🟢 Molecular Entity Ontology

Maturity: 🟢 Released

IRI: https://spec.industrialontologies.org/ontology/biopharma/MolecularEntity/

This module contains terms and relations necessary for representing selected molecular entities in biopharmaceutical manufacturing, including molecular entity populations, molecular entity roles, chemical residues and moieties, biological sequences, proteins, glycans, glycoproteins, and glycosylation- and glycation-related residues. Many molecular entity terms are adapted from ChEBI and represented using IOF annotation conventions and modeling patterns to support consistent description of molecular structure, composition, and role.

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Title

BMIC Molecular Entity Ontology

Classes (112)

Class	Definition
acid-base indicator role	molecular color indicator role held by a molecular entity when it is used or planned to be used so that its color indicates the pH…
acidic charge variant population	protein charge variant population classified by a protein acidic charge variant classifier
amino acid	organic molecular entity that contains a carboxyl group and one or more amino groups
amino acid residue	chemical moiety that is a proper part of a peptide or protein and that is the remaining portion of an amino acid resulting from pe…
amino acid sequence	biological sequence that is the ordered pattern of amino-acid residues that constitute a particular continuous peptide or protein …
anion	ion that is a monoatomic or polyatomic species having one or more elementary charges of the electron
antibody	protein that has the function to selectively bind some antigen
antimicrobial agent role	role held by a molecular entity when it is used or planned to be used to kill, inactivate, or inhibit the growth, proliferation, o…
antioxidant role	role held by a molecular entity when it is used or planned to be used to counteract oxidation or inhibit reactions initiated by di…
basic charge variant population	protein charge variant population classified by a protein basic charge variant classifier
biantennary complex N-glycan moiety	core pentasaccharide N-glycan moiety that has N-acetylglucosamine residues attached to both the α-3 and α-6 mannose branches and c…
biological sequence	generically dependent continuant that is the ordered pattern of residues that constitute a particular continuous DNA, RNA, peptide…
biological sequence variant	DNA or RNA or protein or peptide classified by a biological sequence variant classifier
biological sequence variant classifier	classifier that classifies a DNA molecule, RNA molecule, peptide, or protein which has a biological sequence that differs from a s…
carbohydrate	organic molecular entity that is a polyhydroxy aldehyde, polyhydroxy ketone, derivative of such an entity, or condensation product…
cation	ion that is a monoatomic or polyatomic species having one or more elementary charges of the proton
charge variant classifier	classifier that classifies a population of material entities according to charge-related analytical properties relative to a refer…
chelating agent role	role held by a molecular entity when it is used or planned to be used to bind a metal ion through two or more coordination sites
chemical moiety	material entity consisting of a linked collection of atoms or a single atom and that is a proper continuant part of a molecular en…
complex afucosylated N-glycan moiety	biantennary complex N-glycan moiety that has no fucose residues as parts
complex agalactosylated N-glycan moiety	biantennary complex N-glycan moiety that has no galactose residues as parts
complex asialylated N-glycan moiety	biantennary complex N-glycan moiety that has no sialic acid residues as parts
complex fucosylated N-glycan moiety	biantennary complex N-glycan moiety that has as part one or more fucose residues
complex galactosylated N-glycan moiety	biantennary complex N-glycan moiety that has as part one or more galactose residues
complex N-glycolylneuraminic acid containing N-glycan moiety	complex sialylated N-glycan moiety that has as part one or more N-glycolylneuraminic acid (NGNA) residues
complex sialylated N-glycan moiety	biantennary complex N-glycan moiety that has as part one or more sialic acid residues
core pentasaccharide N-glycan moiety	N-glycan moiety that contains the core pentasaccharide Man₃GlcNAc₂, consisting of a di-N-acetyl-chitobiose unit extended by a bran…
deamidated residue	modified amino acid residue in which a carboxamide group has been converted to a carboxyl group, involving a net gain of oxygen an…
deoxyribonucleic acid	nucleic acid that is composed of nucleotides containing deoxyribose
dioxygen molecule	inorganic molecular entity consisting of two oxygen atoms covalently bonded to each other
endotoxin	lipopolysaccharide with an endotoxin role
endotoxin role	molecular toxin role held by a lipopolysaccharide (LPS) that originates from Gram-negative bacterial cellular material
enzyme activator role	role held by a molecular entity when it increases the catalytic activity of an enzyme without covalently modifying the enzyme
