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
http://resources.openbel.org/belframework/20150611/namespace/chebi.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
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
http://resources.openbel.org/belframework/20150611/namespace/mesh-diseases.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
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 25

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
  • DO
  • DOID
  • EGID
  • GOBPID
  • GOCCID
  • LMSD
  • MESHC
  • MESHCID
  • MESHCS
  • MESHCSID
  • MESHDID
  • MESHPPID
  • PMIBP
  • PMICHEM
  • PMICOMP
  • PMIDIS
  • PMIPFAM
  • SCOMP
  • SDIS
  • 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 http://resources.openbel.org/belframework/20150611/annotation/cell-line.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 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.

  • Anatomy
  • Cell
  • Disease

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
Confidence
  • high
  • low
  • medium
  • very low

Warning Statistics

Syntax Errors 3

Line BEL Message
2851 p(HGNC:BRAF) -| p(HGNC:TGFBRAP1,pmod(P,Serine)) General Parser Failure on line 2851 at pos 31: p(HGNC:BRAF) -| p(HGNC:TGFBRAP1,pmod(P,Serine))
2852 p(HGNC:TGFBRAP1,pmod(P,Serine)) -| bp(MESHPP:"Drug Resistance") General Parser Failure on line 2852 at pos 15: p(HGNC:TGFBRAP1,pmod(P,Serine)) -| bp(MESHPP:"Drug Resistance")
3005 a(SCHEM:"LY 294002") -| p(HGNC:AKT1,pmod(P,Serine,473)) General Parser Failure on line 3005 at pos 35: a(SCHEM:"LY 294002") -| p(HGNC:AKT1,pmod(P,Serine,473))

