Research Article

Causal Biological Network Model for Inflammasome Signaling Applied for Interpreting Transcriptomic Changes in Various Inflammatory States

Table 1

BEL vocabulary for the namespaces used in the inflammasome CBN model.

BEL functionBEL function expandedExample

aAbundancea(CHEBI:“calcium(2+)”)
actActivityact(p(HGNC:NLRP3))
bpBiological processbp(GOBP:autophagy)
complexComplexcomplex(GOCC:“NLRP3 inflammasome complex”)
mMicroRNAm(HGNC:MIR146A)
pProteinp(HGNC:NLRP3)
pathPathologypath(MESHD:Sepsis)
rRNAr(HGNC:IL1B)
SecSecretionsec(p(HGNC:IL18))

Namespace identifierNamespace identifier expandedExample
HGNCHUGO gene nomenclature committeep(HGNC:TLR4)
MGIMouse genome informaticsp(MGI:Tlr4)
RGDRat genome databasep(RGD:Tlr4)
SARSCOV2Severe acute respiratory syndrome coronavirus 2p(SARSCOV2:E)
CHEBIChemical entities of biological interesta(CHEBI:“nitric oxide”)
SCHEMSelventa legacy chemical namesa(SCHEM:“Toxin B, Clostridium difficile”)
GOBPGene ontology biological processbp(GOBP:“mitochondrial depolarization”)
GOCCGene ontology cellular componentscomplex(GOCC:“NF-kappaB complex”)
SCOMPSelventa named complexescomplex(SCOMP:“CHRN Complex”)
SFAMSelventa named protein familyact(p(SFAM:“TNFRSF Family”))
MESHDMedical subject headingspath(MESHD:Inflammation)
PMIBPCustom namespace for biological processesbp(PMIBP:Inflammaging)
PMICOMPCustom namespace for complexescomplex(PMICOMP:“pyrin inflammasome complex”)
PMIDISCustom namespace for diseasespath(PMIDIS:“influenza A virus infection”)
PMIPFAMCustom namespace for protein familiesp(PMIPFAM:“TLR Family”)