enzyme cofactor role	role held by a molecular entity that is realized in an enzymatic reaction through enabling the catalytic activity of a particular …
enzyme inhibitor role	role held by a molecular entity that is realized in an enzyme catalyzed reaction through decreasing or preventing the catalytic ac…
enzyme regulator role	role held by a molecular entity when it binds to an enzyme and modulates its catalytic activity
fucose residue	monosaccharide residue that is the remaining portion of fucose after formation of a glycosidic bond
galactose residue	monosaccharide residue that is the remaining portion of galactose after formation of a glycosidic bond
glycated residue	glycoconjugated residue that is formed by non-enzymatic covalent attachment of a reducing sugar to an amino group of an amino acid…
glycoconjugated residue	modified amino acid residue that has a covalently attached carbohydrate or carbohydrate-derived group, formed either through enzym…
glycoprotein	protein that includes at least one glycosylated residue
glycosylated residue	glycoconjugated residue that results from replacement of a hydrogen atom with a carbohydrate-like group through formation of a gly…
growth factor	protein or peptide with a growth factor role
growth factor role	role held by a peptide or protein that is realized in receptor-mediated signaling processes that stimulate cellular growth, prolif…
heterodimeric antibody	antibody consisting of two heavy chains and two light chains in which the two heavy chains differ in amino acid sequence, the two …
high mannose N-glycan moiety	core pentasaccharide N-glycan moiety whose branches are extended only by mannose residues and whose total mannose count is commonl…
homodimeric antibody	antibody consisting of two heavy chains and two light chains in which the two heavy chains have the same amino acid sequence and t…
hormone	organic molecular entity with a hormone role
hormone role	role held by an organic molecular entity that is realized in receptor-mediated signaling or regulatory processes that modulate the…
hybrid N-glycan moiety	core pentasaccharide N-glycan moiety that contains both unsubstituted terminal mannose residues and at least one mannose residue s…
inorganic molecular entity	molecular entity that contains no carbon
ion	molecular entity having a net electric charge
lipid	organic molecular entity belonging to a structurally diverse class of hydrophobic or amphipathic entities that includes fats, oils…
lipid precursor role	role of a molecular entity that provides carbon or functional groups required for the biosynthetic formation of complex lipids suc…
lipopolysaccharide	organic molecular entity that consists of lipid A covalently linked to a core oligosaccharide and, where present, an O-antigen pol…
main charge variant population	protein charge variant population classified by a protein main charge variant classifier
mannose residue	monosaccharide residue that is the remaining portion of mannose after formation of a glycosidic bond
modified amino acid residue	amino acid residue that has undergone covalent modification of side-chain or backbone atoms while remaining part of an intact pept…
molecular activity regulator role	role held by a molecular entity when it modulates the activity of another molecular entity
molecular color indicator role	molecular visual indicator role held by a molecular entity when it is used or planned to be used so that a change in its color ind…
molecular entity	material entity that is a constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, …
molecular entity population	object aggregate that has one or more molecular entities as member parts and has only molecular entities as member parts
molecular entity role	role of a molecular entity that reflects a chemical or biochemical behavior it may exhibit under specified conditions
molecular indicator role	role held by a molecular entity when it is used or planned to be used so that an observable change in that molecular entity indica…
molecular messenger role	role held by a molecular entity that participates in transmitting biological signals between or within cells, tissues, or organs t…
molecular toxin	molecular entity with a molecular toxin role
molecular toxin role	molecular entity role held by a molecular entity in a biological exposure setting in which its chemical or biochemical activity is…
molecular visual indicator role	molecular indicator role held by a molecular entity when it is used or planned to be used so that a visible change in that molecul…
monosaccharide	carbohydrate that consists of a single polyhydroxy aldehyde or polyhydroxy ketone unit with three or more carbon atoms and is not …
monosaccharide residue	chemical moiety that is a proper part of an oligosaccharide, polysaccharide, or glycoconjugate and that is the remaining portion o…
N-glycan moiety	chemical moiety that is the remaining portion of a glycan resulting from its covalent attachment to the side-chain nitrogen of an …
N-glycolylneuraminic acid residue	sialic acid residue that is the remaining portion of N-glycolylneuraminic acid after formation of a glycosidic bond
