qualified with a valid namespace
11902 a(EHT6706) -| bp(GOBP:"cell growth") [pos:2] "EHT6706" should be qualified with a valid namespace
11907 a(EHT6706) -| bp(GOBP:"cell migration") [pos:2] "EHT6706" should be qualified with a valid namespace
11911 a(EHT6706) -| bp(GOBP:angiogenesis) [pos:2] "EHT6706" should be qualified with a valid namespace
12067 composite(a(CHEBI:parthenolide),a(CHEBI:"5-fluorouracil")) -> tloc(p(HGNC:CYCS)) [pos:66] Unqualified translocation: composite(a(CHEBI:parthenolide),a(CHEBI:"5-fluorouracil")) -> tloc(p(HGNC:CYCS)) [['Protein', 'HGNC', 'CYCS']]

Top Warnings

Error Frequency
[pos:2] "ruthenacycles" should be qualified with a valid namespace 6
[pos:2] "EHT6706" should be qualified with a valid namespace 5
[pos:2] "AIIB2" should be qualified with a valid namespace 5
[pos:2] "MM-1151" should be qualified with a valid namespace 5
[pos:2] "XGFR" should be qualified with a valid namespace 4
[pos:28] "AIIB2" should be qualified with a valid namespace 3
[pos:2] "K-756" should be qualified with a valid namespace 2
[pos:2] "p53 antibody" should be qualified with a valid namespace 2
[pos:2] "Mab#58" should be qualified with a valid namespace 2
[pos:12] "VGX-100" should be qualified with a valid namespace 2
[pos:2] "mAb198.3" should be qualified with a valid namespace 2

Naked Names 13

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.