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 22

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
  • EGID
  • GOBPID
  • GOCCID
  • LMSD
  • MESHCID
  • MESHCS
  • MESHCSID
  • MESHDID
  • MESHPPID
  • PMIBP
  • PMICHEM
  • PMICOMP
  • PMIDIS
  • PMIPFAM
  • 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 17

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

Locally Defined Annotations 23

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 16

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
Confidence
  • high
  • low
  • medium
  • very low
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

Syntax Errors 7

Line BEL Message
2881 p(HGNC:BRAF) -| p(HGNC:TGFBRAP1,pmod(P,Serine)) General Parser Failure on line 2881 at pos 31: p(HGNC:BRAF) -| p(HGNC:TGFBRAP1,pmod(P,Serine))
2882 p(HGNC:TGFBRAP1,pmod(P,Serine)) -| bp(MESHPP:"Drug Resistance") General Parser Failure on line 2882 at pos 15: p(HGNC:TGFBRAP1,pmod(P,Serine)) -| bp(MESHPP:"Drug Resistance")
3035 a(SCHEM:"LY 294002") -| p(HGNC:AKT1,pmod(P,Serine,473)) General Parser Failure on line 3035 at pos 35: a(SCHEM:"LY 294002") -| p(HGNC:AKT1,pmod(P,Serine,473))
3847 composite(p(HGNC:FCGR2A sub(F,158,V)), a("Cetuximab")) causesNoChange bp("survival rate") General Parser Failure on line 3847 at pos 24: composite(p(HGNC:FCGR2A sub(F,158,V)), a("Cetuximab")) causesNoChange bp("survival rate")
4699 p(HGNC:FCGR3A, pmod(V,V,158)) positiveCorrelation bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity") General Parser Failure on line 4699 at pos 13: p(HGNC:FCGR3A, pmod(V,V,158)) positiveCorrelation bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity")
4700 p(HGNC:FCGR3A, pmod(V,F,158)) positiveCorrelation bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity") General Parser Failure on line 4700 at pos 13: p(HGNC:FCGR3A, pmod(V,F,158)) positiveCorrelation bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity")
4706 p(HGNC:FCGR3A, pmod(V,V,158)) positiveCorrelation bp("survival rate") General Parser Failure on line 4706 at pos 13: p(HGNC:FCGR3A, pmod(V,V,158)) positiveCorrelation bp("survival rate")

