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Physical Entities

The following BEL Functions represent classes of abundances of specific types of biological entities like RNAs, proteins, post-translationally modified proteins, and small molecules. Biological experiments frequently involve the manipulation and measurement of entities in samples. These BEL functions specify the type of entity referred to by a namespace value. For example, geneAbundance(hgnc:391 ! AKT1), rnaAbundance(hgnc:391 ! AKT1), and proteinAbundance(hgnc:391 ! AKT1), represent the abundances of the AKT1 gene, RNA, and protein, respectively.

Genes

The protein-coding gene TMTC1 can be encoded in BEL like:

# long form
geneAbundance(hgnc:24099 ! TMTC1)

# short form
g(hgnc:24099 ! TMTC1)

In general, any gene can be encoded using the form:

g(prefix:identifier [! name])

You can encode the genomic relationship between a gene and the RNA(s) to which it is is transcribed like:

g(hgnc:24099 ! TMTC1) transcribedTo r(ensembl:ENST00000539277.6 ! TMTC1-203)
g(hgnc:24099 ! TMTC1) transcribedTo r(ensembl:ENST00000256062.9 ! TMTC1-201)
g(hgnc:24099 ! TMTC1) transcribedTo r(ensembl:ENST00000551659.5 ! TMTC1-206)
g(hgnc:24099 ! TMTC1) transcribedTo r(ensembl:ENST00000552618.5 ! TMTC1-207)
g(hgnc:24099 ! TMTC1) transcribedTo r(ensembl:ENST00000550354.1 ! TMTC1-205)
g(hgnc:24099 ! TMTC1) transcribedTo r(ensembl:ENST00000319685.12 ! TMTC1-202)
g(hgnc:24099 ! TMTC1) transcribedTo r(ensembl:ENST00000552925.5 ! TMTC1-208)
g(hgnc:24099 ! TMTC1) transcribedTo r(ensembl:ENST00000546582.1 ! TMTC1-204)
g(hgnc:24099 ! TMTC1) transcribedTo r(ensembl:ENST00000553189.5 ! TMTC1-209)

You can also encode the binding event between a gene and its transcription factor(s) like:

complex(g(hgnc:24099 ! TMTC1), p(hgnc:3819 ! FOXO1))

More information about complexes can be found below.

The following nomenclatures are recommended for genes:

prefix name species
ncbigene NCBI Entrez Gene all
hgnc HGNC human
fb FlyBase drosophila melanogaster
mgi Mouse Genome Informatics mouse
rgd Rat Genome Database rat
sgd Saccharomyces Genome Database Saccharomyces cerevisiae (baker's yeast)
pombase PomBase Schizosaccharomyces pombe (fission yeast)
wormbase WormBase C elegans (nematode)
xenbase Xenbase xenopus (frogs)
zfin Zebrafish Information Network zebrafish
dbsnp dbSNP human

Some nomenclatures are species-specific (e.g. HGNC covers human genes), and some cover many species (e.g. NCBI Entrez Gene xocrse many.

The orthology between two genes from different species can be written like:

g(hgnc:14064 ! HDAC6) orthologousTo g(mgi:1333752 ! Hdac6)

Genetic Variants

Variants like substitutions, deletions, insertions, and anything that can be represented with the HGVS nomenclature can be added to a gene following the identifier using the variant() / var() function.

For example, the protein-coding gene CFTR (hgnc:1884) when missing phenylalanine 508 (ΔF508) misfolds and leads to cystic fibrosis. This genetic variant can be written in BEL as:

# long form
g(hgnc:1884 ! CFTR, variant("c.1521_1523delCTT"))

# short form
g(hgnc:1884 ! CFTR, var("c.1521_1523delCTT"))

In general, any variant can be encoded like:

var("HGVS string")

This variant has been listed by the dbSNP database as rs113993960. It can be directly encoded in BEL as:

g(dbsnp:rs113993960)

The equivalence between these two BEL terms is different than simple identifier equivalence, so it can be encoded with the equivalentTo / eq relationship like:

g(dbsnp:rs113993960) eq g(hgnc:1884 ! CFTR, var("c.1521_1523delCTT"))

Because a specific position is referenced, a namespace value for a non-ambiguous sequence like the RefSeq ID in the lower example is preferred over the HGNC gene symbol (when possible). The c. within the HGVS string indicates that the numbering is based on a coding DNA reference sequence. The coding DNA reference sequence covers the part of the transcript that is translated into protein; numbering starts at the A of the initiating ATG codon, and ends at the last nucleotide of the translation stop codon.

