Daisuke Shinmachi
Rene Ranzinger
Shujiro Okuda
Kiyoko Aoki-Kinoshita
1.2.1
Issaku Yamada
2013-02-10 23:11:00
Shin Kawano
Philip Toukach
Matthew Campbell
Hiro Sawaki
Masaaki Matsubara
BCSDB
http://csdb.glycoscience.ru/bacterial/core/search_id.php?mode=record&id_list=[?id?]
CCSD
http://www.genome.jp/dbget-bin/www_bget?carbbank+[?id?]
Carint
http://ws.glyconavi.org/carint/entry.php?id=[?id?]
CAZy
http://www.cazy.org/[?id?].html
CFG
http://www.functionalglycomics.org/glycomics/CarbohydrateServlet?pageType=view&view=view&operationType=view&carbId=[?id?]&sideMenu=no%0A%20%20%09%09
CfgGBP
http://www.functionalglycomics.org/glycomics/molecule/jsp/viewGbpMolecule.jsp?gbpId=[?id?]&sideMenu=yes
CfgGlycoenzyme
http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/viewGlycoEnzyme.jsp?gbpId=[?id?]&sideMenu=true&pageType=general
ChEBI
http://www.ebi.ac.uk/chebi/advancedSearchFT.do?searchString='[?id?]'
ChemSpider
http://www.chemspider.com/Chemical-Structure.[?id?].html
GlyAffinity
http://worm.mpi-cbg.de/affinity/structure.action?ID=[?id?]
GlycO
http://glycomics.ccrc.uga.edu/ontologywebapi/service/glycan/id/[?id?]
GlycoBase(Dublin)
GlycoBase(Lille)
http://glycobase.univ-lille1.fr/base/view_mol.php?id=[?id?]
GlycoMapsDB
http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=[?id?]
GlycomeDB
http://www.glycome-db.org/database/showStructure.action?glycomeId=[?id?]
GlycoNAVI
http://ws.glyconavi.org/DbDetail/moldetail.aspx?moleculeID=[?id?]
GlycoNMR
http://glycoinfolab.jp/GlycoNMR/GeneralDetail?spc=[?id?]
GLYCOSCIENCES.de
http://www.glycosciences.de/sweetdb/start.php?action=explore_linucsid&linucsid=[?id?]&show=1#struct%0A%20%20%09%09
JCGGDB
http://jcggdb.jp/idb/jcggdb/[?id?]
KEGG
http://www.genome.jp/dbget-bin/www_bget?gl:[?id?]
MonosaccharideDB
http://www.monosaccharidedb.org/display_monosaccharide.action?id=[?id?]
PDB
http://www.rcsb.org/pdb/explore/explore.do?structureId=[?id?]
PFCSDB
http://csdb.glycoscience.ru/plant_fungal/core/search_id.php?mode=record&id_list=[?id?]
PubChem
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=[?id?]
SMSA
http://ws.glyconavi.org/SM/id.php?Id=[?id?]
UniCarb-DB
http://www.unicarb-db.org/structure/[?id?]
UniCarbKB
http://www.unicarbkb.org/structure/[?id?]
#CE_Digest_Electrogram
CE Digest Electrogram
#CE_Electrogram
CE Electrogram
#CE_Property
Class that contains Capillary Electrophoresis properties.
#CE_Property
CE Property
#Citation
Initial class name is capitalized.
"glycan:Citation"
#Citation
Citation
#D2O
Heavy water, formally called deuterium oxide. Deuterium oxide is used in NMR spectroscopy when the solvent of interest is water and the nuclide of interest is hydrogen.
#D2O
D2O
#DMSO
Dimethyl sulfoxide (DMSO) is an organosulfur compound with the formula (CH3)2SO. This colorless liquid is an important polar aprotic solvent that dissolves both polar and nonpolar compounds and is miscible in a wide range of organic solvents as well as water.
#DMSO
DMSO
#Evidence_HPLC
Normal Phase, a subclass of glycan:evidence_lc, is an experiment for the identification of released glycans based on retention properites run on a HPLC instrument. Retention times are compared to a dextran ladder and represented as GU values.
#Evidence_HPLC
Evidence HPLC
#Evidence_RPUPLC
Reverse Phase, a subclass of glycan:evidence_lc, is an experiment for the identification of released glycans based on retention properites. Retention times are normally compared with an arabinose ladder and assigned arabinose units (AU).
#Evidence_RPUPLC
Evidence RPLC
#Evidence_UPLC
Normal Phase, a subclass of glycan:evidence_lc, is an experiment for the identification of released glycans based on retention properites run on a UPLC instrument. Retention times are compared to a dextran ladder and represented as GU values.
#Evidence_UPLC
Evidence UPLC
#Glycoprotein
Glycoprotein
#Glycoprotein
Initial class name is capitalized.
"glycan:Glycoprotein
#Glycosylation_site
A glycosylation site is an amino acid residue within a peptide that accepts oligosaccharide via amide linkage.