All Parser Warnings 693

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/
282 a("Zuo Jin Wan") -| bp(GOBP:"cell growth") [pos:2] "Zuo Jin Wan" should be qualified with a valid namespace
287 a("Zuo Jin Wan") -| p(HGNC:ABCB1) [pos:2] "Zuo Jin Wan" should be qualified with a valid namespace
288 a("Zuo Jin Wan") -| bp(MESHPP:"Drug Resistance") [pos:2] "Zuo Jin Wan" should be qualified with a valid namespace
546 SET MeSHDisease = "SW620" "SW620" is not defined in the MeSHDisease annotation
548 complex(p(HGNC:CD44),p(HGNC:PROM1)) -- a("cancer stem cells") [pos:41] "cancer stem cells" should be qualified with a valid namespace
566 p(ZFIN:cd44a) negativeCorrelation path(MESHD:Neoplasms) 'g'
660 SET CellLine = "HT_29 cell" "HT_29 cell" is not defined in the CellLine annotation
672 SET Anatomy = "Colon" "Colon" is not defined in the Anatomy annotation
767 a("PX-478") -| p(HGNC:HIF1A) [pos:2] "PX-478" should be qualified with a valid namespace
768 complex(a(SCHEM:Cetuximab),a("PX-478")) -| bp(GOBP:"cell proliferation") [pos:29] "PX-478" should be qualified with a valid namespace
769 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
1026 p(ZFIN:kita) -- path(MESHD:"Testicular Neoplasms") 'g'
1065 p(HGNC:EGFR) biomarkerFor path(MESHD:Head,and,Neck,Neoplasms) "Head" is not in the MESHD namespace
1078 a(thiazol) -| p(HGNC:EGFR) [pos:2] "thiazol" should be qualified with a valid namespace
1104 SET MeSHDisease = {"Multiple Myeloma","Lymphoma","Lung Carcinoma","Mesothelioma","Leukemya","Colorectal Neoplasms","Breast Neoplasms","Pancreatic Neoplasms"} "Lung Carcinoma" is not defined in the MeSHDisease annotation
1111 bp(GOBP:"hydroxymethylglutaryl_CoA reductase activity") -- bp(GOBP:"cell adhesion") "hydroxymethylglutaryl_CoA reductase activity" is not in the GOBP namespace
1141 a("miR-221") -| p(HGNC:ETS1) [pos:2] "miR-221" should be qualified with a valid namespace
1142 a("miR-221") -| p(HGNC:STAT5A) [pos:2] "miR-221" should be qualified with a valid namespace
1143 a("miR-221") -| p(HGNC:KIT) [pos:2] "miR-221" should be qualified with a valid namespace
1147 r("miR-29a") -| p(HGNC:KLF4) [pos:2] "miR-29a" should be qualified with a valid namespace
1150 r("miR-29a") biomarkerFor path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-29a" should be qualified with a valid namespace
1151 r("miR-221") biomarkerFor path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-221" should be qualified with a valid namespace
1156 r("miR-143") -| p(HGNC:KRAS) [pos:2] "miR-143" should be qualified with a valid namespace
1160 r("miR-143") -| p(HGNC:MACC1) [pos:2] "miR-143" should be qualified with a valid namespace
1163 r("miR-143") biomarkerFor path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-143" should be qualified with a valid namespace
1168 r("miR-423") biomarkerFor path(MESHD:"Neoplasm Metastasis") [pos:2] "miR-423" should be qualified with a valid namespace
1169 r("miR-608") biomarkerFor path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-608" should be qualified with a valid namespace
1173 r("pre-miR-34a") -| p(HGNC:AXL) [pos:2] "pre-miR-34a" should be qualified with a valid namespace
1177 r("pre-miR-199a") -| p(HGNC:AXL) [pos:2] "pre-miR-199a" should be qualified with a valid namespace
1178 r("pre-miR-34a") -| path(MESHD:"Neoplasm Metastasis") [pos:2] "pre-miR-34a" should be qualified with a valid namespace
1179 r("pre-miR-199a") -| path(MESHD:"Neoplasm Metastasis") [pos:2] "pre-miR-199a" should be qualified with a valid namespace
1184 r("miR-328") -| p(HGNC:ABCG2) [pos:2] "miR-328" should be qualified with a valid namespace
1185 r("miR-222") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-222" should be qualified with a valid namespace
1186 r("miR-222") -| p(HGNC:ADAM17) [pos:2] "miR-222" should be qualified with a valid namespace
1187 r("miR-328") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-328" should be qualified with a valid namespace
1293 r("miR-145") -| p(HGNC:RAD18) [pos:2] "miR-145" should be qualified with a valid namespace
1294 r("miR-145") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-145" should be qualified with a valid namespace
1301 SET Eco = "Neoplasms" "Neoplasms" is not defined in the Eco annotation
1304 p(HGNC:RAD18) -- bp(GOBP:"ubiquitin_protein ligase activity") "ubiquitin_protein ligase activity" is not in the GOBP namespace
1319 r("miR-145") negativeCorrelation r(HGNC:RAD18) [pos:2] "miR-145" should be qualified with a valid namespace
1323 r("miR-145") -| (p(HGNC:RAD18) -> bp(MESHPP:"DNA Damage")) [pos:2] "miR-145" should be qualified with a valid namespace
1324 r("miR-145") -> bp(MESHPP:"DNA Damage") [pos:2] "miR-145" should be qualified with a valid namespace
1328 r("miR-145") -| p(HGNC:RAD18) [pos:2] "miR-145" should be qualified with a valid namespace
1332 r("miR-145") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-145" should be qualified with a valid namespace
1336 a("miR-145") -| p(HGNC:RAD18) [pos:2] "miR-145" should be qualified with a valid namespace
1496 complex(a("PKD inhibitor"),a(regorafenib)) -> bp(GOBP:"apoptotic process") [pos:10] "PKD inhibitor" should be qualified with a valid namespace
1497 complex(a("PKD inhibitor"),a(regorafenib)) -| p(HGNC:HSPB2) [pos:10] "PKD inhibitor" should be qualified with a valid namespace
1498 complex(a("PKD inhibitor"),a(regorafenib)) -> bp(CHEBI:"poly(ADP-ribose) polymerase inhibitor") [pos:10] "PKD inhibitor" should be qualified with a valid namespace
1503 complex(a("PKD inhibitor"),a(regorafenib)) -| p(HGNC:AKT1) [pos:10] "PKD inhibitor" should be qualified with a valid namespace
1504 complex(a("PKD inhibitor"),a(regorafenib)) -| p(HGNC:NFKB1) [pos:10] "PKD inhibitor" should be qualified with a valid namespace
1579 p(HGNC:MYC) -> r(CDKN1B) [pos:17] "CDKN1B" should be qualified with a valid namespace
1597 p(ZFIN:taz) -- bp(GOBP:"cell proliferation") 'g'
1599 path(MESHD:Neoplasms) -- p(ZFIN:taz) 'g'
1624 p(HGNC:KRAS,sub(G,12,V)) -- r("miR-4689") [pos:30] "miR-4689" should be qualified with a valid namespace
1628 r("miR-4689") -| bp(GOBP:"cell growth") [pos:2] "miR-4689" should be qualified with a valid namespace
1629 r("miR-4689") -> bp(GOBP:"apoptotic process") [pos:2] "miR-4689" should be qualified with a valid namespace
1634 r("miR-4689") -| p(HGNC:AKT1) [pos:2] "miR-4689" should be qualified with a valid namespace
1638 r("miR-4689") -- bp(GOBP:"epidermal growth factor receptor activity") [pos:2] "miR-4689" should be qualified with a valid namespace
1642 r("miR-4689") -| bp(MESHPP:"MAP Kinase Signaling System") [pos:2] "miR-4689" should be qualified with a valid namespace
1646 r("miR-4689") -| bp(GOBP:"phosphatidylinositol 3_kinase activity") [pos:2] "miR-4689" should be qualified with a valid namespace
1798 complex(a(Cryotherapy),a(CHEBI:adjuvant)) -> bp(GOBP:"apoptotic process") [pos:10] "Cryotherapy" should be qualified with a valid namespace
1799 complex(a(Cryotherapy),a(CHEBI:adjuvant)) -> bp(GOBP:"cell death") [pos:10] "Cryotherapy" should be qualified with a valid namespace
1803 complex(a(Cryotherapy),a(CHEBI:adjuvant),a(SCHEM:"Caspase inhibitor")) -| bp(GOBP:"apoptotic process") [pos:10] "Cryotherapy" should be qualified with a valid namespace
1807 complex(a(Cryotherapy),a(CHEBI:adjuvant)) -> p(HGNC:BAX) [pos:10] "Cryotherapy" should be qualified with a valid namespace
1812 complex(a(Cryotherapy),a(CHEBI:adjuvant)) -> bp(GOBP:"apoptotic process") [pos:10] "Cryotherapy" should be qualified with a valid namespace
1841 SET MeSHDisease = "DNA microarray" "DNA microarray" is not defined in the MeSHDisease annotation
1869 SET Disease = "HCT116" "HCT116" is not defined in the Disease annotation
2136 a(SFRE) -> a(CHEBI:"5-fluorouracil") [pos:2] "SFRE" should be qualified with a valid namespace
2140 a(SFRE) -| bp(MESHPP:"Drug Resistance") [pos:2] "SFRE" should be qualified with a valid namespace
2144 a(SFRE) -| p(HGNC:TK1) [pos:2] "SFRE" should be qualified with a valid namespace
2145 a(SFRE) -| p(HGNC:TYMS) [pos:2] "SFRE" should be qualified with a valid namespace
2156 a(HGNC:PDK3) -> bp(MESHPP:"Drug Resistance") Abundance HGNC:PDK3 should be encoded as one of: miRNA, Gene, RNA, Protein
2260 complex(p(HGNC:EGFR),a(panitumumab)) [pos:23] "panitumumab" should be qualified with a valid namespace
2271 a("miR-128") -> bp(MESHPP:"DNA Damage") [pos:2] "miR-128" should be qualified with a valid namespace
2275 a("miR-21") -- path(MESHD:"Carcinoma, Squamous Cell") [pos:2] "miR-21" should be qualified with a valid namespace
2276 a("miR-106b") -- path(MESHD:"Carcinoma, Squamous Cell") [pos:2] "miR-106b" should be qualified with a valid namespace
2280 a("miR-375") -- path(MESHD:"Carcinoma, Squamous Cell") [pos:2] "miR-375" should be qualified with a valid namespace
2319 SET CellLine = "Caco_2 cell" "Caco_2 cell" is not defined in the CellLine annotation
2379 a(hypermethylation) -| r(HGNC:TFAP2E) [pos:2] "hypermethylation" should be qualified with a valid namespace
2398 SET CellLine = {"SW620","HCT15","WiDr"} "WiDr" is not defined in the CellLine annotation
2411 a(SCHEM:"SN 38") -> p(ZFIN:top1) 'g'
2471 a(CHEBI:sulindac) -| tloc(p(HGNC:CTNNB1)) [pos:25] Unqualified translocation: a(CHEBI:sulindac) -| tloc(p(HGNC:CTNNB1)) [['Protein', 'HGNC', 'CTNNB1']]
2504 a(thiazolides) -> bp(GOBP:"apoptotic process") [pos:2] "thiazolides" should be qualified with a valid namespace
2509 a(thiazolides) -> p(HGNC:MAPK9) [pos:2] "thiazolides" should be qualified with a valid namespace
2510 a(thiazolides) -> p(HGNC:MAPK14) [pos:2] "thiazolides" should be qualified with a valid namespace
2511 a(thiazolides) -> (p(HGNC:MAPK9) -> bp(GOBP:"cell death")) [pos:2] "thiazolides" should be qualified with a valid namespace
2512 a(thiazolides) -> (p(HGNC:MAPK14) -> bp(GOBP:"cell death")) [pos:2] "thiazolides" should be qualified with a valid namespace
2539 a(thiazolide) -> kin(p(HGNC:MAPK9)) [pos:2] "thiazolide" should be qualified with a valid namespace
2540 a(thiazolide) -> p(HGNC:BCL2L11) [pos:2] "thiazolide" should be qualified with a valid namespace
2598 complex(a(CHEBI:"5-fluorouracil"),a(SC144)) -| bp(GOBP:"cell growth") [pos:36] "SC144" should be qualified with a valid namespace
2602 complex(a(CHEBI:oxaliplatin),a(SC144)) -| bp(GOBP:"cell growth") [pos:31] "SC144" should be qualified with a valid namespace
2608 complex(a(SC144),a(SCHEM:Paclitaxel)) -| bp(GOBP:"cell growth") [pos:10] "SC144" should be qualified with a valid namespace
2615 complex(a(SC144),a(SCHEM:Paclitaxel)) -| bp(GOBP:"cell growth") [pos:10] "SC144" should be qualified with a valid namespace
2675 bp(GOBP:"histone deacetylase inhibitor activity") -- bp(GOBP:"apoptotic process") "histone deacetylase inhibitor activity" is not in the GOBP namespace
2682 a(LBH589) -| p(HGNC:AKT1) [pos:2] "LBH589" should be qualified with a valid namespace
2709 r("miR-17-5p") -> path(MESHD:"Neoplasm Metastasis") [pos:2] "miR-17-5p" should be qualified with a valid namespace
2713 r("miR-17-5p") -> bp(MESHPP:"Drug Resistance") [pos:2] "miR-17-5p" should be qualified with a valid namespace
2714 r("miR-17-5p") -| p(HGNC:PTEN) [pos:2] "miR-17-5p" should be qualified with a valid namespace
2719 r("miR-17-5p") -> bp(GOBP:"cell invasion") [pos:2] "miR-17-5p" should be qualified with a valid namespace
2730 r("miR-34a") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-34a" should be qualified with a valid namespace
2731 r("miR-34a") -| p(HGNC:SIRT1) [pos:2] "miR-34a" should be qualified with a valid namespace
2732 r("miR-34a") -| p(HGNC:E2F3) [pos:2] "miR-34a" should be qualified with a valid namespace
2738 r("miR-34a") -| path(MESHD:"Neoplasm Metastasis") [pos:2] "miR-34a" should be qualified with a valid namespace
2739 r("miR-34a") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-34a" should be qualified with a valid namespace
2743 r("miR-34a") -| path(MESHD:"Neoplasms") [pos:2] "miR-34a" should be qualified with a valid namespace
2820 p(HGNC:HMGB1) -> bp(GOBP:"vascular endothelial growth factor receptor binding") "vascular endothelial growth factor receptor binding" is not in the GOBP namespace
2881 p(HGNC:BRAF) -| p(HGNC:TGFBRAP1,pmod(P,Serine)) General Parser Failure on line 2881 at pos 31: p(HGNC:BRAF) -| p(HGNC:TGFBRAP1,pmod(P,Serine))
2882 p(HGNC:TGFBRAP1,pmod(P,Serine)) -| bp(MESHPP:"Drug Resistance") General Parser Failure on line 2882 at pos 15: p(HGNC:TGFBRAP1,pmod(P,Serine)) -| bp(MESHPP:"Drug Resistance")
2928 a(SCHEM:"SN 38") -| p(ZFIN:top1) 'g'
3001 a(EHT6706) -- bp(MESHPP:Polymerization) [pos:2] "EHT6706" should be qualified with a valid namespace
3002 a(EHT6706) -| a(GOCC:microtubule) [pos:2] "EHT6706" should be qualified with a valid namespace
3003 a(SCHEM:Colchicine) -| a(GOCC:microtubule) Abundance GOCC:microtubule should be encoded as one of: Complex
3009 a(EHT6706) -| bp(GOBP:"cell growth") [pos:2] "EHT6706" should be qualified with a valid namespace
3014 a(EHT6706) -| bp(GOBP:"cell migration") [pos:2] "EHT6706" should be qualified with a valid namespace
3018 a(EHT6706) -| bp(GOBP:angiogenesis) [pos:2] "EHT6706" should be qualified with a valid namespace
3029 a(ZJW) -| p(SFAM:"AKT Family") [pos:2] "ZJW" should be qualified with a valid namespace
3030 a(ZJW) -| p(HGNC:NFKB1) [pos:2] "ZJW" should be qualified with a valid namespace
3031 a(ZJW) -| bp(MESHPP:"Drug Resistance") [pos:2] "ZJW" should be qualified with a valid namespace
3035 a(SCHEM:"LY 294002") -| p(HGNC:AKT1,pmod(P,Serine,473)) General Parser Failure on line 3035 at pos 35: a(SCHEM:"LY 294002") -| p(HGNC:AKT1,pmod(P,Serine,473))
3036 a(ZJW) -| p(HGNC:NFKB1,pmod(P,Serine,473)) [pos:2] "ZJW" should be qualified with a valid namespace
3038 a(ZJW) -| p(HGNC:NFKB1,pmod(P)) [pos:2] "ZJW" should be qualified with a valid namespace
3062 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']]
3121 a(PZH) -| bp(GOBP:"cell proliferation") [pos:2] "PZH" should be qualified with a valid namespace
3122 a(PZH) -| bp(GOBP:"cell growth") [pos:2] "PZH" should be qualified with a valid namespace