All Parser Warnings 183

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

Line BEL Message
6 SET DOCUMENT Version = "1.0" Version string "1.0" neither is a date like YYYYMMDD nor adheres to semantic versioning. See http://semver.org/
252 a("Zuo Jin Wan") -| bp(GOBP:"cell growth") [pos:2] "Zuo Jin Wan" should be qualified with a valid namespace
257 a("Zuo Jin Wan") -| p(HGNC:ABCB1) [pos:2] "Zuo Jin Wan" should be qualified with a valid namespace
258 a("Zuo Jin Wan") -| bp(MESHPP:"Drug Resistance") [pos:2] "Zuo Jin Wan" should be qualified with a valid namespace
516 SET MeSHDisease = "SW620" "SW620" is not defined in the MeSHDisease annotation
518 complex(p(HGNC:CD44),p(HGNC:PROM1)) -- a("cancer stem cells") [pos:41] "cancer stem cells" should be qualified with a valid namespace
536 p(ZFIN:cd44a) negativeCorrelation path(MESHD:Neoplasms) 'g'
630 SET CellLine = "HT_29 cell" "HT_29 cell" is not defined in the CellLine annotation
642 SET Anatomy = "Colon" "Colon" is not defined in the Anatomy annotation
737 a("PX-478") -| p(HGNC:HIF1A) [pos:2] "PX-478" should be qualified with a valid namespace
738 complex(a(SCHEM:Cetuximab),a("PX-478")) -| bp(GOBP:"cell proliferation") [pos:29] "PX-478" should be qualified with a valid namespace
739 complex(a(SCHEM:Cetuximab),a("PX-478")) -| p(HGNC:KRAS,sub(G,12,V)) [pos:29] "PX-478" should be qualified with a valid namespace
996 p(ZFIN:kita) -- path(MESHD:"Testicular Neoplasms") 'g'
1035 p(HGNC:EGFR) biomarkerFor path(MESHD:Head,and,Neck,Neoplasms) "Head" is not in the MESHD namespace
1048 a(thiazol) -| p(HGNC:EGFR) [pos:2] "thiazol" should be qualified with a valid namespace
1074 SET MeSHDisease = {"Multiple Myeloma","Lymphoma","Lung Carcinoma","Mesothelioma","Leukemya","Colorectal Neoplasms","Breast Neoplasms","Pancreatic Neoplasms"} "Lung Carcinoma" is not defined in the MeSHDisease annotation
1081 bp(GOBP:"hydroxymethylglutaryl_CoA reductase activity") -- bp(GOBP:"cell adhesion") "hydroxymethylglutaryl_CoA reductase activity" is not in the GOBP namespace
1111 a("miR-221") -| p(HGNC:ETS1) [pos:2] "miR-221" should be qualified with a valid namespace
1112 a("miR-221") -| p(HGNC:STAT5A) [pos:2] "miR-221" should be qualified with a valid namespace
1113 a("miR-221") -| p(HGNC:KIT) [pos:2] "miR-221" should be qualified with a valid namespace
1117 r("miR-29a") -| p(HGNC:KLF4) [pos:2] "miR-29a" should be qualified with a valid namespace
1120 r("miR-29a") biomarkerFor path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-29a" should be qualified with a valid namespace
1121 r("miR-221") biomarkerFor path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-221" should be qualified with a valid namespace
1126 r("miR-143") -| p(HGNC:KRAS) [pos:2] "miR-143" should be qualified with a valid namespace
1130 r("miR-143") -| p(HGNC:MACC1) [pos:2] "miR-143" should be qualified with a valid namespace
1133 r("miR-143") biomarkerFor path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-143" should be qualified with a valid namespace
1138 r("miR-423") biomarkerFor path(MESHD:"Neoplasm Metastasis") [pos:2] "miR-423" should be qualified with a valid namespace
1139 r("miR-608") biomarkerFor path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-608" should be qualified with a valid namespace
1143 r("pre-miR-34a") -| p(HGNC:AXL) [pos:2] "pre-miR-34a" should be qualified with a valid namespace
1147 r("pre-miR-199a") -| p(HGNC:AXL) [pos:2] "pre-miR-199a" should be qualified with a valid namespace
1148 r("pre-miR-34a") -| path(MESHD:"Neoplasm Metastasis") [pos:2] "pre-miR-34a" should be qualified with a valid namespace
1149 r("pre-miR-199a") -| path(MESHD:"Neoplasm Metastasis") [pos:2] "pre-miR-199a" should be qualified with a valid namespace
1154 r("miR-328") -| p(HGNC:ABCG2) [pos:2] "miR-328" should be qualified with a valid namespace
1155 r("miR-222") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-222" should be qualified with a valid namespace
1156 r("miR-222") -| p(HGNC:ADAM17) [pos:2] "miR-222" should be qualified with a valid namespace
1157 r("miR-328") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-328" should be qualified with a valid namespace