The CFTR gene can be written with a RefSeq identifier as:

g(refseq:"NM_000492.3", var("c.1521_1523delCTT"))

Example - substitution

Example - double substitution

g(hgnc:2928 ! DMD, var("c.[145C>T;147C>G]")

Example - insertion

TODO

Genetic Modifications

Modifications to the physical genomic sequence can be represented in BEL using the geneModification() / gmod() function following the identifier in a g() function.

For example, the methylation of the NDUFB6 gene causes a decline in its expression in muscles (pubmed:17948130). This can be represented with:

# long form
g(hgnc:7701 ! NDUFB6, geneModification(Methylation))

# short form
g(hgnc:7701 ! NDUFB6, gmod(Me))

In general, the geneModification() / gmod() function takes the following form:

gmod(prefix:identifier [! name])

However, there are several built-in gene modifications in BEL that can be referenced without a CURIE from the following table:

Short Long
Me Methylation
ADPRib ADP-ribosylation

These can be written as:

# long form
gmod(Methylation)
gmod(ADP-ribosylation)

# short form
gmod(Me)
gmod(ADPRib)

While protein modifications have high quality sources like PSI-MOD, genenetic/genomic modifications do not. One source that may grow over time is the DNA modification (go:0006304) branch in the GO biological process namespace. Even though the semantics are not exactly correct, this still may prove a useful source for gene modification nomenclature.

The previous example can be written with DNA methylation (go:0006306) instead of the BEL default name Me like:

g(hgnc:7701 ! NDUFB6, gmod(go:0006306 ! "DNA methylation"))

RNAs

The long non-coding RNA Homo sapiens MAPT antisense RNA 1 (MAPT-AS1) can be encoded in BEL with:

# long form
rnaAbundance(rnacentral:URS000075DB76 ! MAPT-AS1)

# short form
r(rnacentral:URS000075DB76 ! MAPT-AS1)

In general, any RNA type can be encoded using the form, with the exception of miRNAs, which have their own function:

r(prefix:identifier [! name])

Like in the previous example, it can be shown from which gene an RNA is transcribed like:

g(hgnc:43738 ! ) transcribedTo r(rnacentral:URS000075DB76 ! MAPT-AS1)

It can also be shown that an RNA is translated to a protein like:

g(hgnc:6893 ! MAPT) transcribedTo r(ensembl:ENST00000344290.9 ! MAPT-204)
r(ensembl:ENST00000344290.9 ! MAPT-204) translatedTo p(uniprot:P10636 ! TAU_HUMAN)

There are situations when the exact transcript for a given gene is not known, in which case it is common to refer to the RNA transcript using the gene's identifier like:

g(hgnc:6893 ! MAPT) transcribedTo r(hgnc:6893 ! MAPT)

A functional RNA might appear in a relationship in which it causes the regulation of a gene's expression ref:

r(rnacentral:URS000075DB76 ! MAPT-AS1) decreases r(hgnc:6893 ! MAPT)

RNA Variants

Like genes, RNAs can be described with variants using the var() function.