3123 a(PZH) -> bp(GOBP:"apoptotic process") [pos:2] "PZH" should be qualified with a valid namespace
3128 a(PZH) -| bp(GOBP:angiogenesis) [pos:2] "PZH" should be qualified with a valid namespace
3134 a(PHZ) -| bp(GOBP:"cell growth") [pos:2] "PHZ" should be qualified with a valid namespace
3138 a(PHZ) -| p(HGNC:ABCG2) [pos:2] "PHZ" should be qualified with a valid namespace
3139 a(PHZ) -| p(HGNC:ABCB1) [pos:2] "PHZ" should be qualified with a valid namespace
3150 bp(GOBP:"cell proliferation") -- a("cancer stem cells") [pos:35] "cancer stem cells" should be qualified with a valid namespace
3154 bp(MESHPP:"Drug Resistance") -- a("cancer stem cells") [pos:34] "cancer stem cells" should be qualified with a valid namespace
3159 r("miR-451") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-451" should be qualified with a valid namespace
3163 r("miR-451") -| bp(GOBP:"cell growth") [pos:2] "miR-451" should be qualified with a valid namespace
3171 a("miR-451") -- p(HGNC:PTGS2) [pos:2] "miR-451" should be qualified with a valid namespace
3177 r("miR-451") -> p(HGNC:MIF) [pos:2] "miR-451" should be qualified with a valid namespace
3185 r("miR-451") -| p(HGNC:ABCB1) [pos:2] "miR-451" should be qualified with a valid namespace
3196 a(Dbait) -| bp(GOBP:"DNA repair") [pos:2] "Dbait" should be qualified with a valid namespace
3202 a(Dbait) -| bp(MESHPP:"Drug Resistance") [pos:2] "Dbait" should be qualified with a valid namespace
3209 a(Dbait) -> (complex(a(SCHEM:Oxaliplatin),a(SCHEM:"5-fluorouracil")) -| path(MESHD:"Colorectal Neoplasms")) [pos:2] "Dbait" should be qualified with a valid namespace
3214 a(Dbait) -| bp(GOBP:angiogenesis) [pos:2] "Dbait" should be qualified with a valid namespace
3215 a(Dbait) -> bp(GOBP:"necrotic cell death") [pos:2] "Dbait" should be qualified with a valid namespace
3216 a(Dbait) -> bp(GOBP:"apoptotic process") [pos:2] "Dbait" should be qualified with a valid namespace
3217 a(Dbait) -| bp(GOBP:"cell proliferation") [pos:2] "Dbait" should be qualified with a valid namespace
3239 SET MeSHDisease = "MESHD:\"Liver Neoplasms\"" "MESHD:\"Liver Neoplasms\"" is not defined in the MeSHDisease annotation
3245 bp(GOBP:"aldehyde reductase activity") positiveCorrelation path(MESHD:Neoplasms) "aldehyde reductase activity" is not in the GOBP namespace
3266 r("miR-203") -| p(HGNC:ATM) [pos:2] "miR-203" should be qualified with a valid namespace
3270 r("miR-203") -> bp(MESHPP:"Drug Resistance") [pos:2] "miR-203" should be qualified with a valid namespace
3274 r("miR-203") -- bp(MESHPP:"Drug Resistance") [pos:2] "miR-203" should be qualified with a valid namespace
3298 r("miR-203") -| p(HGNC:ATM) [pos:2] "miR-203" should be qualified with a valid namespace
3299 r("miR-203") -> bp(MESHPP:"Drug Resistance") [pos:2] "miR-203" should be qualified with a valid namespace
3315 p(HGNC:KRAS) -- path(MESHD:"Drug Resistance") "Drug Resistance" is not in the MESHD namespace
3334 p(HGNC:CXCR4) -- a(Endostar) [pos:19] "Endostar" should be qualified with a valid namespace
3338 p(HGNC:HIF1A) -- a(Endostar) [pos:19] "Endostar" should be qualified with a valid namespace
3339 p(HGNC:EPAS1) -- a(Endostar) [pos:19] "Endostar" should be qualified with a valid namespace
3343 composite(a(endostar),a(CHEBI:oxaliplatin)) -| bp(GOBP:"cell adhesion") [pos:12] "endostar" should be qualified with a valid namespace
3344 composite(a(endostar),a(CHEBI:oxaliplatin)) -| bp(GOBP:"cell proliferation") [pos:12] "endostar" should be qualified with a valid namespace
3345 composite(a(endostar),a(CHEBI:oxaliplatin)) -| (r(HGNC:CXCR4) -| bp(GOBP:"cell adhesion")) [pos:12] "endostar" should be qualified with a valid namespace
3346 composite(a(endostar),a(CHEBI:oxaliplatin)) -| (r(HGNC:CXCR4) -| bp(GOBP:"cell proliferation")) [pos:12] "endostar" should be qualified with a valid namespace
3351 composite(a(endostar),a(CHEBI:oxaliplatin)) -| r(HGNC:CXCR4) [pos:12] "endostar" should be qualified with a valid namespace
3363 a(endostar) -| p(HGNC:CXCR4) [pos:2] "endostar" should be qualified with a valid namespace
3364 a(endostar) -| p(HGNC:EPAS1) [pos:2] "endostar" should be qualified with a valid namespace
3370 a(endostar) -| bp(MESHPP:"Drug Resistance") [pos:2] "endostar" should be qualified with a valid namespace
3413 SET Anatomy = "Serum" "Serum" is not defined in the Anatomy annotation
3415 SET MeSHDisease = "Colorectal Neoplsms" "Colorectal Neoplsms" is not defined in the MeSHDisease annotation
3431 path(MESHD:"Colorectal Neoplasms") -- p(HGNC:"COMMD3-BMI1") Protein HGNC:COMMD3-BMI1 should be encoded as one of: miRNA, Gene, RNA
3510 r(miRNA) -| p(HGNC:PEBP1) [pos:2] "miRNA" should be qualified with a valid namespace
3621 a(CHEBI:fingolimod) -> bp(GOBP:"autophagic vacuole assembly") "autophagic vacuole assembly" is not in the GOBP namespace
3746 r("miR-328") -- path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-328" should be qualified with a valid namespace
3750 r("miR-328") -| bp(MESHPP:"Drug Resistance") [pos:2] "miR-328" should be qualified with a valid namespace
3754 r("miR-328") -| p(HGNC:ABCG2) [pos:2] "miR-328" should be qualified with a valid namespace
3758 r("miR-328") -| p(HGNC:MMP16) [pos:2] "miR-328" should be qualified with a valid namespace
3779 p(HGNC:EGFR) -> a("PF-04691502") [pos:18] "PF-04691502" should be qualified with a valid namespace
3784 a("PF-04691502") -> p(HGNC:EGFR) [pos:2] "PF-04691502" should be qualified with a valid namespace
3785 a("PF-04691502") -> p(HGNC:ERBB2) [pos:2] "PF-04691502" should be qualified with a valid namespace
3786 a("PF-04691502") -> p(HGNC:ERBB3) [pos:2] "PF-04691502" should be qualified with a valid namespace
3787 a("PF-04691502") -> p(HGNC:FOXO3) [pos:2] "PF-04691502" should be qualified with a valid namespace
3789 bp(GOBP:"phosphatidylinositol-3 kinase activity") -| p(HGNC:FOXO3) "phosphatidylinositol-3 kinase activity" is not in the GOBP namespace
3790 a("PF-04691502") -> (p(HGNC:FOXO3) -> p(HGNC:EGFR)) [pos:2] "PF-04691502" should be qualified with a valid namespace
3791 a("PF-04691502") -> (p(HGNC:FOXO3) -> p(HGNC:ERBB2)) [pos:2] "PF-04691502" should be qualified with a valid namespace
3792 a("PF-04691502") -> (p(HGNC:FOXO3) -> p(HGNC:ERBB3)) [pos:2] "PF-04691502" should be qualified with a valid namespace
3798 a("PF-04691502") -> p(HGNC:EGFR) [pos:2] "PF-04691502" should be qualified with a valid namespace
3804 a(dacomitinib) -| p(HGNC:EGFR) [pos:2] "dacomitinib" should be qualified with a valid namespace
3831 SET Trial = "NCIC CTG CO.17" "Trial" is not defined
3838 g(dbSNP:rs1801274) -> p(HGNC:FCGR2A, sub(H,131,R)) "dbSNP" is not a defined namespace
3839 p(HGNC:FCGR2A, sub(H,131,R)) -- a("Cetuximab related outcomes") [pos:34] "Cetuximab related outcomes" should be qualified with a valid namespace
3840 p(HGNC:FCGR3A, sub(F,158,V)) -- a("Cetuximab related outcomes") [pos:34] "Cetuximab related outcomes" should be qualified with a valid namespace
3846 composite(p(HGNC:FCGR2A), a("Cetuximab")) -> bp("survival rate") [pos:28] "Cetuximab" should be qualified with a valid namespace
3847 composite(p(HGNC:FCGR2A sub(F,158,V)), a("Cetuximab")) causesNoChange bp("survival rate") General Parser Failure on line 3847 at pos 24: composite(p(HGNC:FCGR2A sub(F,158,V)), a("Cetuximab")) causesNoChange bp("survival rate")
3889 a("Cetuximab") =| p(HGNC:EGFR) [pos:2] "Cetuximab" should be qualified with a valid namespace
3915 SET Trial = "GOG 182" "Trial" is not defined
3922 path(DO:"ovarian mucinous neoplasm") -| a("surviva rate") [pos:42] "surviva rate" should be qualified with a valid namespace
3945 composite(a(CHEBI:"oxaliplatin"), a("Cetuximab")) -| path(MESHD:"Colorectal Neoplasms") [pos:36] "Cetuximab" should be qualified with a valid namespace
3958 a("neoadjuvant") -> bp("survival rate") [pos:2] "neoadjuvant" should be qualified with a valid namespace
3970 a("Bevacizumab") -| path(MESHD:"Neoplasms") [pos:2] "Bevacizumab" should be qualified with a valid namespace
3978 composite(a(CHEBI:"lenalidomide"),a("Bevacizumab")) -| path(MESHD:"Neoplasms") [pos:36] "Bevacizumab" should be qualified with a valid namespace
3979 composite(a(CHEBI:"lenalidomide"),a("Bevacizumab")) causesNoChange path("Drug Toxicity") [pos:36] "Bevacizumab" should be qualified with a valid namespace
3989 a("FOLFIRI") hasMember list(a(CHEBI:"Calcium folinate"), a(CHEBI:"5-fluorouracil"), a(CHEBI:"irinotecan")) [pos:2] "FOLFIRI" should be qualified with a valid namespace
3990 composite(a("Bevacizumab"),a("FOLFIRI")) -> bp("survival rate") [pos:12] "Bevacizumab" should be qualified with a valid namespace
4002 a("FOLFOX") hasMember list(a(CHEBI:"Calcium folinate"), a(CHEBI:"5-fluorouracil"), a(CHEBI:"oxaliplatin")) [pos:2] "FOLFOX" should be qualified with a valid namespace
4003 composite(a("Bevacizumab"),a("FOLFOX")) -> bp("survival rate") [pos:12] "Bevacizumab" should be qualified with a valid namespace
4009 composite(a("Bevacizumab"),a("FOLFOX")) -| path(MESHD:"Colorectal Neoplasms") [pos:12] "Bevacizumab" should be qualified with a valid namespace
4021 SET TisueType = "non-cancerous" "TisueType" is not defined
4023 a("FOLFOX") -> a("Chemoresistance") [pos:2] "FOLFOX" should be qualified with a valid namespace
4024 a("FOLFIRI") -> a("Chemoresistance") [pos:2] "FOLFIRI" should be qualified with a valid namespace
4037 a("loaded liposomes") hasMember list(a(CHEBI:"Calcium folinate"), a(CHEBI:"oxaliplatin"), a(CHEBI:"5-fluorouracil"), a("5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin")) [pos:2] "loaded liposomes" should be qualified with a valid namespace
4039 a("loaded liposomes") -| bp(GOBP:"cell growth") [pos:2] "loaded liposomes" should be qualified with a valid namespace
4044 a("drug encapsulation") -| a("Chemoresistance") [pos:2] "drug encapsulation" should be qualified with a valid namespace
4056 g(HGNC:KRAS) biomarkerFor bp("anti-EGFR therapy resistance") [pos:29] "anti-EGFR therapy resistance" should be qualified with a valid namespace
4057 g(HGNC:NRAS) biomarkerFor bp("anti-EGFR therapy resistance") [pos:29] "anti-EGFR therapy resistance" should be qualified with a valid namespace
4062 p(HGNC:BRAF, sub(V,600,E)) biomarkerFor bp("patient prognosis") [pos:43] "patient prognosis" should be qualified with a valid namespace
4067 g(HGNC:UGT1A1) biomarkerFor path("Drug Toxicity") [pos:33] "Drug Toxicity" should be qualified with a valid namespace
4078 composite(a(CHEBI:"oxaliplatin"), a(CHEBI:"5-fluorouracil")) -> a("hematologic event") [pos:66] "hematologic event" should be qualified with a valid namespace
4079 composite(a(CHEBI:"oxaliplatin"), a(CHEBI:"5-fluorouracil")) -> a("grade 3 hematologic toxicity") [pos:66] "grade 3 hematologic toxicity" should be qualified with a valid namespace
4091 a("CapOx") hasMember list(a(CHEBI:"capecitabine"),a(CHEBI:"oxaliplatin")) [pos:2] "CapOx" should be qualified with a valid namespace
4092 a("CapOx") -| path("neuropathy") [pos:2] "CapOx" should be qualified with a valid namespace
4093 a("FOLFOX") -| path("neuropathy") [pos:2] "FOLFOX" should be qualified with a valid namespace
4094 a("FOLFIRI") -| path("neuropathy") [pos:2] "FOLFIRI" should be qualified with a valid namespace
4113 a("ruthenacycles") -| bp(GOBP:"cell growth") [pos:2] "ruthenacycles" should be qualified with a valid namespace
4118 a("ruthenacycles") -> sec(p(HGNC:IFNG)) [pos:2] "ruthenacycles" should be qualified with a valid namespace
4119 a("ruthenacycles") -| sec(p(HGNC:CCL5)) [pos:2] "ruthenacycles" should be qualified with a valid namespace
4120 a("ruthenacycles") -| sec(p(HGNC:IGF1)) [pos:2] "ruthenacycles" should be qualified with a valid namespace
4125 a("ruthenacycles") -- p(RPS21) [pos:2] "ruthenacycles" should be qualified with a valid namespace
4126 a("ruthenacycles") -- bp(GOBP:"regulation of cytokine secretion") [pos:2] "ruthenacycles" should be qualified with a valid namespace
4138 a("Bevacizumab") -> bp("survival rate") [pos:2] "Bevacizumab" should be qualified with a valid namespace
4139 a("Aflibercept") -> bp("survival rate") [pos:2] "Aflibercept" should be qualified with a valid namespace
4140 a(CHEBI:regorafenib) -> bp("survival rate") [pos:27] "survival rate" should be qualified with a valid namespace
4141 a("Ramucirumab") -> bp("survival rate") [pos:2] "Ramucirumab" should be qualified with a valid namespace
4146 a("Fruquintinib") -> bp("survival rate") #On PubChem [pos:2] "Fruquintinib" should be qualified with a valid namespace
4147 a("Famitinib") -> bp("survival rate") #On PubChem [pos:2] "Famitinib" should be qualified with a valid namespace
4148 a("nintedanib") -> bp("survival rate") #On PubChem [pos:2] "nintedanib" should be qualified with a valid namespace
4153 a("VGX-100") =| p(HGNC:VEGFC)) [pos:2] "VGX-100" should be qualified with a valid namespace
4154 composite(a("VGX-100"),a("bevacizumab")) =| p(HGNC:KDR) [pos:12] "VGX-100" should be qualified with a valid namespace
4155 composite(a("VGX-100"),a("bevacizumab")) =| p(HGNC:FLT4) [pos:12] "VGX-100" should be qualified with a valid namespace
4160 a("tanibirumab") =| p(HGNC:KDR) [pos:2] "tanibirumab" should be qualified with a valid namespace
4161 a("vanucizumab") =| p(HGNC:VEGFA) [pos:2] "vanucizumab" should be qualified with a valid namespace
4162 a("vanucizumab") =| p(HGNC:ANGPT2) [pos:2] "vanucizumab" should be qualified with a valid namespace
4175 a("MM-1151") -| bp(GOBP:"cell growth") [pos:2] "MM-1151" should be qualified with a valid namespace
4176 a("MM-1151") -| path(MESHD:"Colorectal Neoplasms") [pos:2] "MM-1151" should be qualified with a valid namespace
4177 a("MM-1151") -| path(MESHD:"Neoplasm Invasiveness") [pos:2] "MM-1151" should be qualified with a valid namespace
4178 a("MM-1151") -| a("Cetuximab resistance") [pos:2] "MM-1151" should be qualified with a valid namespace
4191 a("Cetuximab") -| bp(GOBP:"epidermal growth factor receptor signaling pathway") [pos:2] "Cetuximab" should be qualified with a valid namespace
4192 a("panitumumab") -| bp(GOBP:"epidermal growth factor receptor signaling pathway") [pos:2] "panitumumab" should be qualified with a valid namespace
