Table of Contents

Namespaces

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

ADO
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/alzheimer-disease-ontology/alzheimer-disease-ontology-1.0.2.belns
BRCO
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/brain-region-ontology/brain-region-ontology-1.0.0.belns
CA
http://belief-ptsd.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/ca.belns
CBP
http://belief-ptsd.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/cbp.belns
CCHE
http://belief-ptsd.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/cche.belns
CHEBI
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/chebi/chebi-20170511.belns
DO
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/disease-ontology/disease-ontology-20170511.belns
GFAM
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/hgnc-gene-families/hgnc-gene-families-20170430.belns
GOBP
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/go-biological-process/go-biological-process-20170511.belns
GOCC
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/go-cellular-component/go-cellular-component-20170511.belns
HGNC
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/hgnc-human-genes/hgnc-human-genes-20170511.belns
HP
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/hp/hp-20170724.belns
MESHC
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh-chemicals/mesh-chemicals-20170511.belns
MESHCS
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh-cell-structures/mesh-cell-structures-20170511.belns
MESHD
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh-diseases/mesh-diseases-20170511.belns
MESHPP
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mesh-processes/mesh-processes-20170511.belns
MGI
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/mgi-mouse-genes/mgi-mouse-genes-20170511.belns
NIFT
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/imaging-ontology/imaging-ontology-1.0.0.belns
PMIBP
http://belief-demo.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/pmibp.belns
PMICHEM
http://belief-demo.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/pmichem.belns
PMICOMP
http://belief-demo.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/pmicomp.belns
PMIDIS
http://belief-demo.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/pmidis.belns
PMIPFAM
http://belief-demo.scai.fraunhofer.de/BeliefDashboard/dicten/namespaces/pmipfam.belns
PTS
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/neurodegeneration-pathways/neurodegeneration-pathways-1.0.0.belns
RGD
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/rgd-rat-genes/rgd-rat-genes-20170511.belns
SCOMP
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/selventa-named-complexes/selventa-named-complexes-20170511.belns
SFAM
https://arty.scai.fraunhofer.de/artifactory/bel/namespace/selventa-protein-families/selventa-protein-families-20170511.belns

Unused Namespaces 19

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.

  • ADO
  • BRCO
  • CA
  • CBP
  • CCHE
  • dbSNP
  • GOCC
  • HP
  • MESHCS
  • MGI
  • NIFT
  • PMIBP
  • PMICHEM
  • PMICOMP
  • PMIDIS
  • PMIPFAM
  • PTS
  • RGD
  • SFAM

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
Cell https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell/cell-20170511.belanno View Stratified Summary
CellLine https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell-line/cell-line-20170511.belanno View Stratified Summary
CellStructure https://arty.scai.fraunhofer.de/artifactory/bel/annotation/cell-structure/cell-structure-20170511.belanno View Stratified Summary
Confidence https://arty.scai.fraunhofer.de/artifactory/bel/annotation/confidence/confidence-1.0.0.belanno View Stratified Summary
Disease https://arty.scai.fraunhofer.de/artifactory/bel/annotation/disease/disease-20170511.belanno View Stratified Summary
Gender https://arty.scai.fraunhofer.de/artifactory/bel/annotation/gender/gender-1.0.0.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
Subgraph https://arty.scai.fraunhofer.de/artifactory/bel/annotation/neurommsig/neurommsig-1.0.1.belanno View Stratified Summary

Unused Annotations 22

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
  • BRCO
  • Cell
  • CellStructure
  • Condition
  • Confidence
  • Developmental_Phase__of_patient
  • DiseaseState
  • Duration_of_Chemical_Exposure
  • Encode_Feature_Types
  • Experimental_Group
  • FDASTATUS
  • Gender
  • KnockoutMice
  • MeSHAnatomy
  • NIFT
  • Patient
  • Race
  • Subgraph
  • Transcriptionally_active_region
  • UserdefinedCell
  • UserdefinedCellLine