#Glycosylation_site
Glycosylation Site
#H2O
Water
#N-glycan
A subclass of saccharide primarily found on eukaryotic glycoproteins. This class of glycan typically contains a specific glycan substructure motif (http://jcggdb.jp/idb/motif?id=JCGG-MOTIF1001), and the reducing terminal GlcNAc of the glycan is attached to the N-atom of an asparagine residue of the protein in a beta configuration. A class of glycoconjugate including dolichyl-diphospho esters also involves the same glycan motif, but they are attached in an alpha configuration. The dolichyl-diphosphooligosaccharides are precursors or intermediates in the protein N-glycosylation process, by which the specific dolichyl-diphosphooligosaccharide (http://jcggdb.jp/idb/jcggdb/JCGG-STR015745) is transferred from the dolichyl phospohate ester to an asparagine residue of the protein by an oligosacchayl transferase (GO:0004579).
#N-glycan
N-glycan
#O-glycan
A subclass of saccharide primarily found in glycoproteins This class is subdivided into a variety of subclasses due to its expression in a variety of biological sources. In terms of structure, O-glycans either consist of a GalNAc, Man, Fuc, Glc residue at the reducing end attached to a serine, threonine, hydroxylysine or hydroxyproline residue in a protein sequence in an alpha configuration.
#O-glycan
O-glycan
#PNGaseA_release
Release of glycan that is used PNGaseA.
#PNGaseA_release
PNGaseA release
#PNGaseF_release
Release of glycan that is used PNGaseF.
#PNGaseF_release
PNGaseF release
#Referenced_compound
Initial class name is capitalized.
"glycan:Referenced_compound"
#Referenced_compound
Referenced Compound
#Saccharide
Initial class name is capitalized.
"glycna:Saccharide"
#Saccharide
Saccharide
#Source_natural
Initial class name is capitalized.
"glycan:Source_natural"
#Source_natural
Source Natural
#_Fucosidase
Glycan(s) treated with alpha1-2,4,6 Fucosidase that catalyses the hydrolysis of α1-2, α1-4, and α1-6 linked L-fucopyranosyl residues
#_Fucosidase
Glycan(s) treated with alpha1-3,4 Fucosidase that catalyses the hydrolysis of α1-3 and α1-4 linked fucose residues
#_Fucosidase
alpha1-2,4,6 Fucosidase
#_Fucosidase
alpha1-3,4 Fucosidase
#_Galactosidase
Glycan(s) treated with alpha1-3,6 Galactosidase that catalyses the hydrolysis of α1-3,6 linked D-galactopyranosyl residues
#_Galactosidase
Glycans treated with alpha1-3,4,6 Galactosidase that catalyses the hydrolysis of α1-3, α1-4, and α1-6 linked D-galactopyranosyl residues
#_Galactosidase
alpha1-3,4,6 Galactosidase
#_Galactosidase
alpha1-3,6 Galactosidase
#_Mannosidase
Glycan(s) treated with alpha1-2,3 Mannosidase that catalyses the hydrolysis of α1-2 and α1-3 linked D-Mannopyranosyl residues
#_Mannosidase
alpha1-2,3 Mannosidase
#_Neuraminidase
Glycan(s) treated with alpha2-3,6,8 Neuraminidase that removes α2-3, α2-6, and α2-8 linked N-acetyl-neuraminic acid residues
#_Neuraminidase
alpha2-3,6,8 Neuraminidase
#_Neuraminidase_A
Glycan(s) treated with alpha2-3,6,8,9 Neuraminidase A that removed all terminal sialic acids. Note some enzymes release α2-3 and α2-6 linkages at a higher rate than α2-8 and α2-9.
#_Neuraminidase_A
alpha2-3,6,8,9 Neuraminidase A
#absolute_configuration
Absolute configuration of a monosaccharide basetype. Possible values are D, L or Unknown.
#absolute_configuration
Absolute Configuration
#absolute_configuration_dexter
dexter
#absolute_configuration_laevus
laevus
#absolute_configuration_unknown
unknown
#adduct
Adduct
#adduct_ion
Adduct Ion
#adduct_ion_h
H+
#adduct_ion_na
Na+
#aglycon
Instances of this class represent the aglyca which are covalently attached to the glycans. It contains information about the aglycon, the linkage position in aglycon and glycan.
#aglycon
Aglycon
#alanine
Alanine
#allo
allo
#alpha-N-acetylgalactosaminidase
Glycan(s) treated with alpha-N-acetylgalactosaminidase that catalyzes the hydrolysis of α-linked D-N-acetylgalactosamine
#alpha-N-acetylgalactosaminidase
alpha-N-acetylgalactosaminidase
#alpha1-2_Fucosidase
Glycan(s) treated with alpha1-2 Fucosidase that catalyses the hydrolysis of linear α1-2 linked L-fucopyranosyl residues
#alpha1-2_Fucosidase
alpha1-2 Fucosidase
#alpha1-6_Mannosidase
Glycan(s) treated with alpha1-6 Mannosidase that removes α1-6 linked D-mannopyranosyl residues.