4194 a("Cetuximab") -- p(HGNC:KRAS) [pos:2] "Cetuximab" should be qualified with a valid namespace
4195 a("panitumumab") -- p(HGNC:KRAS) [pos:2] "panitumumab" should be qualified with a valid namespace
4211 composite(a(CHEBI:"5-fluorouracil"), a(CHEBI:"capecitabine")) -| a("mortality") [pos:67] "mortality" should be qualified with a valid namespace
4216 composite(a(CHEBI:"5-fluorouracil"), a(CHEBI:"capecitabine")) causesNoChange a("mortality") [pos:79] "mortality" should be qualified with a valid namespace
4227 p(HGNC:TP53) -> a("p53 antibody") [pos:18] "p53 antibody" should be qualified with a valid namespace
4233 a("p53 antibody") biomarkerFor path(MESHD:"colorectal cancer") [pos:2] "p53 antibody" should be qualified with a valid namespace
4239 a("FOLFOX"), a("Bevacizumab") -| a("CEA") [pos:2] "FOLFOX" should be qualified with a valid namespace
4240 a("FOLFOX"), a("Bevacizumab") -| a("CA19-9") [pos:2] "FOLFOX" should be qualified with a valid namespace
4246 a("FOLFOX"), a("Bevacizumab") -| a("p53 antibody") [pos:2] "FOLFOX" should be qualified with a valid namespace
4251 a("p53 antibody") biomarkerFor path("tumor recurrence") [pos:2] "p53 antibody" should be qualified with a valid namespace
4262 composite(a(CHEBI:"oxaliplatin"),a("traditional plant-based medicines")) -| path(MESHD:"Nausea") [pos:35] "traditional plant-based medicines" should be qualified with a valid namespace
4263 composite(a(CHEBI:"oxaliplatin"),a("traditional plant-based medicines")) -| path(MESHD:"Vomoting") [pos:35] "traditional plant-based medicines" should be qualified with a valid namespace
4275 a("Atractylodes macrocephala") -| path(MESHD:"Nausea") [pos:2] "Atractylodes macrocephala" should be qualified with a valid namespace
4276 a("Atractylodes macrocephala") -| path(MESHD:"Vomiting") [pos:2] "Atractylodes macrocephala" should be qualified with a valid namespace
4277 a("Atractylodes macrocephala") -> bp(GOBP:"antioxidant activity") [pos:2] "Atractylodes macrocephala" should be qualified with a valid namespace
4278 a("Atractylodes macrocephala") -> bp("gastroprotective effects") [pos:2] "Atractylodes macrocephala" should be qualified with a valid namespace
4279 a("Atractylodes macrocephala") -- bp(MESHPPP:"Gastrointestinal Motility") [pos:2] "Atractylodes macrocephala" should be qualified with a valid namespace
4280 a("Poria cocos") -| path(MESHD:"Nausea") [pos:2] "Poria cocos" should be qualified with a valid namespace
4281 a("Poria cocos") -| path(MESHD:"Vomiting") [pos:2] "Poria cocos" should be qualified with a valid namespace
4282 a("Poria cocos") -> bp(GOBP:"antioxidant activity") [pos:2] "Poria cocos" should be qualified with a valid namespace
4283 a("Poria cocos") -> bp("gastroprotective effects") [pos:2] "Poria cocos" should be qualified with a valid namespace
4284 a("Poria cocos") -- bp(MESHPPP:"Gastrointestinal Motility") [pos:2] "Poria cocos" should be qualified with a valid namespace
4285 a("Coix lacryma-jobi") -| path(MESHD:"Nausea") [pos:2] "Coix lacryma-jobi" should be qualified with a valid namespace
4286 a("Coix lacryma-jobi") -| path(MESHD:"Vomiting") [pos:2] "Coix lacryma-jobi" should be qualified with a valid namespace
4287 a("Coix lacryma-jobi") -> bp(GOBP:"antioxidant activity") [pos:2] "Coix lacryma-jobi" should be qualified with a valid namespace
4288 a("Coix lacryma-jobi") -> bp("gastroprotective effects") [pos:2] "Coix lacryma-jobi" should be qualified with a valid namespace
4289 a("Coix lacryma-jobi") -- bp(MESHPPP:"Gastrointestinal Motility") [pos:2] "Coix lacryma-jobi" should be qualified with a valid namespace
4290 a("Astragalus membranaceus") -| path(MESHD:"Nausea") [pos:2] "Astragalus membranaceus" should be qualified with a valid namespace
4291 a("Astragalus membranaceus") -| path(MESHD:"Vomiting") [pos:2] "Astragalus membranaceus" should be qualified with a valid namespace
4292 a("Astragalus membranaceus") -> bp(GOBP:"antioxidant activity") [pos:2] "Astragalus membranaceus" should be qualified with a valid namespace
4293 a("Astragalus membranaceus") -> bp("gastroprotective effects") [pos:2] "Astragalus membranaceus" should be qualified with a valid namespace
4294 a("Astragalus membranaceus") -- bp(MESHPPP:"Gastrointestinal Motility") [pos:2] "Astragalus membranaceus" should be qualified with a valid namespace
4295 a("Glycyrrhiza uralensis") -| path(MESHD:"Nausea") [pos:2] "Glycyrrhiza uralensis" should be qualified with a valid namespace
4296 a("Glycyrrhiza uralensis") -| path(MESHD:"Vomiting") [pos:2] "Glycyrrhiza uralensis" should be qualified with a valid namespace
4297 a("Glycyrrhiza uralensis") -> bp(GOBP:"antioxidant activity") [pos:2] "Glycyrrhiza uralensis" should be qualified with a valid namespace
4298 a("Glycyrrhiza uralensis") -> bp("gastroprotective effects") [pos:2] "Glycyrrhiza uralensis" should be qualified with a valid namespace
4299 a("Glycyrrhiza uralensis") -- bp(MESHPPP:"Gastrointestinal Motility") [pos:2] "Glycyrrhiza uralensis" should be qualified with a valid namespace
4300 a("Panax ginseng") -| path(MESHD:"Nausea") [pos:2] "Panax ginseng" should be qualified with a valid namespace
4301 a("Panax ginseng") -| path(MESHD:"Vomiting") [pos:2] "Panax ginseng" should be qualified with a valid namespace
4302 a("Panax ginseng") -> bp(GOBP:"antioxidant activity") [pos:2] "Panax ginseng" should be qualified with a valid namespace
4303 a("Panax ginseng") -> bp("gastroprotective effects") [pos:2] "Panax ginseng" should be qualified with a valid namespace
4304 a("Panax ginseng") -- bp(MESHPPP:"Gastrointestinal Motility") [pos:2] "Panax ginseng" should be qualified with a valid namespace
4312 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
4321 a("Panitumumab") =| p(HGNC:EGFR) [pos:2] "Panitumumab" should be qualified with a valid namespace
4322 composite(a("Panitumumab"),a("FOLFOXIRI")) -> path(MESHD:"Diarrhea") [pos:12] "Panitumumab" should be qualified with a valid namespace
4323 composite(a("Panitumumab"),a("FOLFOXIRI")) -> path("rash") [pos:12] "Panitumumab" should be qualified with a valid namespace
4329 composite(a("Panitumumab"),a("FOLFOXIRI"),p(HGNC:KRAS)) -| bp("survival rate") [pos:12] "Panitumumab" should be qualified with a valid namespace
4330 composite(a("Panitumumab"),a("FOLFOXIRI"),p(HGNC:KRAS)) -| bp("survival rate") [pos:12] "Panitumumab" should be qualified with a valid namespace
4347 a("bevacizumab") -| bp(GOBP:"Angiogenesis") [pos:2] "bevacizumab" should be qualified with a valid namespace
4348 a("bevacizumab") =| p(HGNC:VEGFA) [pos:2] "bevacizumab" should be qualified with a valid namespace
4349 a("aflibercept") -| bp(GOBP:"Angiogenesis") [pos:2] "aflibercept" should be qualified with a valid namespace
4350 a("aflibercept") =| p(HGNC:VEGFA) [pos:2] "aflibercept" should be qualified with a valid namespace
4351 a("ramucirumab") -| bp(GOBP:"Angiogenesis") [pos:2] "ramucirumab" should be qualified with a valid namespace
4352 a("ramucirumab") =| p(HGNC:KDR) [pos:2] "ramucirumab" should be qualified with a valid namespace
4366 SET Trial = "SIRFLOX" "Trial" is not defined
4368 composite(a("selective internal radiation therapy"), a("FOLFOX")) causesNoChange bp("survival rate") [pos:12] "selective internal radiation therapy" should be qualified with a valid namespace
4369 composite(a("selective internal radiation therapy"), a("FOLFOX")) -| path(MESHD:"Disease Progression") [pos:12] "selective internal radiation therapy" should be qualified with a valid namespace
4383 a(CHEBI:"yttrium atom") -> bp("survival rate") [pos:30] "survival rate" should be qualified with a valid namespace
4384 composite(a(CHEBI:"yttrium atom"),a("chemotherapy")) -> bp("survival rate") [pos:36] "chemotherapy" should be qualified with a valid namespace
4396 a("Cetuximab") -> bp("survival rate") [pos:2] "Cetuximab" should be qualified with a valid namespace
4397 a("Bevacizumab") -> bp("survival rate") [pos:2] "Bevacizumab" should be qualified with a valid namespace
4398 a("Panitumumab") -> bp("survival rate") [pos:2] "Panitumumab" should be qualified with a valid namespace
4399 a("Panitumumab") =| p(HGNC:EGFR) [pos:2] "Panitumumab" should be qualified with a valid namespace
4422 composite(a("Ramucirumab"),a("Chemotherapy")) -| bp(GOBP:"angiogenesis") [pos:12] "Ramucirumab" should be qualified with a valid namespace
4423 composite(a("Ramucirumab"),a("Chemotherapy")) -| path(MESHD:"Colorectal Neoplasms") [pos:12] "Ramucirumab" should be qualified with a valid namespace
4431 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
4436 a(CETIRI) hasMember list(a("Cetuximab"), a(CHEBI:"irinotecan")) [pos:2] "CETIRI" should be qualified with a valid namespace
4437 a(CHEBI:"LSM-1131") -| a("MET Pathway") "LSM-1131" is not in the CHEBI namespace
4438 a("MET pathway") -> bp("anti-EGFR therapy resistance") [pos:2] "MET pathway" should be qualified with a valid namespace
4444 a(CHEBI:"LSM-1131") -> path(MESHD:"Neutropenia") "LSM-1131" is not in the CHEBI namespace
4445 a(CHEBI:"LSM-1131") -> path(MESHD:"Diarrhea") "LSM-1131" is not in the CHEBI namespace
4446 a(CHEBI:"LSM-1131") -> path(MESHD:"Nausea") "LSM-1131" is not in the CHEBI namespace
4447 a(CHEBI:"LSM-1131") -> path("Rash") "LSM-1131" is not in the CHEBI namespace
4460 a("Chemotherapy") -> path(MESHD:"Malnutrition") [pos:2] "Chemotherapy" should be qualified with a valid namespace
4462 path(MESHD:"Malnutrition") -> path("Oncological outcomes") [pos:35] "Oncological outcomes" should be qualified with a valid namespace
4470 path(MESHD:"Malnutrition") -- a("treatment tolerability") [pos:32] "treatment tolerability" should be qualified with a valid namespace
4471 path(MESHD:"Malnutrition") -- path("Anastomotic Leakage") [pos:35] "Anastomotic Leakage" should be qualified with a valid namespace
4472 path(MESHD:"Malnutrition") -- bp("survival rate") [pos:33] "survival rate" should be qualified with a valid namespace
4491 a("biological therapy") -> bp("survival rate") [pos:2] "biological therapy" should be qualified with a valid namespace
4492 a("Bevacizumab") -> bp("survival rate") [pos:2] "Bevacizumab" should be qualified with a valid namespace
4504 a("Cetuximab") -> bp("survival rate") [pos:2] "Cetuximab" should be qualified with a valid namespace
4513 SET DiseaseType = "wild-type KRAS" "wild-type KRAS" is not defined in the DiseaseType annotation
4515 a("Cetuximab") -> bp("survival rate") [pos:2] "Cetuximab" should be qualified with a valid namespace
4517 SET DiseaseType = "mutated KRAS" "mutated KRAS" is not defined in the DiseaseType annotation
4519 a("Cetuximab") causesNoChange bp("survival rate") [pos:2] "Cetuximab" should be qualified with a valid namespace
4526 a("Early Tumor Shrinkage") biomarkerFor a("Cetuximab efficacy") [pos:2] "Early Tumor Shrinkage" should be qualified with a valid namespace
4537 composite(a("FOLFOXIRI"),a("bevacizumab")) -> bp("survival rate") [pos:12] "FOLFOXIRI" should be qualified with a valid namespace
4549 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
4554 a("panitumumab") =| p(HGNC:EGFR) [pos:2] "panitumumab" should be qualified with a valid namespace
4555 a("cetuximab") =| p(HGNC:EGFR) [pos:2] "cetuximab" should be qualified with a valid namespace
4556 g(HGNC:KRAS) biomarkerFor bp("panitumumab lack of response") [pos:29] "panitumumab lack of response" should be qualified with a valid namespace
4557 g(HGNC:KRAS) biomarkerFor bp("cetuximab lack of response") [pos:29] "cetuximab lack of response" should be qualified with a valid namespace
4565 a(RAS) hasMembers list(g(HGNC:KRAS),g(HGNC:NRAS)) [pos:2] "RAS" should be qualified with a valid namespace
4566 g(HGNC:KRAS) biomarkerFor bp("survival rate") [pos:29] "survival rate" should be qualified with a valid namespace
4567 g(HGNC:NRAS) biomarkerFor bp("survival rate") [pos:29] "survival rate" should be qualified with a valid namespace
4579 a("(99m)Tc-duramycin") positiveCorrelation bp(GOBP:"cell death") [pos:2] "(99m)Tc-duramycin" should be qualified with a valid namespace
4580 a("(99m)Tc-duramycin") positiveCorrelation p(HGNC:ANXA5) [pos:2] "(99m)Tc-duramycin" should be qualified with a valid namespace
4581 a("(99m)Tc-duramycin") positiveCorrelation p(HGNC:CASP3) [pos:2] "(99m)Tc-duramycin" should be qualified with a valid namespace
4582 a("(99m)Tc-duramycin") positiveCorrelation p(HGNC:CASP7) [pos:2] "(99m)Tc-duramycin" should be qualified with a valid namespace
4588 a("(99m)Tc-duramycin") positiveCorrelation a(CHEBI:"irinotecan") [pos:2] "(99m)Tc-duramycin" should be qualified with a valid namespace
4596 a("(99m)Tc-duramycin") positiveCorrelation a("Radiotherapy") [pos:2] "(99m)Tc-duramycin" should be qualified with a valid namespace
4597 a("(99m)Tc-duramycin") positiveCorrelation deg(p(HGNC:CASP3)) [pos:2] "(99m)Tc-duramycin" should be qualified with a valid namespace
4613 g(HGNC:ABCA9) biomarkerFor bp("Oxaliplatin treatment") [pos:31] "Oxaliplatin treatment" should be qualified with a valid namespace
4615 g(HGNC:ABCB11) biomarkerFor bp("Oxaliplatin treatment") [pos:31] "Oxaliplatin treatment" should be qualified with a valid namespace
4617 g(HGNC:ABCC10) biomarkerFor bp("Oxaliplatin treatment") [pos:31] "Oxaliplatin treatment" should be qualified with a valid namespace
4619 g(HGNC:ATP1A1) biomarkerFor bp("Oxaliplatin treatment") [pos:31] "Oxaliplatin treatment" should be qualified with a valid namespace
4621 g(HGNC:ATP1B2) biomarkerFor bp("Oxaliplatin treatment") [pos:31] "Oxaliplatin treatment" should be qualified with a valid namespace
4623 g(HGNC:ATP8B3) biomarkerFor bp("Oxaliplatin treatment") [pos:31] "Oxaliplatin treatment" should be qualified with a valid namespace
4625 g(HGNC:GSTM5) biomarkerFor bp("Oxaliplatin treatment") [pos:31] "Oxaliplatin treatment" should be qualified with a valid namespace
4627 g(HGNC:GRHPR) biomarkerFor bp("Oxaliplatin treatment") [pos:31] "Oxaliplatin treatment" should be qualified with a valid namespace