Locally Defined Annotations 22

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 15

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
  • Striatum
  • Parietal_Lobe
  • Frontal_cortex
  • Hippocampus
  • Temporal_Lobe
  • Occipital_cortex
  • Cerebellum
Condition
  • Normal Healthy State
Developmental_Phase__of_patient
  • Developmental stage
  • Old
  • Adult
  • Adolescence
  • Young
DiseaseState
  • Early-onset AD
  • Late-onset AD
  • Moderate AD
  • Pre-dementia
  • Mild 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
Patient
  • APOE e4 -ve
  • AD T2DM -ve
  • AD T2DM +ve
  • APOE e4 +ve
Race
  • Swedish
  • Colombian
  • White
  • silhouettes women
  • Chinese
  • non-Hispanic black
  • Black
  • Taiwanese
  • non-Hispanic white
  • Han Chinese in Taiwan
  • Han Chinese in Singapore
  • Hispanic
  • US women
  • Japanese
  • Caucasian
  • Italian
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
  • App transgenic
  • 293APPwt
  • CHOAPPsw
  • primary cortical neuron
  • INS-1 cells
  • NT2N cells

Warning Statistics

All Parser Warnings 192

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

Line BEL Message
135 a("cancer stem cells") -- path(MESHD:"Cell Transformation, Neoplastic") [pos:2] "cancer stem cells" should be qualified with a valid namespace
136 a("cancer stem cells") -- path(MESHD:"Neoplasm Metastasis") [pos:2] "cancer stem cells" should be qualified with a valid namespace
157 tscript(p(HGNC:ERBB3)) -- a("survival rate") [pos:28] "survival rate" should be qualified with a valid namespace
158 p(HGNC:ERBB3) -> a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
174 a("Mab#58") -- a("HER3/RH7777 cells") [pos:2] "Mab#58" should be qualified with a valid namespace
184 a("Mab#58") biomarkerFor path(MESHD:"Colorectal Neoplasms") [pos:2] "Mab#58" should be qualified with a valid namespace
205 a("cancer stem cells") -- bp(GOBP:"cell growth") [pos:2] "cancer stem cells" should be qualified with a valid namespace
206 a("cancer stem cells") -- path(MESHD:"Neoplasm Metastasis") [pos:2] "cancer stem cells" should be qualified with a valid namespace
207 a("cancer stem cells") -- bp(GOBP:"cell migration") [pos:2] "cancer stem cells" should be qualified with a valid namespace
208 a("cancer stem cells") -- path(MESHD:"Cell Transformation, Neoplastic") [pos:2] "cancer stem cells" should be qualified with a valid namespace
217 a("cancer stem cells") -- p(HGNC:CD44) [pos:2] "cancer stem cells" should be qualified with a valid namespace
218 a("cancer stem cells") -- p(HGNC:PROM1) [pos:2] "cancer stem cells" should be qualified with a valid namespace
219 a("cancer stem cells") -- p(HGNC:CD24) [pos:2] "cancer stem cells" should be qualified with a valid namespace
220 a("cancer stem cells") -- p(HGNC:EPCAM) [pos:2] "cancer stem cells" should be qualified with a valid namespace
221 a("cancer stem cells") -- p(HGNC:LGR5) [pos:2] "cancer stem cells" should be qualified with a valid namespace
222 a("cancer stem cells") -- p(HGNC:ALDH1A1) [pos:2] "cancer stem cells" should be qualified with a valid namespace
223 a("cancer stem cells") -- p(HGNC:BMI1) [pos:2] "cancer stem cells" should be qualified with a valid namespace
248 p(HGNC:DAPK1) negativeCorrelation a("Tumor buds") [pos:36] "Tumor buds" should be qualified with a valid namespace
250 p(HGNC:DAPK1) -| a("survival rate") [pos:19] "survival rate" should be qualified with a valid namespace
299 deg(complex(p(HGNC:ITGB1),p(HGNC:EGFR))) -> a("radiosensitivity") [pos:46] "radiosensitivity" should be qualified with a valid namespace
300 p(HGNC:ITGB1) -> a("radiosensitivity") [pos:19] "radiosensitivity" should be qualified with a valid namespace
301 p(HGNC:EGFR) -> a("radiosensitivity") [pos:18] "radiosensitivity" should be qualified with a valid namespace
318 a(AIIB2) =| p(HGNC:ITGB1) [pos:2] "AIIB2" should be qualified with a valid namespace
319 a(TAE226) =| p(HGNC:PTK2) [pos:2] "TAE226" should be qualified with a valid namespace
320 a(TAE226) =| p(HGNC:PTK2) [pos:2] "TAE226" should be qualified with a valid namespace
321 a(Cetuximab) =| p(HGNC:EGFR) [pos:2] "Cetuximab" should be qualified with a valid namespace
