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Process Entities

Process Functions

The following BEL Functions represent classes of events or phenomena taking place at the level of the cell or the organism which do not correspond to molecular abundances, but instead to a biological process like angiogenesis or a pathology like cancer.

Biological Processes and Pathways

Pathways, biological processes, and high-order molecular-level phenomena can be represented with the biologicalProcess() / bp() function.

For example, the process of angiogenesis can be represented with:

# long form
biologicalProcess(go:0001525 ! angiogenesis)

# short form
bp(go:0001525 ! angiogenesis)

Likewise, the Signaling by Hippo pathway from Reactome can be represented with:

bp(reactome:R-HSA-2028269 ! "Signaling by Hippo")

There are no modifiers to the bp() function.

prefix name
go Gene Ontology
wikipathways WikiPathways
reactome Reactome
prefix name reason
mesh Medical Subject Headings no cross-references to other nomenclatures
ncit National Cancer Institute Thesaurus few cross-references maintained
kegg.pathway Kyoto Encyclopedia of Genes and Genomes data not easily accessible
pid.pathway NCI Pathway Interaction Database not maintained

If you need help mapping between pathway databases, see ComPath.

Phenotypes and Pathologies

Diseases, pathologies, phenotypes, psychiatric conditions, side effects, and organism-level phenomena can be represented with the pathology() / path() function. We're aware that "pathology" is not only inappropriate, but also indelicate in some situations, so an update to the more general term "phenotype" will come with the next backwards-incompatible language update.

For now, disease pathologies like muscle hypotonia can be represented by:

# long form
pathology(mesh:D009123 ! "Muscle Hypotonia")

# short form
path(mesh:D009123 ! "Muscle Hypotonia")

In general, a pathology can be encoded like an abundance, population, or biological process like:

path(prefix:identifier [! name])
prefix name
doid Disease Ontology
efo Experimental Factor Ontology
hpo Human Phenotype Ontology
mondo Monarch Disease Ontology
mesh Medical Subject Headings
prefix name reason
icd9 ICD 9 Not maintained
icd ICD 10 Almost impossible to get data
icd11 ICD 11 You didn't even know there was a version 11, did you?
sdis Selventa Diseases Not maintained