1263 r("miR-145") -| p(HGNC:RAD18) [pos:2] "miR-145" should be qualified with a valid namespace
1264 r("miR-145") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-145" should be qualified with a valid namespace
1271 SET Eco = "Neoplasms" "Neoplasms" is not defined in the Eco annotation
1274 p(HGNC:RAD18) -- bp(GOBP:"ubiquitin_protein ligase activity") "ubiquitin_protein ligase activity" is not in the GOBP namespace
1289 r("miR-145") negativeCorrelation r(HGNC:RAD18) [pos:2] "miR-145" should be qualified with a valid namespace
1293 r("miR-145") -| (p(HGNC:RAD18) -> bp(MESHPP:"DNA Damage")) [pos:2] "miR-145" should be qualified with a valid namespace
1294 r("miR-145") -> bp(MESHPP:"DNA Damage") [pos:2] "miR-145" should be qualified with a valid namespace
1298 r("miR-145") -| p(HGNC:RAD18) [pos:2] "miR-145" should be qualified with a valid namespace
1302 r("miR-145") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-145" should be qualified with a valid namespace
1306 a("miR-145") -| p(HGNC:RAD18) [pos:2] "miR-145" should be qualified with a valid namespace
1466 complex(a("PKD inhibitor"),a(regorafenib)) -> bp(GOBP:"apoptotic process") [pos:10] "PKD inhibitor" should be qualified with a valid namespace
1467 complex(a("PKD inhibitor"),a(regorafenib)) -| p(HGNC:HSPB2) [pos:10] "PKD inhibitor" should be qualified with a valid namespace
1468 complex(a("PKD inhibitor"),a(regorafenib)) -> bp(CHEBI:"poly(ADP-ribose) polymerase inhibitor") [pos:10] "PKD inhibitor" should be qualified with a valid namespace
1473 complex(a("PKD inhibitor"),a(regorafenib)) -| p(HGNC:AKT1) [pos:10] "PKD inhibitor" should be qualified with a valid namespace
1474 complex(a("PKD inhibitor"),a(regorafenib)) -| p(HGNC:NFKB1) [pos:10] "PKD inhibitor" should be qualified with a valid namespace
1549 p(HGNC:MYC) -> r(CDKN1B) [pos:17] "CDKN1B" should be qualified with a valid namespace
1567 p(ZFIN:taz) -- bp(GOBP:"cell proliferation") 'g'
1569 path(MESHD:Neoplasms) -- p(ZFIN:taz) 'g'
1594 p(HGNC:KRAS,sub(G,12,V)) -- r("miR-4689") [pos:30] "miR-4689" should be qualified with a valid namespace
1598 r("miR-4689") -| bp(GOBP:"cell growth") [pos:2] "miR-4689" should be qualified with a valid namespace
1599 r("miR-4689") -> bp(GOBP:"apoptotic process") [pos:2] "miR-4689" should be qualified with a valid namespace
1604 r("miR-4689") -| p(HGNC:AKT1) [pos:2] "miR-4689" should be qualified with a valid namespace
1608 r("miR-4689") -- bp(GOBP:"epidermal growth factor receptor activity") [pos:2] "miR-4689" should be qualified with a valid namespace
1612 r("miR-4689") -| bp(MESHPP:"MAP Kinase Signaling System") [pos:2] "miR-4689" should be qualified with a valid namespace
1616 r("miR-4689") -| bp(GOBP:"phosphatidylinositol 3_kinase activity") [pos:2] "miR-4689" should be qualified with a valid namespace
1768 complex(a(Cryotherapy),a(CHEBI:adjuvant)) -> bp(GOBP:"apoptotic process") [pos:10] "Cryotherapy" should be qualified with a valid namespace
1769 complex(a(Cryotherapy),a(CHEBI:adjuvant)) -> bp(GOBP:"cell death") [pos:10] "Cryotherapy" should be qualified with a valid namespace
1773 complex(a(Cryotherapy),a(CHEBI:adjuvant),a(SCHEM:"Caspase inhibitor")) -| bp(GOBP:"apoptotic process") [pos:10] "Cryotherapy" should be qualified with a valid namespace
1777 complex(a(Cryotherapy),a(CHEBI:adjuvant)) -> p(HGNC:BAX) [pos:10] "Cryotherapy" should be qualified with a valid namespace
1782 complex(a(Cryotherapy),a(CHEBI:adjuvant)) -> bp(GOBP:"apoptotic process") [pos:10] "Cryotherapy" should be qualified with a valid namespace
1811 SET MeSHDisease = "DNA microarray" "DNA microarray" is not defined in the MeSHDisease annotation
1839 SET Disease = "HCT116" "HCT116" is not defined in the Disease annotation
2106 a(SFRE) -> a(CHEBI:"5-fluorouracil") [pos:2] "SFRE" should be qualified with a valid namespace
2110 a(SFRE) -| bp(MESHPP:"Drug Resistance") [pos:2] "SFRE" should be qualified with a valid namespace
2114 a(SFRE) -| p(HGNC:TK1) [pos:2] "SFRE" should be qualified with a valid namespace
2115 a(SFRE) -| p(HGNC:TYMS) [pos:2] "SFRE" should be qualified with a valid namespace