323 deg(complex(p(HGNC:ITGB1),p(HGNC:EGFR))) causesNoChange a("radiosensitivity") [pos:58] "radiosensitivity" should be qualified with a valid namespace
324 deg(p(HGNC:BRAF)) causesNoChange a("radiosensitivity") [pos:35] "radiosensitivity" should be qualified with a valid namespace
325 deg(p(HGNC:KRAS)) causesNoChange a("radiosensitivity") [pos:35] "radiosensitivity" should be qualified with a valid namespace
326 a(CHEBI:"5-fluorouracil") causesNoChange a("radiosensitivity") [pos:43] "radiosensitivity" should be qualified with a valid namespace
328 complex(a(Cetuximab),a(AIIB2)) -- bp(MESHPP:"MAP Kinase Signaling System") [pos:10] "Cetuximab" should be qualified with a valid namespace
329 complex(a(Cetuximab),a(AIIB2)) -- kin(p(HGNC:MAPK8)) [pos:10] "Cetuximab" should be qualified with a valid namespace
330 complex(a(Cetuximab),a(AIIB2)) -- kin(p(HGNC:AKT1)) [pos:10] "Cetuximab" should be qualified with a valid namespace
331 a(Cetuximab) -- bp(MESHPP:"MAP Kinase Signaling System") [pos:2] "Cetuximab" should be qualified with a valid namespace
332 a(Cetuximab) -- kin(p(HGNC:MAPK8)) [pos:2] "Cetuximab" should be qualified with a valid namespace
333 a(Cetuximab) -- kin(p(HGNC:AKT1)) [pos:2] "Cetuximab" should be qualified with a valid namespace
334 a(AIIB2) -- bp(MESHPP:"MAP Kinase Signaling System") [pos:2] "AIIB2" should be qualified with a valid namespace
335 a(AIIB2) -- kin(p(HGNC:MAPK8)) [pos:2] "AIIB2" should be qualified with a valid namespace
336 a(AIIB2) -- kin(p(HGNC:AKT1)) [pos:2] "AIIB2" should be qualified with a valid namespace
344 a(AIIB2) -| path(MESHD:"Neoplasm Invasiveness") [pos:2] "AIIB2" should be qualified with a valid namespace
345 a(TAE226) -| path(MESHD:"Neoplasm Invasiveness") [pos:2] "TAE226" should be qualified with a valid namespace
346 a(TAE226) -| path(MESHD:"Neoplasm Invasiveness") [pos:2] "TAE226" should be qualified with a valid namespace
361 deg(p(HGNC:HGF)) -| bp("Chemoresistance") [pos:23] "Chemoresistance" should be qualified with a valid namespace
367 complex(a("anti-HGF"),a(CHEBI:"Irinotecan")) => a("Irinotecan sensitivity") [pos:10] "anti-HGF" should be qualified with a valid namespace
382 complex(a(anti-HGF),a(CHEBI:"Irinotecan")) =| bp(GOBP:"cell growth") [pos:10] "anti" should be qualified with a valid namespace
384 p(HGNC:HGF) biomarkerFor bp("Chemoresistance") [pos:28] "Chemoresistance" should be qualified with a valid namespace
385 p(HGNC:HGF) -> bp("Chemoresistance") [pos:18] "Chemoresistance" should be qualified with a valid namespace
386 p(HGNC:HGF) -| a("Irinotecan sensitivity") [pos:17] "Irinotecan sensitivity" should be qualified with a valid namespace
387 a("anti-HGF") -| p(HGNC:HGF) [pos:2] "anti-HGF" should be qualified with a valid namespace
388 a("anti-HGF") -| bp("Chemoresistance") [pos:2] "anti-HGF" should be qualified with a valid namespace
417 p(HGNC:KRAS) -> a("anti-EGFR resistance") [pos:18] "anti-EGFR resistance" should be qualified with a valid namespace
418 p(HGNC:NRAS) -> a("anti-EGFR resistance") [pos:18] "anti-EGFR resistance" should be qualified with a valid namespace
426 p(HGNC:KRAS) -- a("Cetuximab resistance") [pos:18] "Cetuximab resistance" should be qualified with a valid namespace
427 p(HGNC:KRAS) -- a("panitumumab resistance") [pos:18] "panitumumab resistance" should be qualified with a valid namespace
428 p(HGNC:PIK3CA) -- a("Cetuximab resistance") [pos:20] "Cetuximab resistance" should be qualified with a valid namespace
429 p(HGNC:PIK3CA) -- a("panitumumab resistance") [pos:20] "panitumumab resistance" should be qualified with a valid namespace
430 p(HGNC:BRAF) -- a("Cetuximab resistance") [pos:18] "Cetuximab resistance" should be qualified with a valid namespace
431 p(HGNC:BRAF) -- a("panitumumab resistance") [pos:18] "panitumumab resistance" should be qualified with a valid namespace
432 p(HGNC:ERBB2) -- a("Cetuximab resistance") [pos:19] "Cetuximab resistance" should be qualified with a valid namespace
433 p(HGNC:ERBB2) -- a("panitumumab resistance") [pos:19] "panitumumab resistance" should be qualified with a valid namespace