Looking back at the CFTR gene that causes ΔF508, the RNA variant would look like:

r(hgnc:1884 ! CFTR, var("r.1653_1655delcuu"))

The RefSeq identifier could be used to more explicitly state the sequence to which the HGVS string is referring.

r(refseq:"NM_000492.3", var("r.1653_1655delcuu"))

The coding gene and protein from this variant could be connected with the following transcribedTo and translatedTo relations:

g(hgnc:1884 ! CFTR, var("c.1521_1523delCTT")) transcribedTo r(hgnc:1884 ! CFTR, var("r.1653_1655delcuu"))
r(hgnc:1884 ! CFTR, var("r.1653_1655delcuu")) translatedTo p(hgnc:1884 ! CFTR, var("p.Phe508del"))

Or using RefSeq:

g(refseq:"NM_000492.3", var("c.1521_1523delCTT")) transcribedTo r(refseq:"NM_000492.3", var("r.1653_1655delcuu"))
r(refseq:"NM_000492.3", var("r.1653_1655delcuu")) translatedTo p(refseq:"NP_000483.3", var("p.Phe508del"))

Because a specific position is referenced, a namespace value for a non-ambiguous sequence like the RefSeq ID in the lower example is preferred over the HGNC gene symbol. The r. within the var("") expression indicates that the numbering is based on an RNA reference sequence. The RNA reference sequence covers the entire transcript except for the poly A-tail; numbering starts at the transcription initiation site and ends at the transcription termination site.

The following nomenclatures are recommended for RNAs:

prefix name species
ensembl Ensembl all
rnacentral RNA Central all
prefix reason
snornabase not maintained

Micro-RNAs

Micro-RNAs (or, miRNAs) are functional RNAs that regulate gene expression. Unlike other non-protein coding RNAs (e.g. lncRNAs, sRNAs, etc.), miRNAs have their own function in BEL. It works exactly the same way as the r() function.

# long form
microRNAAbundance(mirbase:MI0000139 ! mmu-mir-1a-1)

# short form
m(mirbase:MI0000139 ! mmu-mir-1a-1)

Like in the previous two examples, it can be shown from which gene an miRNA is transcribed like:

g(mgi:2676869 ! Mir1a-1) transcribedTo m(mirbase:MI0000139 ! mmu-mir-1a-1)

miRNAs have the unique quality that they have a pre-mature and a mature variant. BEL doesn't have an ontological relationship for this yet, but it's very important to know the related 3' and 5' processed mature miRNAs, which are conveniently listed in miRBase.

m(mirbase:MI0000139 ! mmu-mir-1a-1) -- m(mirbase.mature:MIMAT0016979 ! mmu-miR-1a-1-5p)
m(mirbase:MI0000139 ! mmu-mir-1a-1) -- m(mirbase.mature:MIMAT0000123 ! mmu-miR-1a-3p)

The following nomenclatures are recommended for miRNAs:

prefix species
ensembl all
rnacentral all
mirbase all
mirbase.mature all

Proteins

proteinAbundance(ns:v) or p(ns:v) denotes the abundance of the protein designated by the value +v+ in the namespace +ns+, where +v+ references a gene or a named protein family.

p(hgnc:391 ! AKT1)

Protein Variants

The variant("<expression>") or var("<expression>") function can be used as an argument within a geneAbundance(), rnaAbundance(), microRNAAbundance(), or proteinAbundance() to indicate a sequence variant of the specified abundance. The var("") function takes HGVS variant description expression, e.g., for a substitution, insertion, or deletion variant. Multiple var("") arguments may be applied to an abundance term.

The following BEL functions are special functions that can be used only as an argument within an abundance function. These functions modify the abundance to specify sequence variations (gene, RNA, microRNA, protein), post-translational modifications (protein), fragment resulting from proteolytic processing (protein), or cellular location (most abundance types).

As a follow up to the previous examples showing the gene-level and RNA-level modificaitons that lead to the ΔF508 variant of CFTR, the following is how to express it using the var() function inside a protein with HGVS nomenclature:

p(hgnc:1884 ! CFTR, var("p.Phe508del"))

And mor specifically with RefSeq:

p(refseq:"NP_000483.3", var("p.Phe508del"))

CFTR ΔF508 variant (HGVS NP_000483.3:p.Phe508del). Because a specific position is referenced, a namespace value for a non-ambiguous sequence like the RefSeq ID in the lower example is preferred over the HGNC gene symbol. The p. within the var("") expression indicates that the numbering is based on a protein reference sequence.