2126 a(HGNC:PDK3) -> bp(MESHPP:"Drug Resistance") Abundance HGNC:PDK3 should be encoded as one of: miRNA, Gene, RNA, Protein
2230 complex(p(HGNC:EGFR),a(panitumumab)) [pos:23] "panitumumab" should be qualified with a valid namespace
2241 a("miR-128") -> bp(MESHPP:"DNA Damage") [pos:2] "miR-128" should be qualified with a valid namespace
2245 a("miR-21") -- path(MESHD:"Carcinoma, Squamous Cell") [pos:2] "miR-21" should be qualified with a valid namespace
2246 a("miR-106b") -- path(MESHD:"Carcinoma, Squamous Cell") [pos:2] "miR-106b" should be qualified with a valid namespace
2250 a("miR-375") -- path(MESHD:"Carcinoma, Squamous Cell") [pos:2] "miR-375" should be qualified with a valid namespace
2289 SET CellLine = "Caco_2 cell" "Caco_2 cell" is not defined in the CellLine annotation
2349 a(hypermethylation) -| r(HGNC:TFAP2E) [pos:2] "hypermethylation" should be qualified with a valid namespace
2368 SET CellLine = {"SW620","HCT15","WiDr"} "WiDr" is not defined in the CellLine annotation
2381 a(SCHEM:"SN 38") -> p(ZFIN:top1) 'g'
2441 a(CHEBI:sulindac) -| tloc(p(HGNC:CTNNB1)) [pos:25] Unqualified translocation: a(CHEBI:sulindac) -| tloc(p(HGNC:CTNNB1)) [['Protein', 'HGNC', 'CTNNB1']]
2474 a(thiazolides) -> bp(GOBP:"apoptotic process") [pos:2] "thiazolides" should be qualified with a valid namespace
2479 a(thiazolides) -> p(HGNC:MAPK9) [pos:2] "thiazolides" should be qualified with a valid namespace
2480 a(thiazolides) -> p(HGNC:MAPK14) [pos:2] "thiazolides" should be qualified with a valid namespace
2481 a(thiazolides) -> (p(HGNC:MAPK9) -> bp(GOBP:"cell death")) [pos:2] "thiazolides" should be qualified with a valid namespace
2482 a(thiazolides) -> (p(HGNC:MAPK14) -> bp(GOBP:"cell death")) [pos:2] "thiazolides" should be qualified with a valid namespace
2509 a(thiazolide) -> kin(p(HGNC:MAPK9)) [pos:2] "thiazolide" should be qualified with a valid namespace
2510 a(thiazolide) -> p(HGNC:BCL2L11) [pos:2] "thiazolide" should be qualified with a valid namespace
2568 complex(a(CHEBI:"5-fluorouracil"),a(SC144)) -| bp(GOBP:"cell growth") [pos:36] "SC144" should be qualified with a valid namespace
2572 complex(a(CHEBI:oxaliplatin),a(SC144)) -| bp(GOBP:"cell growth") [pos:31] "SC144" should be qualified with a valid namespace
2578 complex(a(SC144),a(SCHEM:Paclitaxel)) -| bp(GOBP:"cell growth") [pos:10] "SC144" should be qualified with a valid namespace
2585 complex(a(SC144),a(SCHEM:Paclitaxel)) -| bp(GOBP:"cell growth") [pos:10] "SC144" should be qualified with a valid namespace
2645 bp(GOBP:"histone deacetylase inhibitor activity") -- bp(GOBP:"apoptotic process") "histone deacetylase inhibitor activity" is not in the GOBP namespace
2652 a(LBH589) -| p(HGNC:AKT1) [pos:2] "LBH589" should be qualified with a valid namespace
2679 r("miR-17-5p") -> path(MESHD:"Neoplasm Metastasis") [pos:2] "miR-17-5p" should be qualified with a valid namespace
2683 r("miR-17-5p") -> bp(MESHPP:"Drug Resistance") [pos:2] "miR-17-5p" should be qualified with a valid namespace
2684 r("miR-17-5p") -| p(HGNC:PTEN) [pos:2] "miR-17-5p" should be qualified with a valid namespace
2689 r("miR-17-5p") -> bp(GOBP:"cell invasion") [pos:2] "miR-17-5p" should be qualified with a valid namespace
2700 r("miR-34a") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-34a" should be qualified with a valid namespace
2701 r("miR-34a") -| p(HGNC:SIRT1) [pos:2] "miR-34a" should be qualified with a valid namespace
2702 r("miR-34a") -| p(HGNC:E2F3) [pos:2] "miR-34a" should be qualified with a valid namespace
2708 r("miR-34a") -| path(MESHD:"Neoplasm Metastasis") [pos:2] "miR-34a" should be qualified with a valid namespace
2709 r("miR-34a") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-34a" should be qualified with a valid namespace
2713 r("miR-34a") -| path(MESHD:"Neoplasms") [pos:2] "miR-34a" should be qualified with a valid namespace
2790 p(HGNC:HMGB1) -> bp(GOBP:"vascular endothelial growth factor receptor binding") "vascular endothelial growth factor receptor binding" is not in the GOBP namespace
2851 p(HGNC:BRAF) -| p(HGNC:TGFBRAP1,pmod(P,Serine)) General Parser Failure on line 2851 at pos 31: p(HGNC:BRAF) -| p(HGNC:TGFBRAP1,pmod(P,Serine))