434 p(HGNC:MET) -- a("Cetuximab resistance") [pos:17] "Cetuximab resistance" should be qualified with a valid namespace
435 p(HGNC:MET) -- a("panitumumab resistance") [pos:17] "panitumumab resistance" should be qualified with a valid namespace
444 p(HGNC:ERBB3) -> a("anti-EGFR resistance") [pos:19] "anti-EGFR resistance" should be qualified with a valid namespace
445 p(HGNC:MET) -> a("anti-EGFR resistance") [pos:17] "anti-EGFR resistance" should be qualified with a valid namespace
446 p(HGNC:TGFA) -> a("anti-EGFR resistance") [pos:18] "anti-EGFR resistance" should be qualified with a valid namespace
447 p(HGNC:HGF) -> a("anti-EGFR resistance") [pos:17] "anti-EGFR resistance" should be qualified with a valid namespace
465 a("miRNA-497") biomarkerFor a("neoadjuvant sensitivity") [pos:2] "miRNA-497" should be qualified with a valid namespace
466 a("miRNA-497") -| p(HGNC:SMURF1) [pos:2] "miRNA-497" should be qualified with a valid namespace
467 p(HGNC:SMURF1) positiveCorrelation a("5-fluorouracil resistance") [pos:37] "5-fluorouracil resistance" should be qualified with a valid namespace
468 a("miRNA-497") negativeCorrelation a("neoadjuvant") [pos:2] "miRNA-497" should be qualified with a valid namespace
469 deg(a("miRNA-497")) -> a("5-fluorouracil resistance") [pos:6] "miRNA-497" should be qualified with a valid namespace
470 deg(a("miRNA-497")) -> a("neoadjuvant") [pos:6] "miRNA-497" should be qualified with a valid namespace
479 a("miRNA-497") -- a(CHEBI:"5-fluorouracil") [pos:2] "miRNA-497" should be qualified with a valid namespace
480 a("miRNA-497") -| a("5-fluorouracil resistance") [pos:2] "miRNA-497" should be qualified with a valid namespace
481 a("miRNA-497") -| a("chemoresistance") [pos:2] "miRNA-497" should be qualified with a valid namespace
491 deg(a("miRNA-497")) -> bp(GOBP:"cell growth") [pos:6] "miRNA-497" should be qualified with a valid namespace
492 deg(a("miRNA-497")) -> a("5-fluorouracil resistance") [pos:6] "miRNA-497" should be qualified with a valid namespace
508 path(MESHD:"Rectal Neoplasms") positiveCorrelation bp("Chemoresistance") [pos:54] "Chemoresistance" should be qualified with a valid namespace
518 kin(p(HGNC:PIK3CA)) positiveCorrelation bp("Chemoresistance") [pos:43] "Chemoresistance" should be qualified with a valid namespace
519 kin(p(HGNC:PIK3CA)) positiveCorrelation a("neoadjuvant resistance") [pos:42] "neoadjuvant resistance" should be qualified with a valid namespace
533 p(HGNC:IL17A) -> a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
562 a("therapy resistance") -| bp(GOBP:"apoptotic process") [pos:2] "therapy resistance" should be qualified with a valid namespace
570 p(HGNC:BCL2L1) causesNoChange a("survival rate") [pos:32] "survival rate" should be qualified with a valid namespace
571 p(HGNC:MCL1) causesNoChange a("survival rate") [pos:30] "survival rate" should be qualified with a valid namespace
572 p(HGNC:BCL2) -- a("survival rate") [pos:18] "survival rate" should be qualified with a valid namespace
573 deg(p(HGNC:BCL2)) -> a("survival rate") [pos:23] "survival rate" should be qualified with a valid namespace
597 p(HGNC:BRAF) -- a("therapy resistance") [pos:18] "therapy resistance" should be qualified with a valid namespace
655 kin(p(HGNC:AKT1,pmod(P,S,473))) -- a("therapy resistance") [pos:37] "therapy resistance" should be qualified with a valid namespace
715 a("hypoxia") -> a("therapy resistance") [pos:2] "hypoxia" should be qualified with a valid namespace
762 a("tumor microenvironment") -- a("therapy resistance") [pos:2] "tumor microenvironment" should be qualified with a valid namespace
763 a("tumor microenvironment") -- path(MESHD:"Neoplasm Invasiveness") [pos:2] "tumor microenvironment" should be qualified with a valid namespace
764 a("tumor microenvironment") -- path(MESHD:"Neoplasm Metastasis") [pos:2] "tumor microenvironment" should be qualified with a valid namespace
768 SET Citation = {"PubMed","Anticancer Res. 2014 Feb;34(2):845-50.",""} [pos:4] "" is not a valid PubMed identifier
777 a(CHEBI:"capecitabine") -> a("Survival Rate") [pos:29] "Survival Rate" should be qualified with a valid namespace