Example - Protein reference allele

p(hgnc:1884 ! CFTR, var("="))

This is different than p(hgnc:1884 ! CFTR), the root protein abundance, which includes all variants.

Example - Protein unspecified variant

p(hgnc:1884 ! CFTR, var("?"))

Example - Protein substitution 1

p(hgnc:1884 ! CFTR, var("p.Gly576Ala"))

CFTR substitution variant Glycine 576 Alanine (HGVS NP_000483.3:p.Gly576Ala). Because a specific position is referenced, a namespace value for a non-ambiguous sequence like the RefSeq ID in the lower example is preferred over the HGNC gene symbol. The p. within the var("") expression indicates that the numbering is based on a protein sequence.

p(refseq:"NP_000483.3", var("p.Gly576Ala"))

Example - Protein Substitution 2

This term represents the abundance of the human PIK3CA protein in which the glutamic acid residue at position 545 has been substituted with a lysine.

# long form
p(HGNC:PIK3CA, variant("p.Glu545Lys"))

# short form
p(HGNC:PIK3CA, var("p.Glu545Lys"))

Example - Protein frameshift

p(hgnc:1884 ! CFTR, var("p.Thr1220Lysfs"))

CFTR frameshift variant (HGVS NP_000483.3:p.Thr1220Lysfs*7). Because a specific position is referenced, a namespace value for a non-ambiguous sequence RefSeq ID in the lower example is preferred over the HGNC gene symbol. The p. within the var("") expression indicates that the numbering is based on a protein reference sequence.

p(refseq:"NP_000483.3", var("p.Thr1220Lysfs"))

Example - Protein Truncation

The abundances of proteins that are truncated by the introduction of a stop codon can be specified by using the variant("") or var("") function within a protein abundance term.

# long form
p(HGNC:ABCA1, variant("p.Arg1851*"))

# short form
p(HGNC:ABCA1, var("p.Arg1851*"))

Protein Fragments

The fragment() or frag() function can be used within a proteinAbundance() term to specify a protein fragment, e.g., a product of proteolytic cleavage. Protein fragment expressions take the general form:

p(ns:v, frag(, ))

where <range> (required) is an amino acid range, and <descriptor> (optional) is any additional distinguishing information like fragment size or name.

For these examples, HGNC:YFG is ‘your favorite gene’. For the first four examples, only the <range> argument is used. The last examples include use of the optional <descriptor>.

# fragment with known start/stop
p(HGNC:YFG, frag("5_20"))

# amino-terminal fragment of unknown length
p(HGNC:YFG, frag("1_?"))

# carboxyl-terminal fragment of unknown length
p(HGNC:YFG, frag("?_*"))

# fragment with unknown start/stop
p(HGNC:YFG, frag("?"))

# fragment with unknown start/stop and a descriptor
p(HGNC:YFG, frag("?", "55kD"))

Protein Modifications

The proteinModification() / pmod() function can be inside the p() function to indicate modification of the specified protein. Multiple modifications can be applied to the same protein abundance. For example, the phosphorylated Tau protein would look like this:

# long form
p(uniprot:P10636, proteinModification(Phosphorylation))

# short form
p(uniprot:P10636, pmod(Ph))

The first argument of pmod() is the protein modification type. The default BEL namespace includes commonly used protein modification types from the following table:

Label Synonym
Ac acetylation
ADPRib ADP-ribosylation, ADP-rybosylation, adenosine diphosphoribosyl
Farn farnesylation
Gerger geranylgeranylation
Glyco glycosylation
Hy hydroxylation
ISG ISGylation, ISG15-protein conjugation
Me methylation
Me1 monomethylation, mono-methylation
Me2 dimethylation, di-methylation
Me3 trimethylation, tri-methylation
Myr myristoylation
Nedd neddylation
NGlyco N-linked glycosylation
NO Nitrosylation
OGlyco O-linked glycosylation
Palm palmitoylation
Ph phosphorylation
Sulf sulfation, sulphation, sulfur addition, sulphur addition, sulfonation, sulphonation
Sumo SUMOylation
Ub ubiquitination, ubiquitinylation, ubiquitylation
UbK48 Lysine 48-linked polyubiquitination
UbK63 Lysine 63-linked polyubiquitination
UbMono monoubiquitination
UbPoly polyubiquitination

However, any identifier with the form prefix:identifier [! name] can be used.