2852 p(HGNC:TGFBRAP1,pmod(P,Serine)) -| bp(MESHPP:"Drug Resistance") General Parser Failure on line 2852 at pos 15: p(HGNC:TGFBRAP1,pmod(P,Serine)) -| bp(MESHPP:"Drug Resistance")
2898 a(SCHEM:"SN 38") -| p(ZFIN:top1) 'g'
2971 a(EHT6706) -- bp(MESHPP:Polymerization) [pos:2] "EHT6706" should be qualified with a valid namespace
2972 a(EHT6706) -| a(GOCC:microtubule) [pos:2] "EHT6706" should be qualified with a valid namespace
2973 a(SCHEM:Colchicine) -| a(GOCC:microtubule) Abundance GOCC:microtubule should be encoded as one of: Complex
2979 a(EHT6706) -| bp(GOBP:"cell growth") [pos:2] "EHT6706" should be qualified with a valid namespace
2984 a(EHT6706) -| bp(GOBP:"cell migration") [pos:2] "EHT6706" should be qualified with a valid namespace
2988 a(EHT6706) -| bp(GOBP:angiogenesis) [pos:2] "EHT6706" should be qualified with a valid namespace
2999 a(ZJW) -| p(SFAM:"AKT Family") [pos:2] "ZJW" should be qualified with a valid namespace
3000 a(ZJW) -| p(HGNC:NFKB1) [pos:2] "ZJW" should be qualified with a valid namespace
3001 a(ZJW) -| bp(MESHPP:"Drug Resistance") [pos:2] "ZJW" should be qualified with a valid namespace
3005 a(SCHEM:"LY 294002") -| p(HGNC:AKT1,pmod(P,Serine,473)) General Parser Failure on line 3005 at pos 35: a(SCHEM:"LY 294002") -| p(HGNC:AKT1,pmod(P,Serine,473))
3006 a(ZJW) -| p(HGNC:NFKB1,pmod(P,Serine,473)) [pos:2] "ZJW" should be qualified with a valid namespace
3008 a(ZJW) -| p(HGNC:NFKB1,pmod(P)) [pos:2] "ZJW" should be qualified with a valid namespace
3032 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']]
3091 a(PZH) -| bp(GOBP:"cell proliferation") [pos:2] "PZH" should be qualified with a valid namespace
3092 a(PZH) -| bp(GOBP:"cell growth") [pos:2] "PZH" should be qualified with a valid namespace
3093 a(PZH) -> bp(GOBP:"apoptotic process") [pos:2] "PZH" should be qualified with a valid namespace
3098 a(PZH) -| bp(GOBP:angiogenesis) [pos:2] "PZH" should be qualified with a valid namespace
3104 a(PHZ) -| bp(GOBP:"cell growth") [pos:2] "PHZ" should be qualified with a valid namespace
3108 a(PHZ) -| p(HGNC:ABCG2) [pos:2] "PHZ" should be qualified with a valid namespace
3109 a(PHZ) -| p(HGNC:ABCB1) [pos:2] "PHZ" should be qualified with a valid namespace
3120 bp(GOBP:"cell proliferation") -- a("cancer stem cells") [pos:35] "cancer stem cells" should be qualified with a valid namespace
3124 bp(MESHPP:"Drug Resistance") -- a("cancer stem cells") [pos:34] "cancer stem cells" should be qualified with a valid namespace
3129 r("miR-451") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-451" should be qualified with a valid namespace
3133 r("miR-451") -| bp(GOBP:"cell growth") [pos:2] "miR-451" should be qualified with a valid namespace
3141 a("miR-451") -- p(HGNC:PTGS2) [pos:2] "miR-451" should be qualified with a valid namespace
3147 r("miR-451") -> p(HGNC:MIF) [pos:2] "miR-451" should be qualified with a valid namespace
3155 r("miR-451") -| p(HGNC:ABCB1) [pos:2] "miR-451" should be qualified with a valid namespace
3166 a(Dbait) -| bp(GOBP:"DNA repair") [pos:2] "Dbait" should be qualified with a valid namespace
3172 a(Dbait) -| bp(MESHPP:"Drug Resistance") [pos:2] "Dbait" should be qualified with a valid namespace
3179 a(Dbait) -> (complex(a(SCHEM:Oxaliplatin),a(SCHEM:"5-fluorouracil")) -| path(MESHD:"Colorectal Neoplasms")) [pos:2] "Dbait" should be qualified with a valid namespace
3184 a(Dbait) -| bp(GOBP:angiogenesis) [pos:2] "Dbait" should be qualified with a valid namespace
3185 a(Dbait) -> bp(GOBP:"necrotic cell death") [pos:2] "Dbait" should be qualified with a valid namespace
3186 a(Dbait) -> bp(GOBP:"apoptotic process") [pos:2] "Dbait" should be qualified with a valid namespace
3187 a(Dbait) -| bp(GOBP:"cell proliferation") [pos:2] "Dbait" should be qualified with a valid namespace
3209 SET MeSHDisease = "MESHD:\"Liver Neoplasms\"" "MESHD:\"Liver Neoplasms\"" is not defined in the MeSHDisease annotation
3215 bp(GOBP:"aldehyde reductase activity") positiveCorrelation path(MESHD:Neoplasms) "aldehyde reductase activity" is not in the GOBP namespace