#alpha1-6_Mannosidase
alpha1-6 Mannosidase
#alpha2-3_Neuraminidase
Glycan(s) treated with alpha2-3 Neuraminidase that catalyses the hydrolysis of α2-3 N-acetyl-neuraminic acid residues from oligosaccharides. Note some α2-6 linked removed at a lower rate.
#alpha2-3_Neuraminidase
alpha2-3 Neuraminidase
#alpha2-3_Neuraminidase_S
Glycan treated with alpha2-3 Neuraminidase S
#alpha2-3_Neuraminidase_S
alpha2-3 Neuraminidase S
#altro
altro
#amino_acid
Amino Acid
#aminoacridone
Glycan labelled with 2-aminoacridone
#aminoacridone
2-aminoacridone
#aminobenzamide
Glycan labelled with 2-aminobenzamide
#aminobenzamide
2-aminobenzamide
#aminobenzoic_acid
Glycan labelled with 2-aminobenzoic acid
#aminobenzoic_acid
2-aminobenzoic acid
#aminopyridine
Glycan labelled with 2-aminopyridine
#aminopyridine
2-aminopyridine
#anomer
Anomer of a monosaccharide. Possible values are alpha, beta, unknown or none.
#anomer
Anomer
#anomer_alpha
alpha
#anomer_beta
beta
#anomer_none
none
#anomer_unknown
unknown
#antibody
A subclass of glycan_binder which binds to an epitope; in this namespace, this is a glycoepitope, which may be a (part of a) glycan or a part of a glycoconjugate.
#antibody
Antibody
#arabino
arabino
#arginine
arginine
#asparagine
asparagine
#aspartic_acid
aspartic acid
#basetype
Basetype of the monosaccharide in accordance to GlycoCT and MonosaccharideDB definitions.
#basetype
Basetype
#beta-N-Acetylglucosaminidase
Glycan(s) treated with beta-N-Acetylglucosaminidase that catalyses the hydrolysis of terminal, non-reducing β-N-Acetylglucosamine residues
#beta-N-Acetylglucosaminidase
beta-N-Acetylglucosaminidase
#beta-N-Acetylglucosaminidase_S
Glycan treated with beta-N-Acetylglucosaminidase S
#beta-N-Acetylglucosaminidase_S
beta-N-Acetylglucosaminidase S
#beta-N-Acetylhexosaminidase
Glycan treated with beta-N-Acetylhexosaminidase that catalyses the hydrolysis of terminal β-D-N-acetyl-galactosamine and glucosamine residues from oligosaccharides.
#beta-N-Acetylhexosaminidase
beta-N-Acetylhexosaminidase
#beta1-3_Galactosidase
Glycan(s) treated with beta1-3 Galactosidase that catalyses the hydrolysis of β1-3 D-galactopyranosyl residues. Some enzymes known to cleave β1-6 but a lower rate.
#beta1-3_Galactosidase
beta1-3 Galactosidase
#beta1-4_Galactosidase
Glycan(s) treated with beta1-4 Galactosidase that catalyses the hydrolysis of β1-4 linked D-galactopyranosyl residues.
#beta1-4_Galactosidase
beta1-4 Galactosidase
#beta_elimination
Beta elimination that released glycan from glycoconjugate.
#beta_elimination
beta elimination
#biological_repeat_unit
A biological repeat unit contains the monosaccharides of the repetitive oligosaccharide unit in the arrangement as they are synthesized.
#biological_repeat_unit
Biological Repeat Unit
#buffer
A buffer is an aqueous solution consisting of a mixture of a weak acid and its conjugate base or a weak base and its conjugate acid.
#buffer
Buffer
#captured_by
Object is compounds that have affinity to glycan or glycoconjugate.
#carbohydrate_format
Instances of this class are the carbohydrate sequence formats.
#carbohydrate_format
Carbohydrate Format
#carbohydrate_format_carbbank
carbbank
#carbohydrate_format_csdb
csdb
#carbohydrate_format_glycoct
glycoct
#carbohydrate_format_glyde2
glyde2
#carbohydrate_format_iupac_condensed
iupac condensed
#carbohydrate_format_iupac_extended
iupac extended
#carbohydrate_format_iupac_short
iupac short
#carbohydrate_format_kcf
kcf
#carbohydrate_format_linearcode
linearcode
#carbohydrate_format_linucs
linucs
#carbohydrate_format_wurcs
wurcs
#catalyzed_by
Object is a reaction process.
#chemical_release
Release of glycan that is used chemical reaction.
#chemical_release
Chemical Release
#chemical_repeat_unit
A chemical repeat unit is generated when a polysaccharide is chopped down for the analysis. The sequence of the oligomer is based on the reaction chopping down the glycan and may not represent the biological repeat unit.
#chemical_repeat_unit
Chemical Repeat Unit
#citation
References are publications related to the glycan structures or features. This can be journal papers, book chapters, conference articles and so on.
#citation
Citation
#component
Components are used to specify the composition of glycans. A component has a reference to the molecule (monosaccharide, substituent) and a number of occurrences for this molecule in the glycan.
