glycoconjugate
type: Ontology
version info: 1.1.3
creator: Issaku Yamada
creator: Daisuke Shinmachi
modified: 2018-10-26
creator: Kiyoko Aoki-Kinoshita

location
type: ObjectProperty
comment: This is the link between the concept whose location you are annotating and its range or position. For example, when annotating the region that describes an exon, the exon would be the subject and the region would be the object of the triple or: 'active site' 'location' [is] 'position 3'.

glycosylates at
type: ObjectProperty
domain: Class
  union of: Referenced Compound
  union of: set
range: Glycosylation Site
comment: This property is used to specify the glycosylation site of a referenced compound or a collection of saccharides.

has amino acid
type: ObjectProperty
domain: Exact position
range: Class
  union of: Glycosylated Amino Acid
  union of: amino acid
comment: This property is used to specify the amino acid at an Exact position.

has attached referenced saccharide
type: ObjectProperty
domain: Referenced Protein
range: Referenced Saccharide
comment: This property is used to specify the ReferencedSaccharide that glycosylated the Glycoconjugate.

has protein
type: ObjectProperty
sub property of: has compound
domain: Referenced Protein
range: Glycoprotein
comment: This property is used to specify the protein component of a glycoprotein.

has protein part
type: ObjectProperty
domain: Referenced Glycoconjugate
range: Referenced Protein
comment: "has protein part" is a relation between a referenced glycoconjugate and a referenced protein, where the referenced protein is part of referenced glycoconjugete.

has saccharide part
type: ObjectProperty
domain: Referenced Glycoconjugate
range: Referenced Saccharide
comment: "has saccharide part" is a relation between a referenced glycoconjugate and a referenced saccharide, where the referenced saccharide is part of referenced glycoconjugete.

max relative abundance
type: ObjectProperty
domain: Relative Abundance
range: Max relative abundance
comment: This property is used to specify the upper value in the ratio of components.

min relative abundance
type: ObjectProperty
domain: Relative Abundance
range: Min relative abundance
comment: This property is used to specify the lower value in the ratio of components.

relative abundance percentage
type: ObjectProperty
domain: Class
  union of: set
  union of: set item
range: Relative Abundance
comment: This property is userd to specify the ratio at which a saccharide or collection of saccharides is found to glycosylate the glycoconjugate.

glycosylated at
type: ObjectProperty
type: FunctionalProperty
domain: Class
  union of: Referenced Lipid
  union of: Referenced Protein
range: Glycosylation Site
comment: This property is used to specify the glycosylation site of glycoconjugate.

has association
type: ObjectProperty
domain: Referenced Compound
range: association

has compound
type: ObjectProperty

has glycan
type: ObjectProperty
sub property of: has compound
type: FunctionalProperty
domain: Referenced Compound
range: Saccharide
comment: The glycan object referenced by this subject.

has glycosylated amino acid
type: ObjectProperty
domain: Class
  union of: Referenced Protein
  union of: Glycoprotein
range: Glycosylated Amino Acid
comment: This property is used to specify a glycosylated amino acid residue in an object glycoprotein or glycopeptide.

has lipid
type: ObjectProperty
sub property of: has compound
domain: Referenced Lipid
range: Glycolipid
comment: This property is used to specify the lipid component of a glycolipid.

has saccharide set
type: ObjectProperty
domain: Referenced Protein
range: set
comment: This property is used to specify the set of saccharides attached to a protein, when the glycosylation site is unknown or known.

has taxon
type: ObjectProperty
type: FunctionalProperty
domain: Source Natural
range: Taxon
comment: Species information of the source.

is from source
type: ObjectProperty
domain: Referenced Compound
range: Source
comment: Source annotation for a referenced compound.

method
type: ObjectProperty
comment: This property is used to specify the method type of chemical modification process.

published in
type: ObjectProperty
type: FunctionalProperty
domain: Class
  union of: Evidence
  union of: Referenced Compound
range: Citation
comment: Reference information for the subject.

annotation
type: ObjectProperty
domain: Protein
range: Annotation
comment: Attaches an annotation to a resource.

common name
type: ObjectProperty
type: FunctionalProperty
domain: Taxon

has unit
type: ObjectProperty
type: FunctionalProperty
range: unit of measurement
description: has unit is a relation between a quantity and the unit it is a multiple of.
subset: core

is component part of
type: ObjectProperty
inverse of: has component part
domain: set
range: set item
description: is component part of is a relation between a component and a whole, where the component is instrinsic to the whole, and loss of the part would change the kind that the whole is.
subset: core

has component part
type: ObjectProperty
description: has component part is a relation between a whole and a component part where the component is instrinsic to the whole, and loss of the part would change the kind that it is.
example: a human has blood as a component part

refers to
type: ObjectProperty
description: refers to is a relation between one entity and the entity that it makes reference to.
subset: core
subset: nlp+

position
type: DatatypeProperty
domain: Exact position
range: Datatype
  on datatype: integer
  with restrictions:
    min inclusive: 1
comment: Denoted in 1-based closed coordinates, i.e. the position on the first amino acid or nucleotide of a sequence has the value 1. For nucleotide sequences we count from the 5'end of the sequence, while for Aminoacid sequences we start counting from the N-Terminus.
comment: The position value is the offset along the reference where this position is found. Thus the only the position value in combination with the reference determines where a position is.

amino acid length
type: DatatypeProperty
domain: Glycoprotein
range: integer
comment: The number of amino acids of protein or peptide.

has value
type: DatatypeProperty
type: FunctionalProperty
description: A relation between a informational entity and its actual value (numeric, date, text, etc).
subset: core
subset: nlp
subset: relations
subset: sadi

Exact position
type: Class
subclass of: Position
subclass of: Restriction
  on property: position
  cardinality: 1
disjoint with: One of positions
comment: A position that is exactly known.