3236 r("miR-203") -| p(HGNC:ATM) [pos:2] "miR-203" should be qualified with a valid namespace
3240 r("miR-203") -> bp(MESHPP:"Drug Resistance") [pos:2] "miR-203" should be qualified with a valid namespace
3244 r("miR-203") -- bp(MESHPP:"Drug Resistance") [pos:2] "miR-203" should be qualified with a valid namespace
3268 r("miR-203") -| p(HGNC:ATM) [pos:2] "miR-203" should be qualified with a valid namespace
3269 r("miR-203") -> bp(MESHPP:"Drug Resistance") [pos:2] "miR-203" should be qualified with a valid namespace
3285 p(HGNC:KRAS) -- path(MESHD:"Drug Resistance") "Drug Resistance" is not in the MESHD namespace
3304 p(HGNC:CXCR4) -- a(Endostar) [pos:19] "Endostar" should be qualified with a valid namespace
3308 p(HGNC:HIF1A) -- a(Endostar) [pos:19] "Endostar" should be qualified with a valid namespace
3309 p(HGNC:EPAS1) -- a(Endostar) [pos:19] "Endostar" should be qualified with a valid namespace
3313 composite(a(endostar),a(CHEBI:oxaliplatin)) -| bp(GOBP:"cell adhesion") [pos:12] "endostar" should be qualified with a valid namespace
3314 composite(a(endostar),a(CHEBI:oxaliplatin)) -| bp(GOBP:"cell proliferation") [pos:12] "endostar" should be qualified with a valid namespace
3315 composite(a(endostar),a(CHEBI:oxaliplatin)) -| (r(HGNC:CXCR4) -| bp(GOBP:"cell adhesion")) [pos:12] "endostar" should be qualified with a valid namespace
3316 composite(a(endostar),a(CHEBI:oxaliplatin)) -| (r(HGNC:CXCR4) -| bp(GOBP:"cell proliferation")) [pos:12] "endostar" should be qualified with a valid namespace
3321 composite(a(endostar),a(CHEBI:oxaliplatin)) -| r(HGNC:CXCR4) [pos:12] "endostar" should be qualified with a valid namespace
3333 a(endostar) -| p(HGNC:CXCR4) [pos:2] "endostar" should be qualified with a valid namespace
3334 a(endostar) -| p(HGNC:EPAS1) [pos:2] "endostar" should be qualified with a valid namespace
3340 a(endostar) -| bp(MESHPP:"Drug Resistance") [pos:2] "endostar" should be qualified with a valid namespace
3383 SET Anatomy = "Serum" "Serum" is not defined in the Anatomy annotation
3385 SET MeSHDisease = "Colorectal Neoplsms" "Colorectal Neoplsms" is not defined in the MeSHDisease annotation
3401 path(MESHD:"Colorectal Neoplasms") -- p(HGNC:"COMMD3-BMI1") Protein HGNC:COMMD3-BMI1 should be encoded as one of: miRNA, Gene, RNA
3480 r(miRNA) -| p(HGNC:PEBP1) [pos:2] "miRNA" should be qualified with a valid namespace
3591 a(CHEBI:fingolimod) -> bp(GOBP:"autophagic vacuole assembly") "autophagic vacuole assembly" is not in the GOBP namespace
3716 r("miR-328") -- path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-328" should be qualified with a valid namespace
3720 r("miR-328") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-328" should be qualified with a valid namespace
3724 r("miR-328") -| p(HGNC:ABCG2) [pos:2] "miR-328" should be qualified with a valid namespace
3728 r("miR-328") -| p(HGNC:MMP16) [pos:2] "miR-328" should be qualified with a valid namespace
3749 p(HGNC:EGFR) -> a("PF-04691502") [pos:18] "PF-04691502" should be qualified with a valid namespace
3754 a("PF-04691502") -> p(HGNC:EGFR) [pos:2] "PF-04691502" should be qualified with a valid namespace
3755 a("PF-04691502") -> p(HGNC:ERBB2) [pos:2] "PF-04691502" should be qualified with a valid namespace
3756 a("PF-04691502") -> p(HGNC:ERBB3) [pos:2] "PF-04691502" should be qualified with a valid namespace
3757 a("PF-04691502") -> p(HGNC:FOXO3) [pos:2] "PF-04691502" should be qualified with a valid namespace
3759 bp(GOBP:"phosphatidylinositol-3 kinase activity") -| p(HGNC:FOXO3) "phosphatidylinositol-3 kinase activity" is not in the GOBP namespace
3760 a("PF-04691502") -> (p(HGNC:FOXO3) -> p(HGNC:EGFR)) [pos:2] "PF-04691502" should be qualified with a valid namespace
3761 a("PF-04691502") -> (p(HGNC:FOXO3) -> p(HGNC:ERBB2)) [pos:2] "PF-04691502" should be qualified with a valid namespace
3762 a("PF-04691502") -> (p(HGNC:FOXO3) -> p(HGNC:ERBB3)) [pos:2] "PF-04691502" should be qualified with a valid namespace
3768 a("PF-04691502") -> p(HGNC:EGFR) [pos:2] "PF-04691502" should be qualified with a valid namespace
3774 a(dacomitinib) -| p(HGNC:EGFR) [pos:2] "dacomitinib" should be qualified with a valid namespace