#component
Component
#compound
Superclass of types of glycan related molecules and fragments.
#compound
Compound
#configuration
Configuration of a monosaccharide. Each monosaccharide can have several configurations (e.g. dgro-dgal). Each configuration consist of a absolute configuration and a relative configuration.
#configuration
Configuration
#configuration_x
x
#contained_in
The subject is a structurally defined motif, and the object is a glycan structure or motif.
#core_modification
Core modification of a monosaccharide. A core modification consists of a modification type and the position(s) at which this modification happened.
#core_modification
Core Modification
#core_modification_type
List of core modifications that can appear on a monosaccharide.
#core_modification_type
Core Modification Type
#core_modification_type_acid
Carboxyl (COOH) group.
#core_modification_type_acid
acid
#core_modification_type_aldi
Alditol: Reduction of the aldehyde group to CH2OH.
#core_modification_type_aldi
aldi
#core_modification_type_anhydro
Intramolecular anhydride.
#core_modification_type_anhydro
anhydro
#core_modification_type_deoxy
Deoxygenation of a position: The OH group is removed and replaced by a hydrogen atom.
#core_modification_type_deoxy
deoxy
#core_modification_type_en
Double bond in the basetype backbone. This modification implies that - unless explicitly stated with a deoxy modification - hydroxyl groups are preserved.
#core_modification_type_en
en
#core_modification_type_enx
Double bond in the basetype backbone with unknown deoxygenation pattern.
#core_modification_type_enx
enx
#core_modification_type_geminal
Loss of stereochemistry due to identical substituents with DEOXY and H_LOSE linkage types at a single position.
#core_modification_type_geminal
geminal
#core_modification_type_keto
A carbonyl group in the open chain version of a monosaccharide. This modification is omitted if it is only present at position 1 (standard aldose).
#core_modification_type_keto
keto
#core_modification_type_sp
Triple bond to a substituent.
#core_modification_type_sp
sp
#core_modification_type_sp2
Double bond to a substituent.
#core_modification_type_sp2
sp2
#core_modification_type_yn
Triple bond in the basetype backbone.
#core_modification_type_yn
yn
#cyclic_glycan
Cyclic glycans are a special form of glycans which are rarely found in nature. As implied by the name, they form cyclic structures, in contrast to the branched tree structures of commonly known glycans.
#cyclic_glycan
Cyclic Glycan
#cysteine
cysteine
#d-alanine
D-Alanine
#d-arginine
d-arginine
#d-asparagine
d-asparagine
#d-aspartic_acid
d-aspartic acid
#d-cysteine
d-cysteine
#d-glutamic_acid
d-glutamic acid
#d-glutamine
d-glutamine
#d-glycine
d-glycine
#d-histidine
d-histidine
#d-isoleucine
d-isoleucine
#d-leucine
d-leucine
#d-lysine
d-lysine
#d-methionine
d-methionine
#d-phenylalanine
d-phenylalanine
#d-proline
d-proline
#d-selenocysteine
d-selenocysteine
#d-serine
d-serine
#d-threonine
d-threonine
#d-tryptophan
d-tryptophan
#d-tyrosine
d-tyrosine
#d-valine
d-valine
#database_bcsdb
BCSDB
#database_bcsdb
http://csdb.glycoscience.ru/bacterial/
#database_bcsdb
Bacterial Carbohydrate Structure DataBase
#database_carbbank
CarbBank
#database_carbbank
http://www.genome.jp/dbget-bin/www_bfind?carbbank
#database_carbbank
Complex Carbohydrate Structure Database
#database_carint
Carint
#database_carint
http://ws.glyconavi.org/carint/
#database_carint
Carbohydrate Interaction Database
#database_category_bibliography
bibliography
#database_category_cabohydrate_structure
Database containing glycan structure information.
#database_category_cabohydrate_structure
structure
#database_category_carbohydrate_conformation
Database containing carbohydrate conformation
#database_category_carbohydrate_conformation
carbohydrate conformation
#database_category_carbohydrate_interaction
carbohydrate interaction
#database_category_chemical_compound
Database of carbohydrates at the atomic level.
#database_category_chemical_compound
chemical compound
#database_category_experimental
Database of glycomics experiments such as NMR, MS, array data, etc-
#database_category_experimental
experimental
#database_category_glycan_binding_protein
glycan binding protein
#database_category_glycoenzyme
glycoenyzme
#database_category_monosaccharide
Database containing monosaccharide information.
#database_category_monosaccharide
monosaccharide
#database_category_synthesis
synthesis
#database_category_taxonomy
Taxonomical information regarding glycans are available.