4639 composite(g(HGNC:UGT1A1, var(28)),a(CHEBI:"irinotecan")) -> path(MESHD:"Neutropenia") "irinotecan" is not in the CHEBI namespace
4640 composite(g(HGNC:UGT1A1, var(6)),a(CHEBI:"irinotecan")) -> path(MESHD:"Neutropenia") "irinotecan" is not in the CHEBI namespace
4653 composite(a(CHEBI:"lenalidomide"),a("FOLFOX")) -| path(MESHD:"Colorectal Neoplasms") [pos:36] "FOLFOX" should be qualified with a valid namespace
4659 composite(a(CHEBI:"lenalidomide"),a("FOLFOX")) -> path(MESHD:"Neutropenia") [pos:36] "FOLFOX" should be qualified with a valid namespace
4660 composite(a(CHEBI:"lenalidomide"),a("FOLFOX")) -> path(MESHD:"Thrombocytopenia") [pos:36] "FOLFOX" should be qualified with a valid namespace
4661 composite(a(CHEBI:"lenalidomide"),a("FOLFOX")) -> path(MESHD:"Fatigue") [pos:36] "FOLFOX" should be qualified with a valid namespace
4672 a("Cetuximab") =| p(HGNC:EGFR) [pos:2] "Cetuximab" should be qualified with a valid namespace
4673 a("Cetuximab") -> bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity") [pos:2] "Cetuximab" should be qualified with a valid namespace
4678 a("Fcγ receptors") hasMembers list(p(HGNC:FCGBP),p(HGNC:FCGR1A),p(HGNC:FCGR1B),g(HGNC:FCGR1CP),p(HGNC:FCGR2A),p(HGNC:FCGR2B),p(HGNC:FCGR2C),p(HGNC:FCGR3A),p(HGNC:FCGR3B),p(HGNC:FCGRT)) [pos:2] "Fcγ receptors" should be qualified with a valid namespace
4682 g(HGNC:FCGR1CP) -- bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity") "FCGR1CP" is not in the HGNC namespace
4699 p(HGNC:FCGR3A, pmod(V,V,158)) positiveCorrelation bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity") General Parser Failure on line 4699 at pos 13: p(HGNC:FCGR3A, pmod(V,V,158)) positiveCorrelation bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity")
4700 p(HGNC:FCGR3A, pmod(V,F,158)) positiveCorrelation bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity") General Parser Failure on line 4700 at pos 13: p(HGNC:FCGR3A, pmod(V,F,158)) positiveCorrelation bp(MESHPP:"Antibody-Dependent Cell Cytotoxicity")
4706 p(HGNC:FCGR3A, pmod(V,V,158)) positiveCorrelation bp("survival rate") General Parser Failure on line 4706 at pos 13: p(HGNC:FCGR3A, pmod(V,V,158)) positiveCorrelation bp("survival rate")
4711 a("Fcγ receptors") biomarkerFor a("Cetuximab Response") [pos:2] "Fcγ receptors" should be qualified with a valid namespace
4723 a("Bevacizumab") =| p(HGNC:VEGFA) [pos:2] "Bevacizumab" should be qualified with a valid namespace
4724 a("Bevacizumab") causesNoChange path(DO:"hemangioma of liver") [pos:2] "Bevacizumab" should be qualified with a valid namespace
4733 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
4740 a("FOLFIRI") hasMembers list(a(CHEBI:"Calcium folinate"), a(CHEBI:"5-fluorouracil"), a(CHEBI:"irinotecan")) [pos:2] "FOLFIRI" should be qualified with a valid namespace
4741 a("FUPEP") hasMembers list(a(CHEBI:"Calcium folinate"), a(CHEBI:"5-fluorouracil"), a("PEP02")) [pos:2] "FUPEP" should be qualified with a valid namespace
4747 a("FUPEP") -- path(MESHD:"Diarrhea") [pos:2] "FUPEP" should be qualified with a valid namespace
4748 a("FUPEP") -- path(MESHD:"Neutropenia") [pos:2] "FUPEP" should be qualified with a valid namespace
4749 a("FUPEP") -- path(MESHD:"Mucositis") [pos:2] "FUPEP" should be qualified with a valid namespace
4750 a("FUPEP") -- path(MESHD:"Alopecia") [pos:2] "FUPEP" should be qualified with a valid namespace
4751 a("FOLFIRI") -- path(MESHD:"Diarrhea") [pos:2] "FOLFIRI" should be qualified with a valid namespace
4752 a("FOLFIRI") -- path(MESHD:"Neutropenia") [pos:2] "FOLFIRI" should be qualified with a valid namespace
4753 a("FOLFIRI") -- path(MESHD:"Mucositis") [pos:2] "FOLFIRI" should be qualified with a valid namespace
4754 a("FOLFIRI") -- path(MESHD:"Alopecia") [pos:2] "FOLFIRI" should be qualified with a valid namespace
4777 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
4782 composite(a("necitumumab"),a("FOLFOX")) -- path(MESHD:"Neutropenia") [pos:12] "necitumumab" should be qualified with a valid namespace
4783 composite(a("necitumumab"),a("FOLFOX")) -- path(MESHD:"Asthenia") [pos:12] "necitumumab" should be qualified with a valid namespace
4784 composite(a("necitumumab"),a("FOLFOX")) -- path("Rash") [pos:12] "necitumumab" should be qualified with a valid namespace
4789 a("necitumumab") =| p(HGNC:EGFR) [pos:2] "necitumumab" should be qualified with a valid namespace
4790 composite(a("necitumumab"),a("FOLFOX")) -| path(MESHD:"Colorectal Neoplasms") [pos:12] "necitumumab" should be qualified with a valid namespace
4791 composite(a("necitumumab"),a("FOLFOX")) -> bp("survival rate") [pos:12] "necitumumab" should be qualified with a valid namespace
4799 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
4805 a("Bevacizumab") =| p(HGNC:VEGFA) [pos:2] "Bevacizumab" should be qualified with a valid namespace
4806 a("Cetuximab") =| p(HGNC:EGFR) [pos:2] "Cetuximab" should be qualified with a valid namespace
4807 a("Panitumumab") =| p(HGNC:EGFR) [pos:2] "Panitumumab" should be qualified with a valid namespace
4813 composite(a("Bevacizumab"),a("Cetuximab")) causesNoChange path(MESHD:"Colorectal Neoplasms") [pos:12] "Bevacizumab" should be qualified with a valid namespace
4814 composite(a("Bevacizumab"),a("Panitumumab")) causesNoChange path(MESHD:"Colorectal Neoplasms") [pos:12] "Bevacizumab" should be qualified with a valid namespace
4822 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
4829 a("Cetuximab") =| p(HGNC:EGFR) [pos:2] "Cetuximab" should be qualified with a valid namespace
4835 composite(a("Cetuximab"),a(CHEBI:"oxaliplatin")) -| p(HGNC:CASP3) [pos:12] "Cetuximab" should be qualified with a valid namespace
4836 composite(a("Cetuximab"),a(CHEBI:"oxaliplatin")) -| p(HGNC:CASP7) [pos:12] "Cetuximab" should be qualified with a valid namespace
4840 a(CHEBI:"oxaliplatin") -> a("reactive oxigen species") [pos:28] "reactive oxigen species" should be qualified with a valid namespace
4842 a(CHEBI:"oxaliplatin") -> bp("ROS dependent apoptotsis") [pos:29] "ROS dependent apoptotsis" should be qualified with a valid namespace
4843 a(CHEBI:"SN-38") -> a("reactive oxigen species") [pos:22] "reactive oxigen species" should be qualified with a valid namespace
4852 a("Cetuximab") -| p(HGNC:DUOX2) [pos:2] "Cetuximab" should be qualified with a valid namespace
4853 p(HGNC:DUOX2) -| bp("oxaliplatin cytotoxicity") [pos:20] "oxaliplatin cytotoxicity" should be qualified with a valid namespace
4854 a("Cetuximab") -> p(HGNC:MAPK14) [pos:2] "Cetuximab" should be qualified with a valid namespace
4855 p(HGNC:MAPK14) -| bp("oxaliplatin cytotoxicity") [pos:21] "oxaliplatin cytotoxicity" should be qualified with a valid namespace
4861 a("Cetuximab") -| p(HGNC:STAT1) [pos:2] "Cetuximab" should be qualified with a valid namespace
4862 a("Cetuximab") -| (p(HGNC:DUOX2) -> bp("ROS generation")) [pos:2] "Cetuximab" should be qualified with a valid namespace
4863 a("Cetuximab") -| (p(HGNC:MAPK14) -> bp(GOBP:"apoptotic process")) [pos:2] "Cetuximab" should be qualified with a valid namespace
4864 a("Cetuximab") -| a(CHEBI"oxaliplatin") [pos:2] "Cetuximab" should be qualified with a valid namespace
4889 a("Neoadjuvant concurrent chemoradiotherapy") -> path(MESHD:"Neutropenia") [pos:2] "Neoadjuvant concurrent chemoradiotherapy" should be qualified with a valid namespace
4904 a("irinotecan resistance") causesNoChange a("DEBIRI") [pos:2] "irinotecan resistance" should be qualified with a valid namespace
4905 a("DEBIRI") -| a("adverse events") [pos:2] "DEBIRI" should be qualified with a valid namespace
4917 a("Adjuvant FOLFOX chemotherapy") -> a("received dose intensity") [pos:2] "Adjuvant FOLFOX chemotherapy" should be qualified with a valid namespace
4925 SET DiseaseType = "mutated KRAS" "mutated KRAS" is not defined in the DiseaseType annotation
4930 p(HGNC:KRAS) biomarkerFor bp("therapy resistance") [pos:29] "therapy resistance" should be qualified with a valid namespace
4935 bp(GOBP:"regulation of Ras protein signal transduction") -> bp("cell growth") [pos:63] "cell growth" should be qualified with a valid namespace
4936 bp(GOBP:"MAPK cascade") -> bp("cell growth") [pos:30] "cell growth" should be qualified with a valid namespace
4941 composite(a(CHEBI:"selumetinib"),a("Cetuximab")) -> path("Rash") "selumetinib" is not in the CHEBI namespace
4942 composite(a(CHEBI:"selumetinib"),a("Cetuximab")) -> path(MESHD:"Nausea") "selumetinib" is not in the CHEBI namespace
4943 composite(a(CHEBI:"selumetinib"),a("Cetuximab")) -> path(MESHD:"Vomiting") "selumetinib" is not in the CHEBI namespace
4944 composite(a(CHEBI:"selumetinib"),a("Cetuximab")) -> path(MESHD:"Diarrhea") "selumetinib" is not in the CHEBI namespace
4945 composite(a(CHEBI:"selumetinib"),a("Cetuximab")) -> path(MESHD:"Fatigue") "selumetinib" is not in the CHEBI namespace
4966 SET DiseaseType = {"metastatic", "wild-type RAS"} "metastatic" is not defined in the DiseaseType annotation
4968 composite(a("Panitumumab"), a("FOLFOX")) -> bp("survival rate") [pos:12] "Panitumumab" should be qualified with a valid namespace
4980 composite(a("Bevacizumab"), a(CHEBI:"sorafenib")) -| path(MESHD:"Colorectal Neoplasms") [pos:12] "Bevacizumab" should be qualified with a valid namespace
4987 composite(a("Bevacizumab"), a(CHEBI:"sorafenib"), a("FOLFIRI")) -> a("disease stabilization") [pos:12] "Bevacizumab" should be qualified with a valid namespace
4998 SET DiseaseType = "wild-type KRAS" "wild-type KRAS" is not defined in the DiseaseType annotation
5000 composite(a("liver-specific intensive chemotherapy"),a("surgery")) -> bp("survival rate") [pos:12] "liver-specific intensive chemotherapy" should be qualified with a valid namespace
5021 composite(a("FOLFOX"), a("bevacizumab")) -| path(MESHD:"Colorectal Neoplasm") [pos:12] "FOLFOX" should be qualified with a valid namespace
5034 composite(a("FOLFIRI"),a("CT guided (125)I-seed implantation")) -> bp("survival rate") [pos:12] "FOLFIRI" should be qualified with a valid namespace
5050 a("early post operative chemotherapy") causesNoChange bp("survival rate") [pos:2] "early post operative chemotherapy" should be qualified with a valid namespace
5058 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
5064 composite(a("Bevacizumab"),a(CHEBI:"capecitabine")) -> path(MESHD:"Hand-Foot Syndrome") [pos:12] "Bevacizumab" should be qualified with a valid namespace
5070 composite(a("Bevacizumab"),a(CHEBI:"capecitabine")) -| path(MESHD:"Colorectal Neoplasms") [pos:12] "Bevacizumab" should be qualified with a valid namespace
5081 SET DiseaseType = "wild-type KRAS" "wild-type KRAS" is not defined in the DiseaseType annotation
5083 a("Cetuximab") =| p(HGNC:EGFR) [pos:2] "Cetuximab" should be qualified with a valid namespace
5093 a("Cetuximab") causesNoChange bp(GOBP:"cell growth") [pos:2] "Cetuximab" should be qualified with a valid namespace
5098 a("Cetuximab") causesNoChange bp(GOBP:"cell growth") [pos:2] "Cetuximab" should be qualified with a valid namespace
5104 composite(a(CHEBI:"zoledronic acid"),a("Cetuximab")) =| bp(GOBP:"MAPK cascade") [pos:39] "Cetuximab" should be qualified with a valid namespace
5105 composite(a(CHEBI:"zoledronic acid"),a("Cetuximab")) =| bp(GOBP:"protein kinase B signaling") [pos:39] "Cetuximab" should be qualified with a valid namespace
5128 composite(a(CHEBI:"zoledronic acid"),a("Cetuximab")) =| path(MESHD:"Colorectal Neoplasms") [pos:39] "Cetuximab" should be qualified with a valid namespace
5129 composite(a(CHEBI:"zoledronic acid"),a("Cetuximab")) =| bp(GOBP:"cell growth") [pos:39] "Cetuximab" should be qualified with a valid namespace
5137 a("Peritoneal metastases") -| bp("survival rate") [pos:2] "Peritoneal metastases" should be qualified with a valid namespace
5146 a(CHEBI:"camptothecin") -> bp("survival rate") [pos:30] "survival rate" should be qualified with a valid namespace
5147 a(CHEBI:"oxaliplatin") -> bp("survival rate") [pos:29] "survival rate" should be qualified with a valid namespace
5161 a("XELOX") hasMembers list(a(CHEBI:"capecitabine"), a(CHEBI:"oxaliplatin")) [pos:2] "XELOX" should be qualified with a valid namespace
5168 composite(a("bevacizumab"),a("XELOX")) -> bp(GOBP:"transaminase activity") [pos:12] "bevacizumab" should be qualified with a valid namespace
5169 composite(a("bevacizumab"),a("XELOX")) -> path(MESHD:"Neutropenia") [pos:12] "bevacizumab" should be qualified with a valid namespace
5170 composite(a("bevacizumab"),a("XELOX")) -> path(MESHD:"Fatigue") [pos:12] "bevacizumab" should be qualified with a valid namespace
5171 composite(a("bevacizumab"),a("XELOX")) -> path(MESHD:"Anemia") [pos:12] "bevacizumab" should be qualified with a valid namespace
5172 composite(a("bevacizumab"),a("XELOX")) -> path(MESHD:"Neuropathy") [pos:12] "bevacizumab" should be qualified with a valid namespace
5178 composite(a("bevacizumab"),a("XELOX")) -> bp("survival rate") [pos:12] "bevacizumab" should be qualified with a valid namespace
5196 a(CHEBI:"irinotecan") -> path(MESHD:"Neutropenia") "irinotecan" is not in the CHEBI namespace
5197 a(CHEBI:"irinotecan") -> path(MESHD:"Diarrhea") "irinotecan" is not in the CHEBI namespace
5202 bp(MESHPP:"Fasting") -| a(CHEBI:"irinotecan") "irinotecan" is not in the CHEBI namespace
5203 a(CHEBI:"irinotecan") -> path(MESHD:"Diarrhea")) "irinotecan" is not in the CHEBI namespace
5208 a(CHEBI:"irinotecan") positiveCorrelation path(MESHD:"Leukopenia") "irinotecan" is not in the CHEBI namespace
5209 composite(a(CHEBI:"irinotecan"),bp(MESHPP:"Fasting")) negativeCorrelation path(MESHD:"Leukopenia") "irinotecan" is not in the CHEBI namespace
5214 a(CHEBI:"irinotecan") -| bp(GOBP:"cell growth") "irinotecan" is not in the CHEBI namespace
5215 a(CHEBI:"irinotecan") -| path(MESHD:"Colorectal Neoplasms") "irinotecan" is not in the CHEBI namespace
5223 composite(a(CHEBI:"irinotecan"),bp(MESHPP:"Fasting")) negativeCorrelation a(CHEBI:"SN-38") "irinotecan" is not in the CHEBI namespace
5227 composite(a(CHEBI:"irinotecan"),bp(MESHPP:"Fasting")) negativeCorrelation a(CHEBI:"SN-38") "irinotecan" is not in the CHEBI namespace
