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 function | BEL function expanded | Example |
| a | Abundance | a(CHEBI:“calcium(2+)”) | act | Activity | act(p(HGNC:NLRP3)) | bp | Biological process | bp(GOBP:autophagy) | complex | Complex | complex(GOCC:“NLRP3 inflammasome complex”) | m | MicroRNA | m(HGNC:MIR146A) | p | Protein | p(HGNC:NLRP3) | path | Pathology | path(MESHD:Sepsis) | r | RNA | r(HGNC:IL1B) | Sec | Secretion | sec(p(HGNC:IL18)) |
| Namespace identifier | Namespace identifier expanded | Example | HGNC | HUGO gene nomenclature committee | p(HGNC:TLR4) | MGI | Mouse genome informatics | p(MGI:Tlr4) | RGD | Rat genome database | p(RGD:Tlr4) | SARSCOV2 | Severe acute respiratory syndrome coronavirus 2 | p(SARSCOV2:E) | CHEBI | Chemical entities of biological interest | a(CHEBI:“nitric oxide”) | SCHEM | Selventa legacy chemical names | a(SCHEM:“Toxin B, Clostridium difficile”) | GOBP | Gene ontology biological process | bp(GOBP:“mitochondrial depolarization”) | GOCC | Gene ontology cellular components | complex(GOCC:“NF-kappaB complex”) | SCOMP | Selventa named complexes | complex(SCOMP:“CHRN Complex”) | SFAM | Selventa named protein family | act(p(SFAM:“TNFRSF Family”)) | MESHD | Medical subject headings | path(MESHD:Inflammation) | PMIBP | Custom namespace for biological processes | bp(PMIBP:Inflammaging) | PMICOMP | Custom namespace for complexes | complex(PMICOMP:“pyrin inflammasome complex”) | PMIDIS | Custom namespace for diseases | path(PMIDIS:“influenza A virus infection”) | PMIPFAM | Custom namespace for protein families | p(PMIPFAM:“TLR Family”) |
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