Top Warnings

Error Frequency
[pos:2] "miR-145" should be qualified with a valid namespace 8
[pos:2] "PF-04691502" should be qualified with a valid namespace 8
[pos:2] "Dbait" should be qualified with a valid namespace 7
[pos:2] "miR-328" should be qualified with a valid namespace 6
[pos:2] "miR-4689" should be qualified with a valid namespace 6
[pos:2] "miR-34a" should be qualified with a valid namespace 6
'g' 6
[pos:10] "PKD inhibitor" should be qualified with a valid namespace 5
[pos:2] "ZJW" should be qualified with a valid namespace 5
[pos:2] "thiazolides" should be qualified with a valid namespace 5
[pos:2] "miR-203" should be qualified with a valid namespace 5
[pos:2] "EHT6706" should be qualified with a valid namespace 5
[pos:10] "Cryotherapy" should be qualified with a valid namespace 5
[pos:2] "miR-451" should be qualified with a valid namespace 5
[pos:12] "endostar" should be qualified with a valid namespace 5
[pos:2] "miR-221" should be qualified with a valid namespace 4
[pos:2] "miR-17-5p" should be qualified with a valid namespace 4
[pos:2] "SFRE" should be qualified with a valid namespace 4
[pos:2] "PZH" should be qualified with a valid namespace 4
[pos:2] "Zuo Jin Wan" should be qualified with a valid namespace 3

Naked Names 43

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 2

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.