#database_category_taxonomy
taxonomy
#database_category_tissue
tissue
#database_cazy
CAZy
#database_cazy
http://www.cazy.org
#database_cazy
Carbhoydrate-Active enZYmes
#database_cfg
CFG
#database_cfg
http://www.functionalglycomics.org/glycomics/molecule/jsp/carbohydrate/carbMoleculeHome.jsp
#database_cfg
Consortium for Functional Glycomics Structure Database
#database_cfg_gbp
CfgGBP
#database_cfg_gbp
http://www.functionalglycomics.org/glycomics/molecule/jsp/gbpMolecule-home.jsp
#database_cfg_gbp
CFG Glycan Binding Proteins
#database_cfg_glycoenzymes
CfgGlycoenzyme
#database_cfg_glycoenzymes
http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/geMolecule.jsp
#database_cfg_glycoenzymes
CFG Glycosyltransferases DB
#database_chebi
ChEBI
#database_chebi
http://www.ebi.ac.uk/chebi/
#database_chebi
Chemical Entities of Biological Interest
#database_chemspider
ChemSpider
#database_chemspider
http://www.chemspider.com/
#database_chemspider
ChemSpider
#database_glyaffinity
GlyAffinity
#database_glyaffinity
http://www.glycosciences.de/affinity/browse.action
#database_glyaffinity
GlyAffinity
#database_glyco
GlycO
#database_glyco
http://ccrc.uga.edu/ontology/GlycO/GlycO.owl
#database_glyco
Glycomics Ontology
#database_glycobase_dublin
GlycoBase(Dublin)
#database_glycobase_dublin
http://glycobase.nibrt.ie/glycobase/show_nibrt.action
#database_glycobase_dublin
GlycoBase(Dublin)
#database_glycobase_lille
GlycoBase(Lille)
#database_glycobase_lille
http://glycobase.univ-lille1.fr/base/
#database_glycobase_lille
GlycoBase(Lille)
#database_glycomapsdb
GlycoMapsDB
#database_glycomapsdb
http://www.glycosciences.de/modeling/glycomapsdb/
#database_glycomapsdb
GlycoMapsDB
#database_glycomedb
GlycomeDB
#database_glycomedb
http://www.glycome-db.org/
#database_glycomedb
GlycomeDB
#database_glyconavi
GlycoNAVI
#database_glyconavi
http://ws.glyconavi.org/
#database_glyconavi
GlycoNAVI
#database_glyconmr
GlycoNMR
#database_glyconmr
http://glycoinfolab.jp/GlycoNMR/
#database_glyconmr
GlycoNMR
#database_glycosciences_de
GLYCOSCIENCES.de
#database_glycosciences_de
http://www.glycosciences.de/database/
#database_glycosciences_de
GLYCOSCIENCES.de
#database_jcggdb
JCGGDB
#database_jcggdb
http://jcggdb.jp/index_en.html
#database_jcggdb
Japan Consortium for Glycobiology and Glycotechnology DataBase
#database_kegg
KEGG
#database_kegg
http://www.genome.jp/kegg/glycan/
#database_kegg
Kyoto Encyclopedia of Genes and Genomes
#database_monosaccharidedb
MonosaccharideDB
#database_monosaccharidedb
http://www.monosaccharidedb.org
#database_monosaccharidedb
MonosaccharideDB
#database_pdb
PDB
#database_pdb
http://www.rcsb.org/pdb/home/home.do
#database_pdb
RCSB Protein Data Bank
#database_pfcsdb
PFCSDB
#database_pfcsdb
http://csdb.glycoscience.ru/plant_fungal/
#database_pfcsdb
Plant and Fungal Carbohydrate Structure DataBase
#database_pubchem
PubChem
#database_pubchem
http://pubchem.ncbi.nlm.nih.gov/
#database_pubchem
PubChem
#database_smsa
SMSA
#database_smsa
http://ws.glyconavi.org/SM/
#database_smsa
Small Molecule for Spectral Analysis
#database_unicarb_db
UniCarb-DB
#database_unicarb_db
http://www.unicarb-db.org
#database_unicarb_db
UniCarb-DB
#database_unicarbkb
UniCarbKB
#database_unicarbkb
http://www.unicarbkb.org
#database_unicarbkb
UniCarbKB
#degraded_by
Object is a reaction process, which degrades the subject.
#elucidated
if this glycan was elucidated (rather than just studied) in this publication
#enzymatic_release
Release of glycan by an enzymatic reaction.
#enzymatic_release
Enzymatic Release
#enzyme
Enzyme that take part in synthesis anddegradation of glycan.
#enzyme
Enzyme
#erythro
erythro
#evidence
An evidence is any kind of experimental data that can be linked to glycans. These are mainly experiments that elucidate the carbohydrate structure or feature but can also include experiments for creating carbohydrates for example by synthesis.
#evidence
Evidence
#evidence_IGOT
Is an IGOT experiment, subclass of glycan:evidence_lc_ms. IGOT experiment is a procedure for the large-scale identification of N-glycosylated proteins, with isotope-coded glycosylation-site-specific tagging. (PMID: 12754521)
#evidence_IGOT
Evidence IGOT
#evidence_binding
Entities of this class represent molecular interactions between instances of glycan:saccharide and glycan:glycan_binder, elucidated by experimental results.
#evidence_binding
Evidence Binding
#evidence_binding_antibody
Entities of this class represent molecular interactions between instances of epitope and antibody, elucidated by experimental results.