778 a(CHEBI:"gemcitabine") -> a("Survival Rate") [pos:28] "Survival Rate" should be qualified with a valid namespace
795 p(HGNC:KRAS) -- bp("anti-EGFR therapy resistance") [pos:19] "anti-EGFR therapy resistance" should be qualified with a valid namespace
796 p(HGNC:BRAF) -- bp("anti-EGFR therapy resistance") [pos:19] "anti-EGFR therapy resistance" should be qualified with a valid namespace
797 p(HGNC:NRAS) -- bp("anti-EGFR therapy resistance") [pos:19] "anti-EGFR therapy resistance" should be qualified with a valid namespace
798 p(HGNC:PIK3CA) -- bp("anti-EGFR therapy resistance") [pos:21] "anti-EGFR therapy resistance" should be qualified with a valid namespace
799 p(HGNC:ERCC1) -- bp("therapy resistance") [pos:20] "therapy resistance" should be qualified with a valid namespace
800 p(HGNC:MET) -- bp("therapy resistance") [pos:18] "therapy resistance" should be qualified with a valid namespace
801 p(HGNC:PTEN) -- bp("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
802 p(HGNC:ERBB2) -- bp("therapy resistance") [pos:20] "therapy resistance" should be qualified with a valid namespace
803 p(HGNC:ERBB3) -- bp("therapy resistance") [pos:20] "therapy resistance" should be qualified with a valid namespace
810 p(HGNC:KRAS) biomarkerFor bp("anti-EGFR therapy resistance") [pos:29] "anti-EGFR therapy resistance" should be qualified with a valid namespace
811 p(HGNC:BRAF) biomarkerFor bp("anti-EGFR therapy resistance") [pos:29] "anti-EGFR therapy resistance" should be qualified with a valid namespace
812 p(HGNC:NRAS) biomarkerFor bp("anti-EGFR therapy resistance") [pos:29] "anti-EGFR therapy resistance" should be qualified with a valid namespace
813 p(HGNC:PIK3CA) biomarkerFor bp("anti-EGFR therapy resistance") [pos:31] "anti-EGFR therapy resistance" should be qualified with a valid namespace
814 p(HGNC:ERCC1) biomarkerFor bp("therapy resistance") [pos:30] "therapy resistance" should be qualified with a valid namespace
815 p(HGNC:MET) biomarkerFor bp("therapy resistance") [pos:28] "therapy resistance" should be qualified with a valid namespace
816 p(HGNC:PTEN) biomarkerFor bp("therapy resistance") [pos:29] "therapy resistance" should be qualified with a valid namespace
817 p(HGNC:ERBB2) biomarkerFor bp("therapy resistance") [pos:30] "therapy resistance" should be qualified with a valid namespace
818 p(HGNC:ERBB3) biomarkerFor bp("therapy resistance") [pos:30] "therapy resistance" should be qualified with a valid namespace
857 a(GSH-PX) hasMember list(p(HGNC:GPX1),p(HGNC:GPX2),p(HGNC:GPX3),p(HGNC:GPX4),p(HGNC:GPX6)) [pos:2] "GSH" should be qualified with a valid namespace
858 a(CHEBI:"Salinomycin") -| a(GSH-PX) [pos:28] "GSH" should be qualified with a valid namespace
902 a(CHEBI:"oxaliplatin") -> a("DNA cross-links") [pos:28] "DNA cross-links" should be qualified with a valid namespace
903 a(CHEBI:"oxaliplatin") -> a("chemoresistance") [pos:28] "chemoresistance" should be qualified with a valid namespace
926 m("miR-27b") negativeCorrelation path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-27b" should be qualified with a valid namespace
927 m("miR-27b") -| path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-27b" should be qualified with a valid namespace
928 m("miR-27b") -| bp(GOBP:"cell growth") [pos:2] "miR-27b" should be qualified with a valid namespace
929 m("miR-27b") -| p(HGNC:VEGFC) [pos:2] "miR-27b" should be qualified with a valid namespace
930 m("miR-27b") -| bp(GOBP:"angiogenesis") [pos:2] "miR-27b" should be qualified with a valid namespace
931 g("miR-27b",) -| tscript(m("miR-27b")) #MI: I don't see how to express something as CpG islands [pos:2] "miR-27b" should be qualified with a valid namespace
932 m("miR-27b") -> bp(MESHPP:Necrosis) [pos:2] "miR-27b" should be qualified with a valid namespace
982 p(HGNC:SLC29A1) positiveCorrelation a("5-fluorouracil resistance") [pos:38] "5-fluorouracil resistance" should be qualified with a valid namespace
983 deg(p(HGNC:SLC29A1)) -| a("5-fluorouracil resistance") [pos:26] "5-fluorouracil resistance" should be qualified with a valid namespace