Fuzzy position
type: Class
subclass of: Position
comment: A position that lacks exact data.

One of positions
type: Class
subclass of: Fuzzy position
comment: The position is known to be one of the more detailed positions listed by the location predicate.

Position
type: Class
comment: Position
comment: Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate.

Compound Disease Association
type: Class
subclass of: association

Max relative abundance
type: Class
comment: Maximum percentage of abundance

Min relative abundance
type: Class
comment: Minimum percentage of abundance

Referenced Glycoconjugate
type: Class
subclass of: Referenced Compound
comment: Correlation class, which connects a referenced saccharide, referenced protein and referenced lipd classes.

Referenced Lipid
type: Class
subclass of: Referenced Compound
comment: Correlation class, which connects a Glycolipid, Glycosylation_site, and Referenced_Saccharide class.

Referenced Protein
type: Class
subclass of: Referenced Compound
comment: Correlation class, which connects a protein compex, Glycoprotein, Glycosylation_site, glycosylated_AA and Referenced_Saccharide class.

Referenced Saccharide
type: Class
subclass of: Referenced Compound
comment: Correlation class, which connects a Saccharide, Relative_abundance, Saccharide_set, Glycosylation_site and Referenced_protein/lipid class.

Relative Abundance
type: Class
comment: Relative abundance (percentage) of saccharides. e.g.,

Citation
type: Class
equivalent class: citation
comment: Initial class name is capitalized. "glycan:Citation"
comment: References are publications related to the glycan structures or features. This can be journal papers, book chapters, conference articles and so on.

Glycolipid
type: Class
equivalent class: glycolipid
subclass of: Glycoconjugate
comment: Lipid with saccharide(s) attached by glycosidic bond(s).

Glycoprotein
type: Class
equivalent class: glycoprotein
subclass of: Glycoconjugate
subclass of: Protein
comment: A compound that consists of protein and glycan parts; they are covalently attached to each other by a glycosidic bond. There are reasons or traces that at least one amino acid residue of the protein is glycosylated.
comment: Initial class name is capitalized. "glycan:Glycoprotein

Glycosylated Amino Acid
type: Class
equivalent class: glycosylated AA
subclass of: Glycoconjugate
comment: An amino acid residue, in a glycoprotein or glycopeptide sequence, that a glycan is covalently attached. To specify glycosylation type or bond of glycoprotein.

Glycosylation Site
type: Class
subclass of: Glycosylation Annotation
comment: A glycosylation site is an amino acid residue within a peptide that accepts oligosaccharide via amide linkage.

Referenced Compound
type: Class
equivalent class: referenced compound
comment: Initial class name is capitalized. "glycan:Referenced_compound"
comment: Previously correlation instances, which connects a compound class and other information (source, references, evidence) that belong to one data set. That allows to specify that a compound instance, which has been found in a certain source was published by a certain publication.

Saccharide
type: Class
equivalent class: saccharide
subclass of: Compound
comment: Initial class name is capitalized. "glycna:Saccharide"
comment: Instances of this class represent the molecule information of the glycans. That includes chemical composition, molecular weight but also related information such as images of the glycans.

Source
type: Class
equivalent class: source
comment: Initial class name is capitalized. "glycan:Source"
comment: Source of the glycan or glycoconjugate. The source can be a biological organism that the compound was found in, a synthesis procedure trying to reproduce a natural glycan or a modeling approach for the glycan.

Source Natural
type: Class
equivalent class: source natural
subclass of: Source
comment: Class for sources from biological organism. Instances contain information about the species, cell type, tissue and so on.
comment: Initial class name is capitalized. "glycan:Source_natural"

purity percentage
type: Class
equivalent class: Class
  one of: purity percentage
type: NamedIndividual
comment: "A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED]

Annotation
type: Class
comment: Description of a resource on a specific topic.

Glycosylation Annotation
type: Class
comment: Describes the occurrence of the attachment of a glycan (mono- or polysaccharide) to a residue of a protein.

Protein
type: Class
comment: Description of a protein.

Taxon
type: Class
comment: An element of a taxonomy for classifying life forms.

entity
type: Class
description: Every thing is an entity.
subset: core

unit of measurement
type: Class
description: A unit of measurement is a definite magnitude of a physical quantity, defined and adopted by convention and/or by law, that is used as a standard for measurement of the same physical quantity.

mathematical entity
type: Class
description: A mathematical entity is an information content entity that are components of a mathematical system or can be defined in mathematical terms.
subset: math+

set
type: Class
subclass of: mathematical entity
description: A set is a collection of entities, for which there may be zero members.

association
type: Class
subclass of: mathematical entity
subclass of: Restriction
  on property: refers to
  min qualified cardinality: 2
  on class: entity
description: An assocation is a relationship between two or more entities derived by some informational analysis.

ratio
type: Class
description: A ratio is a relationship between two numbers of the same kind expressed arithmetically as a dimensionless quotient of the two which explicitly indicates how many times the first number contains the second.

amino acid
type: Class
description: An amino acid is an organic molecule composed of a carbon bonded to four different groups: a carboxyl group, an amino group, an R group, and a hydrogen atom. In the case of glycine, the R group is another hydrogen atom.

set item
type: Class
subclass of: mathematical entity
description: set item is an item in a set.

protein complex
type: Class
description: A protein complex is a molecular complex composed of at least two polypeptide chains.