Optionally, the amino acid residue which is modified can be specified with its three letter code:

p(uniprot:P10636, pmod(Ph, Ser))

The following amino acids are supported in BEL:

Amino Acid 1-Letter Code 3-Letter Code
Alanine A Ala
Arginine R Arg
Asparagine N Asn
Aspartic Acid D Asp
Cysteine C Cys
Glutamic Acid E Glu
Glutamine Q Gln
Glycine G Gly
Histidine H His
Isoleucine I Ile
Leucine L Leu
Lysine K Lys
Methionine M Met
Phenylalanine F Phe
Proline P Pro
Serine S Ser
Threonine T Thr
Tryptophan W Trp
Tyrosine Y Tyr
Valine V Val

Optionally, the position which is modified can be specified

p(uniprot:P10636, pmod(Ph, Ser, 519))

More information about this phosphorylation can be found on PhosphoSitePlus.

Modified protein abundance term expressions have the general form:

p(prefix:identifier [! name], pmod(prefix:identifier [! name], <code>, <pos>))

Example - AKT1 phosphorylated at Serine 473

Default BEL namespace and 3-letter amino acid code:

p(hgnc:391 ! AKT1, pmod(Ph, Ser, 473))

PSI-MOD namespace and 3-letter amino acid code:

p(hgnc:391 ! AKT1, pmod(MOD:PhosRes, Ser, 473))

Example - MAPK1 phosphorylated at both Threonine 185 and Tyrosine 187

default BEL namespace and 3-letter amino acid code:

p(hgnc:6871 ! MAPK1, pmod(Ph, Thr, 185), pmod(Ph, Tyr, 187))

Example - Palmitoylated HRAS

HRAS palmitoylated at an unspecified residue. Default BEL namespace:

p(hgnc:5173 ! HRAS, pmod(Palm))

Example - Hydroxylation

This term represents the abundance of human HIF1A protein hydroxylated at asparagine 803.

# long form
p(hgnc:4910 ! HIF1A, proteinModification(Hy, Asn, 803))

# short form
p(hgnc:4910 ! HIF1A, pmod(Hy, Asn, 803))

Example - Phosphorylation

This term represents the phosphorylation of the human AKT protein family at an unspecified amino acid residue.

p(fplx:AKT, pmod(Ph))

Example - Acetylation

This term represents the abundance of mouse RELA protein acetylated at lysine 315.

p(mgi:103290 ! Rela, pmod(Ac, Lys, 315))

Example - Glycosylation

This term represents the abundance of human SP1 protein glycosylated at an unspecified amino acid residue.

p(hgnc:11205 ! SP1, pmod(Glyco))

Example - Methylation

This term represents the abundance of rat STAT1 protein methylated at an unspecified arginine residue:

p(rgd:3771 ! STAT1, pmod(Me, Arg))

Ubiquitination

This term represents the abundance of human MYC protein ubiquitinated at an unspecified lysine residue:

p(hgnc:7553 ! MYC, pmod(Ub, Lys))

Protein Families

Families of proteins can be expressed using the p() function as well.