5229 SET UserdefinedCell = "Tumor" "Tumor" is not defined in the UserdefinedCell annotation
5231 composite(a(CHEBI:"irinotecan"),bp(MESHPP:"Fasting")) positiveCorrelation a(CHEBI:"SN-38") "irinotecan" is not in the CHEBI namespace
5236 bp(MESHPP:"Fasting") -| a("side effects") [pos:26] "side effects" should be qualified with a valid namespace
5237 bp(MESHPP:"Fasting") causesNoChange a(CHEBI:"irinotecan") "irinotecan" is not in the CHEBI namespace
5238 a(CHEBI:"irinotecan") -| bp(GOBP:"cell growth") "irinotecan" is not in the CHEBI namespace
5249 a("Cetuximab") =| p(HGNC:EGFR) [pos:2] "Cetuximab" should be qualified with a valid namespace
5250 a("Cetuximab") -> path(MESHD:"Acneiform Eruptions") [pos:2] "Cetuximab" should be qualified with a valid namespace
5261 p(HGNC:KDR) -- bp("survival rate") [pos:18] "survival rate" should be qualified with a valid namespace
5262 p(HGNC:KDR) negativeCorrelation bp("survival rate") [pos:35] "survival rate" should be qualified with a valid namespace
5267 composite(p(HGNC:KDR),a("chemotherapy"),a("bevacizumab")) -> bp("survival rate") [pos:24] "chemotherapy" should be qualified with a valid namespace
5277 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
5282 a("resection of metastases") -> bp("survival rate") [pos:2] "resection of metastases" should be qualified with a valid namespace
5288 composite(a("bevacizumab"),a(CHEBI:"irinotecan")) -> bp("survival rate") [pos:12] "bevacizumab" should be qualified with a valid namespace
5303 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
5305 a("Bevacizumab") -- path(MESHD:"Venous Thromoembolisms") [pos:2] "Bevacizumab" should be qualified with a valid namespace
5313 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
5319 tscript(p(HGNC:AREG)) -- bp("survival rate") [pos:28] "survival rate" should be qualified with a valid namespace
5324 tscript(p(HGNC:EREG)) -- bp("survival rate") [pos:28] "survival rate" should be qualified with a valid namespace
5330 tscript(p(HGNC:EREG)) biomarkerFor bp("survival rate") [pos:38] "survival rate" should be qualified with a valid namespace
5342 SET DiseaseType = "metastatic" "metastatic" is not defined in the DiseaseType annotation
5350 composite(a("FOLFOX"),a("bevacizumab"),a("FOLFIRI")) -- path(MESHD:"Neutropenia") [pos:12] "FOLFOX" should be qualified with a valid namespace
5351 composite(a("FOLFOX"),a("bevacizumab"),a("FOLFIRI")) -- path(MESHD:"Leukopenia") [pos:12] "FOLFOX" should be qualified with a valid namespace
5352 composite(a("FOLFOX"),a("bevacizumab"),a("FOLFIRI")) -- path(MESHD:"Anorexia") [pos:12] "FOLFOX" should be qualified with a valid namespace
5353 composite(a("FOLFOX"),a("bevacizumab"),a("FOLFIRI")) -- path(MESHD:"Fatigue") [pos:12] "FOLFOX" should be qualified with a valid namespace
5354 composite(a("FOLFOX"),a("bevacizumab"),a("FOLFIRI")) -- path(MESHD:"Nausea") [pos:12] "FOLFOX" should be qualified with a valid namespace
5355 composite(a("FOLFOX"),a("bevacizumab"),a("FOLFIRI")) -- path(MESHD:"Vomiting") [pos:12] "FOLFOX" should be qualified with a valid namespace
5356 a("bevacizumab") -- path(MESHD:"Hypertension") [pos:2] "bevacizumab" should be qualified with a valid namespace
5357 a("bevacizumab") -- path(MESHD:"Thrombosis") [pos:2] "bevacizumab" should be qualified with a valid namespace
5363 composite(a("FOLFOX"),a("bevacizumab"),a("FOLFIRI")) -| path(MESHD:"Colorectal Neoplasms") [pos:12] "FOLFOX" should be qualified with a valid namespace
5364 composite(a("FOLFOX"),a("bevacizumab"),a("FOLFIRI")) -| path(MESHD:"Colorectal Neoplasms") [pos:12] "FOLFOX" should be qualified with a valid namespace
5397 p(HGNC:UBE3D) -| a("irinotecan sensitivity") [pos:19] "irinotecan sensitivity" should be qualified with a valid namespace
5398 p(HGNC:UBE3D) -| a("SN-38 sensitivity") [pos:19] "SN-38 sensitivity" should be qualified with a valid namespace
5399 p(HGNC:UBE3D) -| a("cetuximab sensitivity") [pos:19] "cetuximab sensitivity" should be qualified with a valid namespace
5401 p(HGNC:AKT1) -- a("irinotecan sensitivity") [pos:18] "irinotecan sensitivity" should be qualified with a valid namespace
5402 p(HGNC:AKT1) -- a("SN-38 sensitivity") [pos:18] "SN-38 sensitivity" should be qualified with a valid namespace
5403 p(HGNC:AKT1) -- a("cetuximab sensitivity") [pos:18] "cetuximab sensitivity" should be qualified with a valid namespace
5411 p(HGNC:UBE3D) biomarkerFor bp("Chemoresistance") [pos:30] "Chemoresistance" should be qualified with a valid namespace
5448 a("cancer stem cells") -- path(MESHD:"Cell Transformation, Neoplastic") [pos:2] "cancer stem cells" should be qualified with a valid namespace
5449 a("cancer stem cells") -- path(MESHD:"Neoplasm Metastasis") [pos:2] "cancer stem cells" should be qualified with a valid namespace
5470 tscript(p(HGNC:ERBB3)) -- a("survival rate") [pos:28] "survival rate" should be qualified with a valid namespace
5471 p(HGNC:ERBB3) -> a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
5487 a("Mab#58") -- a("HER3/RH7777 cells") [pos:2] "Mab#58" should be qualified with a valid namespace
5497 a("Mab#58") biomarkerFor path(MESHD:"Colorectal Neoplasms") [pos:2] "Mab#58" should be qualified with a valid namespace
5518 a("cancer stem cells") -- bp(GOBP:"cell growth") [pos:2] "cancer stem cells" should be qualified with a valid namespace
5519 a("cancer stem cells") -- path(MESHD:"Neoplasm Metastasis") [pos:2] "cancer stem cells" should be qualified with a valid namespace
5520 a("cancer stem cells") -- bp(GOBP:"cell migration") [pos:2] "cancer stem cells" should be qualified with a valid namespace
5521 a("cancer stem cells") -- path(MESHD:"Cell Transformation, Neoplastic") [pos:2] "cancer stem cells" should be qualified with a valid namespace
5530 a("cancer stem cells") -- p(HGNC:CD44) [pos:2] "cancer stem cells" should be qualified with a valid namespace
5531 a("cancer stem cells") -- p(HGNC:PROM1) [pos:2] "cancer stem cells" should be qualified with a valid namespace
5532 a("cancer stem cells") -- p(HGNC:CD24) [pos:2] "cancer stem cells" should be qualified with a valid namespace
5533 a("cancer stem cells") -- p(HGNC:EPCAM) [pos:2] "cancer stem cells" should be qualified with a valid namespace
5534 a("cancer stem cells") -- p(HGNC:LGR5) [pos:2] "cancer stem cells" should be qualified with a valid namespace
5535 a("cancer stem cells") -- p(HGNC:ALDH1A1) [pos:2] "cancer stem cells" should be qualified with a valid namespace
5536 a("cancer stem cells") -- p(HGNC:BMI1) [pos:2] "cancer stem cells" should be qualified with a valid namespace
5561 p(HGNC:DAPK1) negativeCorrelation a("Tumor buds") [pos:36] "Tumor buds" should be qualified with a valid namespace
5563 p(HGNC:DAPK1) -| a("survival rate") [pos:19] "survival rate" should be qualified with a valid namespace
5612 deg(complex(p(HGNC:ITGB1),p(HGNC:EGFR))) -> a("radiosensitivity") [pos:46] "radiosensitivity" should be qualified with a valid namespace
5613 p(HGNC:ITGB1) -> a("radiosensitivity") [pos:19] "radiosensitivity" should be qualified with a valid namespace
5614 p(HGNC:EGFR) -> a("radiosensitivity") [pos:18] "radiosensitivity" should be qualified with a valid namespace
5618 SET CellLine = {"DLD1","HT-29"} "DLD1" is not defined in the CellLine annotation
5631 a(AIIB2) =| p(HGNC:ITGB1) [pos:2] "AIIB2" should be qualified with a valid namespace
5632 a(TAE226) =| p(HGNC:PTK2) [pos:2] "TAE226" should be qualified with a valid namespace
5633 a(TAE226) =| p(HGNC:PTK2) [pos:2] "TAE226" should be qualified with a valid namespace
5634 a(Cetuximab) =| p(HGNC:EGFR) [pos:2] "Cetuximab" should be qualified with a valid namespace
5636 deg(complex(p(HGNC:ITGB1),p(HGNC:EGFR))) causesNoChange a("radiosensitivity") [pos:58] "radiosensitivity" should be qualified with a valid namespace
5637 deg(p(HGNC:BRAF)) causesNoChange a("radiosensitivity") [pos:35] "radiosensitivity" should be qualified with a valid namespace
5638 deg(p(HGNC:KRAS)) causesNoChange a("radiosensitivity") [pos:35] "radiosensitivity" should be qualified with a valid namespace
5639 a(CHEBI:"5-fluorouracil") causesNoChange a("radiosensitivity") [pos:43] "radiosensitivity" should be qualified with a valid namespace
5641 complex(a(Cetuximab),a(AIIB2)) -- bp(MESHPP:"MAP Kinase Signaling System") [pos:10] "Cetuximab" should be qualified with a valid namespace
5642 complex(a(Cetuximab),a(AIIB2)) -- kin(p(HGNC:MAPK8)) [pos:10] "Cetuximab" should be qualified with a valid namespace
5643 complex(a(Cetuximab),a(AIIB2)) -- kin(p(HGNC:AKT1)) [pos:10] "Cetuximab" should be qualified with a valid namespace
5644 a(Cetuximab) -- bp(MESHPP:"MAP Kinase Signaling System") [pos:2] "Cetuximab" should be qualified with a valid namespace
5645 a(Cetuximab) -- kin(p(HGNC:MAPK8)) [pos:2] "Cetuximab" should be qualified with a valid namespace
5646 a(Cetuximab) -- kin(p(HGNC:AKT1)) [pos:2] "Cetuximab" should be qualified with a valid namespace
5647 a(AIIB2) -- bp(MESHPP:"MAP Kinase Signaling System") [pos:2] "AIIB2" should be qualified with a valid namespace
5648 a(AIIB2) -- kin(p(HGNC:MAPK8)) [pos:2] "AIIB2" should be qualified with a valid namespace
5649 a(AIIB2) -- kin(p(HGNC:AKT1)) [pos:2] "AIIB2" should be qualified with a valid namespace
5657 a(AIIB2) -| path(MESHD:"Neoplasm Invasiveness") [pos:2] "AIIB2" should be qualified with a valid namespace
5658 a(TAE226) -| path(MESHD:"Neoplasm Invasiveness") [pos:2] "TAE226" should be qualified with a valid namespace
5659 a(TAE226) -| path(MESHD:"Neoplasm Invasiveness") [pos:2] "TAE226" should be qualified with a valid namespace
5674 deg(p(HGNC:HGF)) -| bp("Chemoresistance") [pos:23] "Chemoresistance" should be qualified with a valid namespace
5680 complex(a("anti-HGF"),a(CHEBI:"Irinotecan")) => a("Irinotecan sensitivity") [pos:10] "anti-HGF" should be qualified with a valid namespace
5695 complex(a(anti-HGF),a(CHEBI:"Irinotecan")) =| bp(GOBP:"cell growth") [pos:10] "anti" should be qualified with a valid namespace
5697 p(HGNC:HGF) biomarkerFor bp("Chemoresistance") [pos:28] "Chemoresistance" should be qualified with a valid namespace
5698 p(HGNC:HGF) -> bp("Chemoresistance") [pos:18] "Chemoresistance" should be qualified with a valid namespace
5699 p(HGNC:HGF) -| a("Irinotecan sensitivity") [pos:17] "Irinotecan sensitivity" should be qualified with a valid namespace
5700 a("anti-HGF") -| p(HGNC:HGF) [pos:2] "anti-HGF" should be qualified with a valid namespace
5701 a("anti-HGF") -| bp("Chemoresistance") [pos:2] "anti-HGF" should be qualified with a valid namespace
5730 p(HGNC:KRAS) -> a("anti-EGFR resistance") [pos:18] "anti-EGFR resistance" should be qualified with a valid namespace
5731 p(HGNC:NRAS) -> a("anti-EGFR resistance") [pos:18] "anti-EGFR resistance" should be qualified with a valid namespace
5739 p(HGNC:KRAS) -- a("Cetuximab resistance") [pos:18] "Cetuximab resistance" should be qualified with a valid namespace
5740 p(HGNC:KRAS) -- a("panitumumab resistance") [pos:18] "panitumumab resistance" should be qualified with a valid namespace
5741 p(HGNC:PIK3CA) -- a("Cetuximab resistance") [pos:20] "Cetuximab resistance" should be qualified with a valid namespace
5742 p(HGNC:PIK3CA) -- a("panitumumab resistance") [pos:20] "panitumumab resistance" should be qualified with a valid namespace
5743 p(HGNC:BRAF) -- a("Cetuximab resistance") [pos:18] "Cetuximab resistance" should be qualified with a valid namespace
5744 p(HGNC:BRAF) -- a("panitumumab resistance") [pos:18] "panitumumab resistance" should be qualified with a valid namespace
5745 p(HGNC:ERBB2) -- a("Cetuximab resistance") [pos:19] "Cetuximab resistance" should be qualified with a valid namespace
5746 p(HGNC:ERBB2) -- a("panitumumab resistance") [pos:19] "panitumumab resistance" should be qualified with a valid namespace
5747 p(HGNC:MET) -- a("Cetuximab resistance") [pos:17] "Cetuximab resistance" should be qualified with a valid namespace
5748 p(HGNC:MET) -- a("panitumumab resistance") [pos:17] "panitumumab resistance" should be qualified with a valid namespace
5757 p(HGNC:ERBB3) -> a("anti-EGFR resistance") [pos:19] "anti-EGFR resistance" should be qualified with a valid namespace
5758 p(HGNC:MET) -> a("anti-EGFR resistance") [pos:17] "anti-EGFR resistance" should be qualified with a valid namespace
5759 p(HGNC:TGFA) -> a("anti-EGFR resistance") [pos:18] "anti-EGFR resistance" should be qualified with a valid namespace
5760 p(HGNC:HGF) -> a("anti-EGFR resistance") [pos:17] "anti-EGFR resistance" should be qualified with a valid namespace
5778 a("miRNA-497") biomarkerFor a("neoadjuvant sensitivity") [pos:2] "miRNA-497" should be qualified with a valid namespace
5779 a("miRNA-497") -| p(HGNC:SMURF1) [pos:2] "miRNA-497" should be qualified with a valid namespace
5780 p(HGNC:SMURF1) positiveCorrelation a("5-fluorouracil resistance") [pos:37] "5-fluorouracil resistance" should be qualified with a valid namespace
5781 a("miRNA-497") negativeCorrelation a("neoadjuvant") [pos:2] "miRNA-497" should be qualified with a valid namespace
5782 deg(a("miRNA-497")) -> a("5-fluorouracil resistance") [pos:6] "miRNA-497" should be qualified with a valid namespace
5783 deg(a("miRNA-497")) -> a("neoadjuvant") [pos:6] "miRNA-497" should be qualified with a valid namespace
5792 a("miRNA-497") -- a(CHEBI:"5-fluorouracil") [pos:2] "miRNA-497" should be qualified with a valid namespace
5793 a("miRNA-497") -| a("5-fluorouracil resistance") [pos:2] "miRNA-497" should be qualified with a valid namespace
5794 a("miRNA-497") -| a("chemoresistance") [pos:2] "miRNA-497" should be qualified with a valid namespace
5802 SET CellLine = "LoVo" "LoVo" is not defined in the CellLine annotation
5804 deg(a("miRNA-497")) -> bp(GOBP:"cell growth") [pos:6] "miRNA-497" should be qualified with a valid namespace
5805 deg(a("miRNA-497")) -> a("5-fluorouracil resistance") [pos:6] "miRNA-497" should be qualified with a valid namespace
5821 path(MESHD:"Rectal Neoplasms") positiveCorrelation bp("Chemoresistance") [pos:54] "Chemoresistance" should be qualified with a valid namespace