#evidence_binding_antibody
Evidence Binding Antibody
#evidence_binding_lectin
Entities of this class represent molecular interactions between instances of glycan and lectin, elucidated by experimental results.
#evidence_binding_lectin
Evidence Binding Lectin
#evidence_ce
Experiments using capillary electrophoresis to identify and characterize carbohydrate structures.
#evidence_ce
Evidence CE
#evidence_lc
Experiments using LC techniques to identify and characterize carbohydrates or used for separating glycans by charge or other retention properties.
#evidence_lc
Evidence LC
#evidence_lc_ms
Evidence LC MS
#evidence_ms
Experiments using mass spectrometry to identify the carbohydrate structures.
#evidence_ms
Evidence MS
#evidence_nmr
Experiments using NMR to identify the carbohydrate structure.
#evidence_nmr
Evidence NMR
#evidence_type
List of evidence types.
#evidence_type
Evidence Type
#evidence_type_ce
ce
#evidence_type_hplc
hplc
#evidence_type_lc
lc
#evidence_type_lc_ms
lc ms
#evidence_type_lc_msms
lc msms
#evidence_type_ms
ms
#evidence_type_msms
msms
#evidence_type_nmr
nmr
#from_sample
A brief descripition of the sample analysed. This may be required if taxon, tissue, and disease are not sufficient. An example may include analysis of a sample with no specified background e.g. commerical project.
#from_sample
from_sample
#furanose
A furanose is a five member ring structure containing four carbon atoms and one oxygen atom.
#furanose
furanose
#galacto
galacto
#gluco
gluco
#glutamic_acid
glutamic acid
#glutamine
glutamine
#glycan_binder
A class of compound that has affinity to a glycan or glycoconjugate. Usually a reference to a lectin, virus, bacteria, etc.
#glycan_binder
Glycan Binder
#glycan_database
A class representing databases that store glycans and related information. If possible, owl:sameAs should be used referencing the biosharing entry for this database.
#glycan_database
Glycan Database
#glycan_database_category
Instances of this class are the categories for the classification of glycan databases.
#glycan_database_category
Glycan Database Category
#glycan_epitope
A glycan epitope is a special motif which has a known biological function.
#glycan_epitope
Glycan Epitope
#glycan_motif
A glycan motif is a sub-structure of glycans that has been named because of its frequent appearance or because of the biological meaning.
#glycan_motif
Glycan Motif
#glycan_release
A class for process of glycan release, including chemical and enzymatic reaction.
#glycan_release
Glycan Release
#glycero
glycero
#glycine
glycine
#glycoconjugate
Superclass of biomolecules consisting of a glycan part and an aglycon part, that are covalently attached to each other.
#glycoconjugate
Glycoconjugate
#glycoconjugate_sequence
Sequence of the glycoconjugate that includes the carbohydrate and the aglyca. Predicates should be selected based on the format used to represent the structure.
#glycoconjugate_sequence
Glycoconjugate Sequence
#glycolipid
Lipid with saccharide(s) attached by glycosidic bond(s).
#glycolipid
Glycolipid
#glycopeptide
A class involves artificial degradation products of glycoproteins with protease digestion, which typically results from a proteomics experiment. There are reasons or traces that at least one amino acid residue of the peptide is glycosylated.
#glycopeptide
Glycopeptide
#glycoprotein
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.
#glycoprotein
Glycoprotein
#glycosequence
Sequence of the glycan in a specified sequence format.
#glycosequence
Glycosequence
#glycoside
Glycoside
#glycosyl_hydrolase_reaction
Instances of this class are glycosyl hydrolase reactions which releases monosaccharide or oligosaccharides from the glycan or glycoconjugate.
#glycosyl_hydrolase_reaction
Glycosyl Hydrolase Reaction
#glycosylated_AA
An amino acid residue, in a glycoprotein or glycopeptide sequence, that a glycan is covalently attached. To specify glycosylation type or bond of glycoprotein.
#glycosylated_AA
Glycosylated Amino Acid
#glycosylates
glycosylates
#glycosyltransferase_reaction
Instances of this class are glycosyltransferase reactions that build up glycans or glycoconjugates by attaching additional monosaccharides or oligosaccharides to them.
#glycosyltransferase_reaction
Glycosyltransferase Reaction
#gradient
Gradient
#gulo
gulo
#has_AA_sequence
Amino acid sequence is represented in the standard IUPAC-IUB amino acid code. Even if any modification are known, any modified amino acid residues are represented with a single letter of a nascent residue.
#has_abbreviation
Abbreviation of the database
#has_absolute_configuration
Subject is a monosaccharide basetype. The object values for the predicate can be D, L or unknown.
#has_affinity_to
Subject is a glycan or glycoconjugate, which non-covalently binds to the object, usually :glycan_binder.
#has_affinity_value
Binding affinity value for the lectin or antibody.
#has_aglycon
This property is used to specify the aglycon portion of a glycoconjugate compound.