N-glycosylated residue	glycosylated residue in which a carbohydrate or carbohydrate-derived group is attached to a nitrogen atom through formation of an …
N4-glycosyl-L-asparagine	N-glycosylated residue in which a glycan is covalently attached to the side-chain nitrogen of an L-asparagine residue
non-proteinogenic amino acid	amino acid that is not normally incorporated into polypeptide chains by ribosomal translation
nucleic acid	organic molecular entity composed of two or more nucleotides linked by phosphodiester bonds
nucleoside	organic molecular entity that consists of a nucleobase linked through a nitrogen atom to a sugar such as ribose or deoxyribose
nucleotide	organic molecular entity that consists of a nucleoside having one or more phosphate groups attached to its sugar moiety
nucleotide sequence	biological sequence that is the ordered pattern of nucleotide residues that constitute a particular continuous DNA or RNA molecule
O-glycan moiety	chemical moiety that is the remaining portion of a glycan resulting from its covalent attachment to the side-chain hydroxyl oxygen…
O-glycosylated residue	glycosylated residue in which a carbohydrate or carbohydrate-derived group is attached to an oxygen atom through formation of an O…
organic molecular entity	molecular entity that contains carbon
oxidized residue	modified amino acid residue that results from covalent changes involving loss of hydrogen atoms or addition of oxygen atoms to the…
peptide	organic molecular entity consisting of two or more amino acid residues linked by peptide bonds
polyamine	organic molecular entity that contains two or more amino groups
polypeptide	peptide containing ten or more amino acid residues
polysaccharide	carbohydrate consisting of large numbers of monosaccharide residues linked glycosidically
protein	organic molecular entity that consists of one or more polypeptide chains of sufficient length or molecular mass to be distinguishe…
protein acidic charge variant classifier	protein charge variant classifier that classifies a molecular entity population composed of proteins or protein fragments as diffe…
protein aggregate	organic molecular entity that consists of two or more protein molecules or protein fragments associated through non-covalent inter…
protein basic charge variant classifier	protein charge variant classifier that classifies a molecular entity population composed of proteins or protein fragments as diffe…
protein charge variant classifier	charge variant classifier that classifies a molecular entity population composed of proteins or protein fragments according to cha…
protein charge variant population	molecular entity population classified by a protein charge variant classifier
protein fragment	peptide or protein that was a proper part of a protein molecule and resulted from cleavage of one or more peptide bonds within tha…
protein high molecular weight population	protein size variant population classified by a protein high molecular weight variant classifier
protein high molecular weight variant classifier	protein size variant classifier that classifies a molecular entity population composed of proteins or protein aggregates as having…
protein low molecular weight population	protein size variant population classified by a protein low molecular weight variant classifier
protein low molecular weight variant classifier	protein size variant classifier that classifies a molecular entity population composed of proteins or protein fragments as having …
protein main charge variant classifier	protein charge variant classifier that classifies a molecular entity population composed of proteins or protein fragments as havin…
protein size variant classifier	size variant classifier that classifies a molecular entity population composed of proteins, protein fragments, or protein aggregat…
protein size variant population	molecular entity population classified by a protein size variant classifier
proteinogenic amino acid	amino acid that is normally incorporated into polypeptide chains by ribosomal translation
ribonucleic acid	nucleic acid that is composed of nucleotide units containing ribose
ribonucleoside	nucleoside where the sugar component is D-ribose
salt	molecular entity that is an assembly of cations and anions
sialic acid residue	monosaccharide residue that is the remaining portion of sialic acid after formation of a glycosidic bond
size variant classifier	classifier that classifies a population of material entities according to size-related analytical properties relative to a referen…
steroid	lipid that has a core structure of four fused carbon rings, consisting of three six-membered rings and one five-membered ring
trace element role	role held by a molecular entity composed of a single chemical element that originates from a source external to cells, is present …
vitamin	organic molecular entity with a vitamin role
vitamin role	role held by an organic molecular entity that is used in small amounts to support metabolic or physiological functions and whose a…
water molecule	inorganic molecular entity consisting of an oxygen atom that is covalently bonded to two hydrogen atoms