1000 p(HGNC:RAD51) negativeCorrelation a("survival rate") [pos:36] "survival rate" should be qualified with a valid namespace
1014 a(MLH) hasMember list(p(HGNC:MLH1),p(HGNC:PMS1),p(HGNC:MLH3),p(HGNC:PMS2)) [pos:2] "MLH" should be qualified with a valid namespace
1015 p(HGNC:RAD51) negativeCorrelation a(MHL) [pos:36] "MHL" should be qualified with a valid namespace
1034 p(HGNC:GSN) negativeCorrelation a("survival rate") [pos:34] "survival rate" should be qualified with a valid namespace
1035 p(HGNC:GSN) positiveCorrelation a("therapy resistance") [pos:34] "therapy resistance" should be qualified with a valid namespace
1089 p(HGNC:BIRC5) -> a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
1099 m("survivin-miRNA") =| p(HGNC:BIRC5) [pos:2] "survivin-miRNA" should be qualified with a valid namespace
1100 m("survivin-miRNA") -| a("therapy resistance") [pos:2] "survivin-miRNA" should be qualified with a valid namespace
1170 a("cancer stem cells") -> bp(GOBP:"cell growth") [pos:2] "cancer stem cells" should be qualified with a valid namespace
1187 a("cancer stem cells") -- path(MESHD:"Cell Transformation, Neoplastic") [pos:2] "cancer stem cells" should be qualified with a valid namespace
1188 a("cancer stem cells") -- bp(GOBP:"cell growth") [pos:2] "cancer stem cells" should be qualified with a valid namespace
1189 p(HGNC:PROM1) -- a("cancer stem cells") [pos:19] "cancer stem cells" should be qualified with a valid namespace
1190 p(HGNC:CD44) -- a("cancer stem cells") [pos:18] "cancer stem cells" should be qualified with a valid namespace
1191 p(HGNC:CD24) -- a("cancer stem cells") [pos:18] "cancer stem cells" should be qualified with a valid namespace
1192 p(HGNC:ITGB1) -- a("cancer stem cells") [pos:19] "cancer stem cells" should be qualified with a valid namespace
1193 p(HGNC:ALCAM) -- a("cancer stem cells") [pos:19] "cancer stem cells" should be qualified with a valid namespace
1194 p(HGNC:LGR5) -- a("cancer stem cells") [pos:18] "cancer stem cells" should be qualified with a valid namespace
1208 a("hypoxia resistance") -- bp(GOBP:"cell growth") [pos:2] "hypoxia resistance" should be qualified with a valid namespace
1209 a("hypoxia resistance") -- a("therapy resistance") [pos:2] "hypoxia resistance" should be qualified with a valid namespace
1210 a("hypoxia resistance") -- p(HGNC:HIF1A) [pos:2] "hypoxia resistance" should be qualified with a valid namespace
1245 p(HGNC:LOX) -> a("hypoxia resistance") [pos:17] "hypoxia resistance" should be qualified with a valid namespace
1246 p(HGNC:HIF1A) -> a("hypoxia resistance") [pos:19] "hypoxia resistance" should be qualified with a valid namespace
1285 a("cancer stem cells") -> a("therapy resistance") [pos:2] "cancer stem cells" should be qualified with a valid namespace
1290 bp(GOBP:"Wnt signaling pathway") -> a("cancer stem cells") [pos:38] "cancer stem cells" should be qualified with a valid namespace
1303 p(HGNC:PROM1) -- a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
1309 p(HGNC:PROM1) negativeCorrelation a("survival rate") [pos:36] "survival rate" should be qualified with a valid namespace
1342 p("Cep55/c10orf3_193(10)(VYVKGLLAKI)") => bp(GOBP:"antibody-dependent cellular cytotoxicity") [pos:2] "Cep55/c10orf3_193(10)(VYVKGLLAKI)" should be qualified with a valid namespace
1343 p("anti-Cep55/c10orf3 antibody (# 11-55)") => bp(GOBP:"antibody-dependent cellular cytotoxicity") [pos:2] "anti-Cep55/c10orf3 antibody (# 11-55)" should be qualified with a valid namespace
1360 a("cancer stem cells") -- a("therapy resistance") [pos:2] "cancer stem cells" should be qualified with a valid namespace
1361 a("cancer stem cells") -> path(MESHD:"Neoplasm Metastasis") [pos:2] "cancer stem cells" should be qualified with a valid namespace
1362 a("cancer stem cells") -- a("chemoresistance") [pos:2] "cancer stem cells" should be qualified with a valid namespace
1382 p(HGNC:SPARC) -| a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
1413 p(HGNC:SPARC) -| bp("Chemoresistance") [pos:20] "Chemoresistance" should be qualified with a valid namespace
1414 p(HGNC:SPARC) -| a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