#has_alias
reference to aliases for the monosaccharide
#has_alias_name
Alias name of a monosaccharide.
#has_alternative_name
Name of compound. Use if name is not with compliant with Oxford Shorthand format, IUPAC, GlycoCT/WURCS, or Motif/Epitope.
#has_anomer
Anomeric state of the basetype.
#has_arabinose_unit
Structure has an arabinose unit
#has_association
has association
#has_attached_glycan
This property is used to specify a glycan portion of a glycoconjugate compound.
#has_average_molecular_weight
literal numeric with decimal, calculated from monosaccharide composition with average atomic weight
#has_basetype
Object is the basetype of the monosaccharide (subject).
#has_basetype_id
Id of the basetype in MonosaccharideDB.
#has_basetype_linkage_position
Linkage position at the basetype.
#has_cardinality
Number of occurrences of an element (e.g. a monosaccharide) in the subject. This information can be missing in case the cardinality cannot be defined (e.g. repeat units with unknown or under-defined repeats). Missing for non-stoichiometrical residues.
#has_cardinality_per_repeat
Number of occurrences of an element (e.g. a monosaccharide) in the repeat unit. Applicable to :repeatUnits only. Missing for non-stoichiometrical residues.
#has_category
category of a glycan database
#has_ce_electrogram
Glycan annotation with associated CE electrogram evidence
#has_ce_peak
Peak description
#has_cell_line
Cell line information of the source
#has_cell_type
Cell type information of the source
#has_charge
Charge state of the MS peak
#has_chemical_shift
chemical shift (may be multiple e.g. for CH2 groups in 1H spectra. May be missing if unknown)
#has_chemical_shift_max
Maximum value of chemical shift.
#has_chemical_shift_min
Minimum value of chemical shift.
#has_code
Code for compound. This may be linked with a commerically available compound and its catalogue number or in-house available compound e.g. synthesied standard.
#has_component
Object is a component, representing the monosaccharide composition of the subject.
#has_compound
has_compound
#has_configuration
Instance of class is configuration.
#has_configuration
configuration
#has_core_modification
reference to another RDF describing a core modification that is present in this basetype
#has_core_modification_type
Type of the core modification. Instances of class are core modification types.
#has_core_modification_type
has_core_modification_type
#has_coupling_constant
values in Hz
#has_default_linkage_bondorder
Object is bond order that is number of linkage in default.
#has_default_linkage_bondorder2
Object is second bond order that is number of linkage in default.
#has_default_linkage_type
Instances of this class are linkage type .
#has_default_linkage_type2
Instances of this class are second linkage type.
#has_default_linking_position
A position that is number of linkage in default.
#has_default_linking_position2
A position that is number of second linkage in default.
#has_destination_organism
glycan of which organism authors wanted to synthesize or model
#has_diameter
diameter of the column in micro meter
#has_disease
MESH reference for disease
#has_enzyme
Object is an enzyme, which performs the reaction.
#has_epitope
The object is a structural motif with biological relevance; subproperty of has_motif.
#has_evidence
evidence for a given set of information (glycan, publication). An evidence can be any type of experimental data.
#has_exoglycosidase_chromatogram
Relation to exoglycosidase treated sample
#has_extended_stereocode
Extended stereocode of the basetype
#has_external_substituent
Reference to a :substituent.
#has_first_configuration
Reference to another RDF resource with URI describing the first monosaccharide configuration
#has_fluid
either tissue or fluid
#has_fragment
sequence as peak annotation
#has_glucose_unit
Structure has an glucose unit
#has_glycan
The glycan object referenced by this subject.
#has_glycoconjugate_sequence
Sequence information to object of rdf:type :glycoconjugate_sequence if the subject is part of a glycoconjugate.
#has_glycosequence
glycan sequence information to object of rdf:type :glycosequence representing the subject in a text format.
#has_glycosylated_AA
This property is used to specify a glycosylated amino acid residue in an object glycoprotein or glycopeptide.
#has_image
Object is a URI to an image instance describing a graphical representation of the glycan.
#has_intensity
intensity value of the MS peak
#has_keyword
Keyword for the publication. Object is a URI in MeSH.
#has_lc_chromatogram_peak
Peak description
#has_length
Length of the column in milli meter
#has_life_stage
Life stage information of the source.
#has_linkage_path
path from the reducing end or from the rightmost residue in repeat
#has_linkage_position
Monosaccharide can be linked to other residues via standard glycosidic linkage at the given backbone position.
#has_linkage_type
GlycoCT linkage type of the monosaccharide to the substituent
#has_manufacturer
Manufacturer of the device used in the experiment.
#has_material
Column packing material
#has_method
experimental procedures described in the article
#has_model
Model of the device used in the experiment.
#has_modification_position
Position of the modification at the monosaccharide.
#has_modification_position2
Second position of the modification at the monosaccharide (eg. for double bounds)
#has_monoisotopic_molecular_weight
Literal numeric with decimal, calculated from monosaccharide composition with atomic weight of monoisotope.