For example, the Protein Kinase B (a.k.a., AKT family) can be expressed using any of these several namespaces:

p(fplx:AKT)

# see: https://signor.uniroma2.it/relation_result.php?id=SIGNOR-PF24&organism=human
p(signor:SIGNOR-PF24 ! AKT)

# see: https://identifiers.org/ncit:C41625
# NCIT not recommended because they do not provide mappings
p(ncit:C41625 ! "Protein Kinase B")

# The selventa namespace is not maintained. Please do not use.
p(sfam:F0014 ! "AKT Family")

While many resources (such as Bio2BEL repositories) can be used to enrich BEL graphs with protein family's members, they can be encoded directly with the isA relationship as in:

p(hgnc:391 ! AKT1) isA p(fplx:AKT)
p(hgnc:392 ! AKT2) isA p(fplx:AKT)
p(hgnc:393 ! AKT3) isA p(fplx:AKT)

Warning: some nomenclatures, such as InterPro, are not organism specific. This results in protein families that contain proteins that are orthologs.

Protein families may share a position that is post-translationally modified or a variant. Both the pmod() and var() functions are allowed for protein families, but use with care. For example, the entire AKT family shares the Ser473 phosphorylation.

p(fplx:AKT, pmod(Ph, Ser, 473))
prefix name
fplx FamPlex
interpro InterPro
signor SIGNOR
pro Protein Ontology
prefix reason
ncit no mappings available to other resources
mesh no mappings available to other resources
sfam Selventa families are not maintained. Please upgrade to FamPlex (fplx)

A community maintained list of equivalences between protein families is maintained at https://github.com/sorgerlab/famplex/blob/master/equivalences.csv. This is a useful tool for moving away from deprecated namespaces.

Protein Domains

Protein domains and functional are considered similarly to protein families in BEL because it's useful to think of groups of proteins with the same domain having the same (putative) molecular function (think GO annotations).

The Zinc finger, AN1-type can be expressed using the p() tag as in:

# See also: https://identifiers.org/interpro:IPR000058
p(interpro:IPR000058 ! "Zinc finger, AN1-type")

The fact that the AN1-type zinc finger protein 2B has the Zinc finger, AN1-type domain can be encoded with the following:

p(uniprot:B4DEN4 ! "AN1-type zinc finger protein 2B") isA p(interpro:IPR000058 ! "Zinc finger, AN1-type")

In general, these kinds of relationships can be automatically extracted from InterPro and shouldn't be manually curated.

prefix name
prosite ProSite
interpro InterPro

Populations

The populationAbundance() / pop() function allow for capturing Taxon and Cell population level changes due to environment or treatments. For example, a population of Streptococcus entericus can be encoded as:

# long form
populationAbundance(taxonomy:1123302 ! "Streptococcus entericus DSM 14446")

# short form
pop(taxonomy:1123302 ! "Streptococcus entericus DSM 14446")

Similarly, a population of white adipocytes can be encoded as:

pop(mesh:D052436 ! "Adipocytes, White")

Unlike the gene, RNA, and protein, there are no var() or modification functions for pop().

This function was added in BEL 2.1. The following are example use cases:

# Penicillin decreases the population of Streptococcus entericus
a(chebi:17334 ! penicillin) decreases pop(taxonomy:1123302 ! "Streptococcus entericus DSM 14446")

# Firmicutes bacteria increases obesity
pop(taxonomy:1239 ! Firmicutes) increases path(mesh:D009765 ! Obesity)

# A drug decreases the population of adipocytes
a(chebi:6801 ! metformin) decreases pop(mesh:D052436 ! "Adipocytes, White")

# P. falciparum invasion of RBCs increases malaria
complex(pop(taxonomy:5833 ! "Plasmodium falciparum"), pop(bto:0000424 ! erythrocyte)) increases path(doid:12365 ! malaria)

#S. typhimurium in complex with L-ficolin (an opsonin) enhances phagocytosis [PMID:8576206]
complex(pop(taxonomy:90371), p(hgnc:3624 ! FCN2)) increases bp(go:0006909 ! phagocytosis)
prefix name
taxonomy NCBI Taxonomy
bto Brenda Tissue Ontology
cl Cell Type Ontology
clo Cell Line Ontology
efo Experimental Factor Ontology

Other Physical Entities

Small molecules, chemicals, and drugs can be represented with the abundance() / a() function. For example, the drug Viagra can be encoded as:

# long form
abundance(chebi:58987 ! "sildenafil citrate")

# short form
a(chebi:58987 ! "sildenafil citrate")

Classes of chemicals can be encoded with a() as well:

a(chebi:26523 ! "reactive oxygen species")

Chemicals that are part of a class can be denoted using the isA relationship, though these relationships can often be programatically extracted from ontologies such as ChEBI:

a(chebi:16240 ! hydrogen peroxide) isA a(chebi:26523 ! "reactive oxygen species") 
a(chebi:25935 ! hydroperoxyl) isA a(chebi:26523 ! "reactive oxygen species") 
a(chebi:29191 ! hydroxyl) isA a(chebi:26523 ! "reactive oxygen species") 
...

In general, an abundance can be written like:

a(prefix:identifier [! name])

Abundances do not have variant() modifiers like genes, RNAs, and proteins.

prefix name
chebi Chemical Entities of Biological Interest
drugbank DrugBank
pubchem.compound PubChem
chembl.compound ChEMBL
prefix name reason
mesh Medical Subject Headings no cross-references to other nomenclatures or structural information
schem Selventa chemicals not maintained

Other Entity Types

Other entity types can be encoded as abundances() that do not fit well into the paradigm of protein, such as functional nucleic acids, cellular structures, and small functional peptides.

# cellular structure
a(go:0022904 ! "respiratory electron transport chain")

# aggregates of proteins
a(conso:CONSO00358 ! TDP-43 oligomers)

Complexes of Physical Entities

The complexAbundance() or complex() function can be used with either a namespace value or with a list of abundance terms.

complexAbundance(ns:v) or complex(ns:v) denotes the abundance of the molecular complex designated by the value v in the namespace ns. This form is generally used to identify abundances of named complexes.

complexAbundance(<abundance term list>) denotes the abundance of the molecular complex of members of the abundances denoted by <abundance term list>, a list of abundance terms supplied as arguments. The list is unordered, thus different orderings of the arguments should be interpreted as the same term. Members of a molecular complex retain their individual identities. ThecomplexAbundance() function does not specify the duration or stability of the interaction of the members of the complex.

The abundances of molecular complexes are represented using the complexAbundance() function. This function can take either a list of abundance terms or a value from a namespace of molecular complexes as its argument.

Both BEL Terms represent the IkappaB kinase complex. The first by referencing a named protein complex within the GO namespace.

# long form
complexAbundance(go:0008385 ! "IkappaB kinase complex")

# short form
complex(go:0008385 ! "IkappaB kinase complex")

Define the enumerating the IkappaB kinase complex by composition of its member proteins: CHUK, IKBKB, and IKBKG.

# long form
complexAbundance(p(hgnc:1974 ! CHUK), p(hgn:c5960 ! IKBKB), p(hgnc:5961 ! IKBKG))

# short form
complex(p(hgnc:1974 ! CHUK), p(hgnc:5960 ! IKBKB), p(hgnc:5961 ! IKBKG))

Members of a complex can be annotated to it using the partOf like in

p(hgnc:1974 ! CHUK)  partOf complex(go:0008385 ! "IkappaB kinase complex")
p(hgnc:5960 ! IKBKB) partOf complex(go:0008385 ! "IkappaB kinase complex")
p(hgnc:5961 ! IKBKG) partOf complex(go:0008385 ! "IkappaB kinase complex")

However, resources like FamPlex usually provide these relationships that can be automatically added.

Example - composed complex of proteins

complex(p(hgnc:3796 ! FOS), p(hgnc:6204 ! JUN))

Example - composed complex of protein and ligand

complex(a(chebi:132964 ! "fluazifop-P-butyl"), p(ec-code:6.4.1.2 ! "acetyl-CoA carboxylase"))

Example - composed complex of virus and cell

complex(pop(taxonomy:5833 ! "Plasmodium falciparum"), pop(bto:0000424 ! erythrocyte))

Example - a protein bound to gene

complex(p(hgnc:11364 ! STAT3), g(hgnc:10610 ! CCL11))