5831 kin(p(HGNC:PIK3CA)) positiveCorrelation bp("Chemoresistance") [pos:43] "Chemoresistance" should be qualified with a valid namespace
5832 kin(p(HGNC:PIK3CA)) positiveCorrelation a("neoadjuvant resistance") [pos:42] "neoadjuvant resistance" should be qualified with a valid namespace
5846 p(HGNC:IL17A) -> a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
5875 a("therapy resistance") -| bp(GOBP:"apoptotic process") [pos:2] "therapy resistance" should be qualified with a valid namespace
5883 p(HGNC:BCL2L1) causesNoChange a("survival rate") [pos:32] "survival rate" should be qualified with a valid namespace
5884 p(HGNC:MCL1) causesNoChange a("survival rate") [pos:30] "survival rate" should be qualified with a valid namespace
5885 p(HGNC:BCL2) -- a("survival rate") [pos:18] "survival rate" should be qualified with a valid namespace
5886 deg(p(HGNC:BCL2)) -> a("survival rate") [pos:23] "survival rate" should be qualified with a valid namespace
5896 p(GFAM:"BCL2 family") biomarkerFor path(MESHD:"Rectal Neoplasms") "GFAM" is not a defined namespace
5910 p(HGNC:BRAF) -- a("therapy resistance") [pos:18] "therapy resistance" should be qualified with a valid namespace
5968 kin(p(HGNC:AKT1,pmod(P,S,473))) -- a("therapy resistance") [pos:37] "therapy resistance" should be qualified with a valid namespace
6028 a("hypoxia") -> a("therapy resistance") [pos:2] "hypoxia" should be qualified with a valid namespace
6075 a("tumor microenvironment") -- a("therapy resistance") [pos:2] "tumor microenvironment" should be qualified with a valid namespace
6076 a("tumor microenvironment") -- path(MESHD:"Neoplasm Invasiveness") [pos:2] "tumor microenvironment" should be qualified with a valid namespace
6077 a("tumor microenvironment") -- path(MESHD:"Neoplasm Metastasis") [pos:2] "tumor microenvironment" should be qualified with a valid namespace
6081 SET Citation = {"PubMed","Anticancer Res. 2014 Feb;34(2):845-50.",""} [pos:4] "" is not a valid PubMed identifier
6090 a(CHEBI:"capecitabine") -> a("Survival Rate") [pos:29] "Survival Rate" should be qualified with a valid namespace
6091 a(CHEBI:"gemcitabine") -> a("Survival Rate") [pos:28] "Survival Rate" should be qualified with a valid namespace
6108 p(HGNC:KRAS) -- bp("anti-EGFR therapy resistance") [pos:19] "anti-EGFR therapy resistance" should be qualified with a valid namespace
6109 p(HGNC:BRAF) -- bp("anti-EGFR therapy resistance") [pos:19] "anti-EGFR therapy resistance" should be qualified with a valid namespace
6110 p(HGNC:NRAS) -- bp("anti-EGFR therapy resistance") [pos:19] "anti-EGFR therapy resistance" should be qualified with a valid namespace
6111 p(HGNC:PIK3CA) -- bp("anti-EGFR therapy resistance") [pos:21] "anti-EGFR therapy resistance" should be qualified with a valid namespace
6112 p(HGNC:ERCC1) -- bp("therapy resistance") [pos:20] "therapy resistance" should be qualified with a valid namespace
6113 p(HGNC:MET) -- bp("therapy resistance") [pos:18] "therapy resistance" should be qualified with a valid namespace
6114 p(HGNC:PTEN) -- bp("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
6115 p(HGNC:ERBB2) -- bp("therapy resistance") [pos:20] "therapy resistance" should be qualified with a valid namespace
6116 p(HGNC:ERBB3) -- bp("therapy resistance") [pos:20] "therapy resistance" should be qualified with a valid namespace
6123 p(HGNC:KRAS) biomarkerFor bp("anti-EGFR therapy resistance") [pos:29] "anti-EGFR therapy resistance" should be qualified with a valid namespace
6124 p(HGNC:BRAF) biomarkerFor bp("anti-EGFR therapy resistance") [pos:29] "anti-EGFR therapy resistance" should be qualified with a valid namespace
6125 p(HGNC:NRAS) biomarkerFor bp("anti-EGFR therapy resistance") [pos:29] "anti-EGFR therapy resistance" should be qualified with a valid namespace
6126 p(HGNC:PIK3CA) biomarkerFor bp("anti-EGFR therapy resistance") [pos:31] "anti-EGFR therapy resistance" should be qualified with a valid namespace
6127 p(HGNC:ERCC1) biomarkerFor bp("therapy resistance") [pos:30] "therapy resistance" should be qualified with a valid namespace
6128 p(HGNC:MET) biomarkerFor bp("therapy resistance") [pos:28] "therapy resistance" should be qualified with a valid namespace
6129 p(HGNC:PTEN) biomarkerFor bp("therapy resistance") [pos:29] "therapy resistance" should be qualified with a valid namespace
6130 p(HGNC:ERBB2) biomarkerFor bp("therapy resistance") [pos:30] "therapy resistance" should be qualified with a valid namespace
6131 p(HGNC:ERBB3) biomarkerFor bp("therapy resistance") [pos:30] "therapy resistance" should be qualified with a valid namespace
6170 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
6171 a(CHEBI:"Salinomycin") -| a(GSH-PX) [pos:28] "GSH" should be qualified with a valid namespace
6215 a(CHEBI:"oxaliplatin") -> a("DNA cross-links") [pos:28] "DNA cross-links" should be qualified with a valid namespace
6216 a(CHEBI:"oxaliplatin") -> a("chemoresistance") [pos:28] "chemoresistance" should be qualified with a valid namespace
6239 m("miR-27b") negativeCorrelation path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-27b" should be qualified with a valid namespace
6240 m("miR-27b") -| path(MESHD:"Colorectal Neoplasms") [pos:2] "miR-27b" should be qualified with a valid namespace
6241 m("miR-27b") -| bp(GOBP:"cell growth") [pos:2] "miR-27b" should be qualified with a valid namespace
6242 m("miR-27b") -| p(HGNC:VEGFC) [pos:2] "miR-27b" should be qualified with a valid namespace
6243 m("miR-27b") -| bp(GOBP:"angiogenesis") [pos:2] "miR-27b" should be qualified with a valid namespace
6244 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
6245 m("miR-27b") -> bp(MESHPP:Necrosis) [pos:2] "miR-27b" should be qualified with a valid namespace
6295 p(HGNC:SLC29A1) positiveCorrelation a("5-fluorouracil resistance") [pos:38] "5-fluorouracil resistance" should be qualified with a valid namespace
6296 deg(p(HGNC:SLC29A1)) -| a("5-fluorouracil resistance") [pos:26] "5-fluorouracil resistance" should be qualified with a valid namespace
6313 p(HGNC:RAD51) negativeCorrelation a("survival rate") [pos:36] "survival rate" should be qualified with a valid namespace
6327 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
6328 p(HGNC:RAD51) negativeCorrelation a(MHL) [pos:36] "MHL" should be qualified with a valid namespace
6347 p(HGNC:GSN) negativeCorrelation a("survival rate") [pos:34] "survival rate" should be qualified with a valid namespace
6348 p(HGNC:GSN) positiveCorrelation a("therapy resistance") [pos:34] "therapy resistance" should be qualified with a valid namespace
6402 p(HGNC:BIRC5) -> a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
6412 m("survivin-miRNA") =| p(HGNC:BIRC5) [pos:2] "survivin-miRNA" should be qualified with a valid namespace
6413 m("survivin-miRNA") -| a("therapy resistance") [pos:2] "survivin-miRNA" should be qualified with a valid namespace
6483 a("cancer stem cells") -> bp(GOBP:"cell growth") [pos:2] "cancer stem cells" should be qualified with a valid namespace
6500 a("cancer stem cells") -- path(MESHD:"Cell Transformation, Neoplastic") [pos:2] "cancer stem cells" should be qualified with a valid namespace
6501 a("cancer stem cells") -- bp(GOBP:"cell growth") [pos:2] "cancer stem cells" should be qualified with a valid namespace
6502 p(HGNC:PROM1) -- a("cancer stem cells") [pos:19] "cancer stem cells" should be qualified with a valid namespace
6503 p(HGNC:CD44) -- a("cancer stem cells") [pos:18] "cancer stem cells" should be qualified with a valid namespace
6504 p(HGNC:CD24) -- a("cancer stem cells") [pos:18] "cancer stem cells" should be qualified with a valid namespace
6505 p(HGNC:ITGB1) -- a("cancer stem cells") [pos:19] "cancer stem cells" should be qualified with a valid namespace
6506 p(HGNC:ALCAM) -- a("cancer stem cells") [pos:19] "cancer stem cells" should be qualified with a valid namespace
6507 p(HGNC:LGR5) -- a("cancer stem cells") [pos:18] "cancer stem cells" should be qualified with a valid namespace
6521 a("hypoxia resistance") -- bp(GOBP:"cell growth") [pos:2] "hypoxia resistance" should be qualified with a valid namespace
6522 a("hypoxia resistance") -- a("therapy resistance") [pos:2] "hypoxia resistance" should be qualified with a valid namespace
6523 a("hypoxia resistance") -- p(HGNC:HIF1A) [pos:2] "hypoxia resistance" should be qualified with a valid namespace
6558 p(HGNC:LOX) -> a("hypoxia resistance") [pos:17] "hypoxia resistance" should be qualified with a valid namespace
6559 p(HGNC:HIF1A) -> a("hypoxia resistance") [pos:19] "hypoxia resistance" should be qualified with a valid namespace
6598 a("cancer stem cells") -> a("therapy resistance") [pos:2] "cancer stem cells" should be qualified with a valid namespace
6603 bp(GOBP:"Wnt signaling pathway") -> a("cancer stem cells") [pos:38] "cancer stem cells" should be qualified with a valid namespace
6616 p(HGNC:PROM1) -- a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
6622 p(HGNC:PROM1) negativeCorrelation a("survival rate") [pos:36] "survival rate" should be qualified with a valid namespace
6655 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
6656 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
6673 a("cancer stem cells") -- a("therapy resistance") [pos:2] "cancer stem cells" should be qualified with a valid namespace
6674 a("cancer stem cells") -> path(MESHD:"Neoplasm Metastasis") [pos:2] "cancer stem cells" should be qualified with a valid namespace
6675 a("cancer stem cells") -- a("chemoresistance") [pos:2] "cancer stem cells" should be qualified with a valid namespace
6695 p(HGNC:SPARC) -| a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
6726 p(HGNC:SPARC) -| bp("Chemoresistance") [pos:20] "Chemoresistance" should be qualified with a valid namespace
6727 p(HGNC:SPARC) -| a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
6744 m("CASP8 small-interfering RNA") -| bp(GOBP:"apoptotic process") [pos:2] "CASP8 small-interfering RNA" should be qualified with a valid namespace
6761 p(HGNC:SPARC) =| bp("Chemoresistance") [pos:20] "Chemoresistance" should be qualified with a valid namespace
6762 g(HGNC:SPARC) =| bp("Chemoresistance") [pos:20] "Chemoresistance" should be qualified with a valid namespace
6764 p(HGNC:SPARC) =| a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
6765 g(HGNC:SPARC) =| a("therapy resistance") [pos:19] "therapy resistance" should be qualified with a valid namespace
6784 a(CHEBI:"vitamin D") =| bp("Chemoresistance") [pos:27] "Chemoresistance" should be qualified with a valid namespace
6801 composite(p(HGNC:SPARC),a(CHEBI:"vitamin D")) =| a("therapy resistance") [pos:51] "therapy resistance" should be qualified with a valid namespace
6817 a("limited resection of the colon") -> a("survival rate") [pos:2] "limited resection of the colon" should be qualified with a valid namespace
6834 a("Tumor-infiltrating lymphocytes") biomarkerFor a("solid tumors") [pos:2] "Tumor-infiltrating lymphocytes" should be qualified with a valid namespace
6835 a("regulatory T cells (Treg)") -- bp(GOBP:"cell growth") [pos:2] "regulatory T cells (Treg)" should be qualified with a valid namespace
6836 a("B+ cytotoxic cells") positiveCorrelation bp(GOBP:"cell growth") [pos:2] "B+ cytotoxic cells" should be qualified with a valid namespace
6851 a(Cetuximab) -| p(HGNC:EGFR) [pos:2] "Cetuximab" should be qualified with a valid namespace
6852 composite(a(Cetuximab),a(CHEBI:"irinotecan")) -| p(HGNC:EGFR) [pos:12] "Cetuximab" should be qualified with a valid namespace
6874 composite(a(CHEBI:"dexamethasone"),a("gamma-irradiation")) -| bp(GOBP:"apoptotic process") [pos:37] "gamma-irradiation" should be qualified with a valid namespace
6876 a(CHEBI:"dexamethasone") -> a("therapy resistance") [pos:30] "therapy resistance" should be qualified with a valid namespace
6897 tscript(p(HGNC:SPARC)) -| a("therapy resistance") [pos:28] "therapy resistance" should be qualified with a valid namespace
6899 tscript(p(HGNC:SPARC)) -> a("Irinotecan sensitivity") [pos:28] "Irinotecan sensitivity" should be qualified with a valid namespace
6900 tscript(p(HGNC:SPARC)) -> a("5-fluorouracil sensitivity") [pos:28] "5-fluorouracil sensitivity" should be qualified with a valid namespace
6901 tscript(p(HGNC:SPARC)) -> a("radiosensitivity") [pos:28] "radiosensitivity" should be qualified with a valid namespace
6930 bp(GOBP:"cell adhesion") causesNoChange a("therapy resistance") [pos:42] "therapy resistance" should be qualified with a valid namespace
6931 p(HGNC:ITGB1) causesNoChange a("therapy resistance") [pos:31] "therapy resistance" should be qualified with a valid namespace
6947 p(HGNC:MT1A) -- a("therapy resistance") [pos:18] "therapy resistance" should be qualified with a valid namespace
6958 p(HGNC:MT1A) -| a("survival rate") [pos:18] "survival rate" should be qualified with a valid namespace
6961 p(HGNC:MT1A) biomarkerFor bp("poor survival") [pos:29] "poor survival" should be qualified with a valid namespace
6980 p(HGNC:MT1A) -- a("therapy resistance") [pos:18] "therapy resistance" should be qualified with a valid namespace
7010 a(CHEBI:"5-fluorouracil") -| a("5-fluorouracil resistance") [pos:31] "5-fluorouracil resistance" should be qualified with a valid namespace
7022 composite(p(HGNC:IFNA2), a(CHEBI:"5-fluorouracil")) -> path("Drug Toxicity") [pos:60] "Drug Toxicity" should be qualified with a valid namespace
7030 a(CHEBI:"5-fluorouracil") -> a("5-fluorouracil resistance") [pos:31] "5-fluorouracil resistance" should be qualified with a valid namespace
7045 a("chemotherapy") -- path(MESHD:Necrosis) [pos:2] "chemotherapy" should be qualified with a valid namespace
7061 a("microsatellite instability") -- path(MESHD:"Prostatic Neoplasms") [pos:2] "microsatellite instability" should be qualified with a valid namespace
7062 a("microsatellite instability") -- p(HGNC:AR) [pos:2] "microsatellite instability" should be qualified with a valid namespace
7063 a("microsatellite instability") -| a("survival rate") [pos:2] "microsatellite instability" should be qualified with a valid namespace

