Issaku Yamada
Daisuke Shinmachi
Kiyoko Aoki-Kinoshita
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'.
This property is used to specify the glycosylation site of a referenced compound or a collection of saccharides.
glycosylates at
This property is used to specify the amino acid at an Exact position.
has amino acid
This property is used to specify the ReferencedSaccharide that glycosylated the Glycoconjugate.
has attached referenced saccharide
This property is used to specify the protein component of a glycoprotein.
has protein
"has protein part" is a relation between a referenced glycoconjugate and a referenced protein, where the referenced protein is part of referenced glycoconjugete.
has protein part
"has saccharide part" is a relation between a referenced glycoconjugate and a referenced saccharide, where the referenced saccharide is part of referenced glycoconjugete.
has saccharide part
This property is used to specify the upper value in the ratio of components.
max relative abundance
This property is used to specify the lower value in the ratio of components.
min relative abundance
This property is userd to specify the ratio at which a saccharide or collection of saccharides is found to glycosylate the glycoconjugate.
relative abundance percentage
This property is used to specify the glycosylation site of glycoconjugate.
glycosylated at
has association
The glycan object referenced by this subject.
This property is used to specify a glycosylated amino acid residue in an object glycoprotein or glycopeptide.
This property is used to specify the lipid component of a glycolipid.
has lipid
This property is used to specify the set of saccharides attached to a protein, when the glycosylation site is unknown or known.
has saccharide set
Source annotation for a referenced compound.
This property is used to specify the method type of chemical modification process.
method
has unit is a relation between a quantity and the unit it is a multiple of.
has unit
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.
is component part of
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.
a human has blood as a component part
has component part
refers to is a relation between one entity and the entity that it makes reference to.
refers to
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.
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.
The number of amino acids of protein or peptide.
amino acid length
A relation between a informational entity and its actual value (numeric, date, text, etc).
sadi
has value
The position is known to be one of the more detailed positions listed by the location predicate.
Superclass for the general concept of a position on a sequence. The sequence is designated with the reference predicate.
Compound Disease Association
Maximum percentage of abundance
Max relative abundance
Minimum percentage of abundance
Min relative abundance
Correlation class, which connects a referenced saccharide, referenced protein and referenced lipd classes.
Referenced Glycoconjugate
Correlation class, which connects a Glycolipid, Glycosylation_site, and Referenced_Saccharide class.
Referenced Lipid
Correlation class, which connects a protein compex, Glycoprotein, Glycosylation_site, glycosylated_AA and Referenced_Saccharide class.
Referenced Protein
Correlation class, which connects a Saccharide, Relative_abundance, Saccharide_set, Glycosylation_site and Referenced_protein/lipid class.
Referenced Saccharide
Relative abundance (percentage) of saccharides. e.g.,
Relative Abundance
Initial class name is capitalized. "glycan:Citation"
References are publications related to the glycan structures or features. This can be journal papers, book chapters, conference articles and so on.
Lipid with saccharide(s) attached by glycosidic bond(s).
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.
Initial class name is capitalized. "glycan:Glycoprotein
An amino acid residue, in a glycoprotein or glycopeptide sequence, that a glycan is covalently attached. To specify glycosylation type or bond of glycoprotein.
A glycosylation site is an amino acid residue within a peptide that accepts oligosaccharide via amide linkage.
Glycosylation Site
Initial class name is capitalized. "glycan:Referenced_compound"
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.
Initial class name is capitalized. "glycna:Saccharide"
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.
Initial class name is capitalized. "glycan:Source"
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.
Class for sources from biological organism. Instances contain information about the species, cell type, tissue and so on.
Initial class name is capitalized. "glycan:Source_natural"
Description of a resource on a specific topic.
Describes the occurrence of the attachment of a glycan (mono- or polysaccharide) to a residue of a protein.
An element of a taxonomy for classifying life forms.
Every thing is an entity.
entity
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.
unit of measurement
A mathematical entity is an information content entity that are components of a mathematical system or can be defined in mathematical terms.
mathematical entity
A set is a collection of entities, for which there may be zero members.
set
An assocation is a relationship between two or more entities derived by some informational analysis.
association
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.
ratio
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.
amino acid
set item is an item in a set.
set item
A protein complex is a molecular complex composed of at least two polypeptide chains.
protein complex
"A dimensionless percent unit which denotes the homogeneity of a biomaterial." [MGED:MGED]