1431 m("CASP8 small-interfering RNA") -| bp(GOBP:"apoptotic process") [pos:2] "CASP8 small-interfering RNA" should be qualified with a valid namespace
1448 p(HGNC:SPARC) =| bp("Chemoresistance") [pos:20] "Chemoresistance" should be qualified with a valid namespace
1449 g(HGNC:SPARC) =| bp("Chemoresistance") [pos:20] "Chemoresistance" should be qualified with a valid namespace
1451 p(HGNC:SPARC) =| a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
1452 g(HGNC:SPARC) =| a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
1471 a(CHEBI:"vitamin D") =| bp("Chemoresistance") [pos:27] "Chemoresistance" should be qualified with a valid namespace
1488 composite(p(HGNC:SPARC),a(CHEBI:"vitamin D")) =| a("therapy resistance") [pos:51] "therapy resistance" should be qualified with a valid namespace
1504 a("limited resection of the colon") -> a("survival rate") [pos:2] "limited resection of the colon" should be qualified with a valid namespace
1521 a("Tumor-infiltrating lymphocytes") biomarkerFor a("solid tumors") [pos:2] "Tumor-infiltrating lymphocytes" should be qualified with a valid namespace
1522 a("regulatory T cells (Treg)") -- bp(GOBP:"cell growth") [pos:2] "regulatory T cells (Treg)" should be qualified with a valid namespace
1523 a("B+ cytotoxic cells") positiveCorrelation bp(GOBP:"cell growth") [pos:2] "B+ cytotoxic cells" should be qualified with a valid namespace
1538 a(Cetuximab) -| p(HGNC:EGFR) [pos:2] "Cetuximab" should be qualified with a valid namespace
1539 composite(a(Cetuximab),a(CHEBI:"irinotecan")) -| p(HGNC:EGFR) [pos:12] "Cetuximab" should be qualified with a valid namespace
1561 composite(a(CHEBI:"dexamethasone"),a("gamma-irradiation")) -| bp(GOBP:"apoptotic process") [pos:37] "gamma-irradiation" should be qualified with a valid namespace
1563 a(CHEBI:"dexamethasone") -> a("therapy resistance") [pos:30] "therapy resistance" should be qualified with a valid namespace
1584 tscript(p(HGNC:SPARC)) -| a("therapy resistance") [pos:28] "therapy resistance" should be qualified with a valid namespace
1586 tscript(p(HGNC:SPARC)) -> a("Irinotecan sensitivity") [pos:28] "Irinotecan sensitivity" should be qualified with a valid namespace
1587 tscript(p(HGNC:SPARC)) -> a("5-fluorouracil sensitivity") [pos:28] "5-fluorouracil sensitivity" should be qualified with a valid namespace
1588 tscript(p(HGNC:SPARC)) -> a("radiosensitivity") [pos:28] "radiosensitivity" should be qualified with a valid namespace
1617 bp(GOBP:"cell adhesion") causesNoChange a("therapy resistance") [pos:42] "therapy resistance" should be qualified with a valid namespace
1618 p(HGNC:ITGB1) causesNoChange a("therapy resistance") [pos:31] "therapy resistance" should be qualified with a valid namespace
1634 p(HGNC:MT1A) -- a("therapy resistance") [pos:18] "therapy resistance" should be qualified with a valid namespace
1645 p(HGNC:MT1A) -| a("survival rate") [pos:18] "survival rate" should be qualified with a valid namespace
1648 p(HGNC:MT1A) biomarkerFor bp("poor survival") [pos:29] "poor survival" should be qualified with a valid namespace
1667 p(HGNC:MT1A) -- a("therapy resistance") [pos:18] "therapy resistance" should be qualified with a valid namespace
1697 a(CHEBI:"5-fluorouracil") -| a("5-fluorouracil resistance") [pos:31] "5-fluorouracil resistance" should be qualified with a valid namespace
1709 composite(p(HGNC:IFNA2), a(CHEBI:"5-fluorouracil")) -> path("Drug Toxicity") [pos:60] "Drug Toxicity" should be qualified with a valid namespace
1717 a(CHEBI:"5-fluorouracil") -> a("5-fluorouracil resistance") [pos:31] "5-fluorouracil resistance" should be qualified with a valid namespace
1732 a("chemotherapy") -- path(MESHD:Necrosis) [pos:2] "chemotherapy" should be qualified with a valid namespace
1748 a("microsatellite instability") -- path(MESHD:"Prostatic Neoplasms") [pos:2] "microsatellite instability" should be qualified with a valid namespace
1749 a("microsatellite instability") -- p(HGNC:AR) [pos:2] "microsatellite instability" should be qualified with a valid namespace
1750 a("microsatellite instability") -| a("survival rate") [pos:2] "microsatellite instability" should be qualified with a valid namespace