Top Warnings

Error Frequency
[pos:2] "Cetuximab" should be qualified with a valid namespace 27
[pos:2] "cancer stem cells" should be qualified with a valid namespace 20
"irinotecan" is not in the CHEBI namespace 15
"metastatic" is not defined in the DiseaseType annotation 13
[pos:12] "Bevacizumab" should be qualified with a valid namespace 9
[pos:19] "therapy resistance" should be qualified with a valid namespace 9
[pos:12] "FOLFOX" should be qualified with a valid namespace 9
[pos:31] "Oxaliplatin treatment" should be qualified with a valid namespace 8
[pos:2] "miR-145" should be qualified with a valid namespace 8
[pos:2] "FOLFIRI" should be qualified with a valid namespace 8
[pos:2] "PF-04691502" should be qualified with a valid namespace 8
[pos:2] "Bevacizumab" should be qualified with a valid namespace 8
[pos:2] "miR-27b" should be qualified with a valid namespace 7
[pos:2] "Dbait" should be qualified with a valid namespace 7
[pos:12] "bevacizumab" should be qualified with a valid namespace 7
[pos:2] "(99m)Tc-duramycin" 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] "miRNA-497" should be qualified with a valid namespace 6
'g' 6

Naked Names 157

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.

Undefined Namespaces 2

The source BEL script contained references to the following namespaces, but they were never defined. Click the links to download them as enumerated namespaces, and update the BEL script accordingly.

Namespaces with Incorrect Names 4

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.