Top Warnings

Error Frequency
[pos:2] "cancer stem cells" should be qualified with a valid namespace 20
[pos:19] "therapy resistance" should be qualified with a valid namespace 9
[pos:2] "miR-27b" should be qualified with a valid namespace 7
[pos:2] "miRNA-497" should be qualified with a valid namespace 6
[pos:2] "AIIB2" should be qualified with a valid namespace 5
[pos:2] "Cetuximab" should be qualified with a valid namespace 5
[pos:18] "therapy resistance" should be qualified with a valid namespace 4
[pos:30] "therapy resistance" should be qualified with a valid namespace 4
[pos:6] "miRNA-497" should be qualified with a valid namespace 4
[pos:2] "TAE226" should be qualified with a valid namespace 4
[pos:2] "hypoxia resistance" should be qualified with a valid namespace 3
[pos:20] "Chemoresistance" should be qualified with a valid namespace 3
[pos:18] "cancer stem cells" should be qualified with a valid namespace 3
[pos:18] "anti-EGFR resistance" should be qualified with a valid namespace 3
[pos:2] "tumor microenvironment" should be qualified with a valid namespace 3
[pos:10] "Cetuximab" should be qualified with a valid namespace 3
[pos:19] "cancer stem cells" should be qualified with a valid namespace 3
[pos:19] "anti-EGFR therapy resistance" should be qualified with a valid namespace 3
[pos:20] "therapy resistance" should be qualified with a valid namespace 3
[pos:29] "anti-EGFR therapy resistance" should be qualified with a valid namespace 3

Naked Names 44

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.

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.