#has_monosaccharide
URI to a RDF resource describing the monosaccharide (usually MonosaccharideDB).
#has_monosaccharide_notation_scheme
One of GLYCOSCIENCES, GLYCOCT, IUPAC, CARBBANK, CFG, BCSDB, PDB, or GLYCAM, see http://www.monosaccharidedb.org/notation.action?topic=schemes
#has_motif
The object is a structurally defined motif E.g. for Neo-lacto motif http://jcggdb.jp/idb/motif?id=JCGG-MOTIF3009.rdf inverse of ”contained_in”. should have sequence, composition, image ...
#has_msdb_id
Id of the monosaccharide in MonosaccharideDB.
#has_multiplicity
single-character literal (S,M,D,T ,Q) or combination
#has_mz
MZ value of the MS peak
#has_nucleus
Nucleus
#has_organ
Organ of the source.
#has_particle_size
Size of the particle in micro meter.
#has_peak_area
Integrated peak area.
#has_phase_description
Description / short hand of the phase e.g. HILIC, PGC
#has_phase_description
has_phase_description
#has_polymerization_degree
Used only if the specified glycan structure (subject) itself is the oligomeric part forming a repeating unit. Repeating unit information to object of rdf:type :repeat_count.
#has_precursor_peak
URI of the precursor peak of a MS^n spectra.
#has_product
Object is generated by the reaction.
#has_protein_name
Protein name in accordance with UniProt accession with information available.
#has_reference
Reference between :compound, :citation, :evidence, :source and :referenced_compound.
#has_relative_configuration
IUPAC monosaccharide basetype information. Without absolute configuration D or L
#has_repeat_attribute
(min, max, exact, average, unknown) part of repeating unit
#has_repeat_count
value of repeat_attribute in resource, if known
#has_residue
Monosaccharide annotation of the subspectrum.
#has_resource_entry
Assigns a resource entry to a compound.
#has_retention_time
Retention time of the molecule in the experiment in minutes.
#has_ring_end
position of last carbon involved in ring closure
#has_ring_start
position of first carbon involved in ring closure
#has_ring_type
Assigns the ring type to a basetype.
#has_sample_type
Sample type of the source.
#has_second_configuration
Reference to another RDF resource with URI describing the second monosaccharide configuration in case there are more than four stereocenters
#has_sequence
Sequence of the Glycan
#has_signal
Resource to a :signal
#has_size
number of backbone carbon atoms
#has_stereocode
Stereocode describing the backbone stereochemistry
#has_strain
Object is bacterial strain.
#has_structure_location
The location of the referenced compound in a publication (e.g. Figure 1).
#has_substituent_linkage
linkage of the substituent
#has_substituent_linkage_position
Linkage position at the substituent.
#has_substituent_linkage_position2
Second linkage position at the substituent.
#has_substituent_type
linkage type of the substituent
#has_substitution
The substituent is linked to the basetype in this monosaccharide.
#has_substitution_name
Name of substitution.
#has_substrate
Object is consumed by the reaction.
#has_symbol_format
URL to explanation of symbol? The display style of the glycan. (cfg, uoxf, atoms)
#has_synthesis_type
Allows to specify the synthesis type used to generated the glycan.
#has_taxon
Species information of the source.
#has_third_configuration
Reference to another RDF resource with URI describing the third monosaccharide configuration in case there are more than eight stereocenters
#has_tissue
either tissue or fluid
#has_unassigned_signal
Link to an unassigned signal which is just a chemical shift.
#has_uniprot_accession
When the subject of this predicate is :glycoprotein, the range instance is equivalent to proteineous part of the subject glycoprotein.
#has_uoxf
Glycan sequence in a text format.
#has_uoxf
has_uoxf
#has_url_template
xsd:string such as http://foo.bar.com/someglycan?id=%s
#has_valence
Object is a valence of substituent.
#has_version
Version of the software used
#histidine
histidine
#hosted_by
Reference to another biological source representing the host organism.
#hybrid_with
An offspring of two different taxons.
#ido
ido
#image
Image class for representing glycan images.
#image
Image
#in_carbohydrate_format
carbohydrate sequence format of the sequence given in the glycosequence instance
#in_glycan_database
Glycan is present in the glycan database specified by the URI.
#is_ambiguous
Boolean indicating whether the subject is a fully defined structure including all linkage information, or not.
#is_fragment
If the synthesised or modeled molecule is just a fragment or the complete target molecule
#is_from_profile
A profile can have many peaks and saccharides. It represents a single LC run (parent or digest).
#is_from_report
Reference to a report (internal, contract, method development or similar) with no associated publication.
#is_from_source
Source annotation for a referenced compound.
#is_fuzzy
If a substituent is fuzzy.
#is_glycosylated_on
is glycosylated on
#is_linkable
If a substituent is linkable.
#is_missing
If true unassigned signal. NO if a signal can not exist, rather than its unknown.
#is_primary_name
indicates whether this is the name that should be used to uniquely identify this monosaccharide in the given :notation_scheme, or whether this is a secondary alias name (e.g. to indicate whether a trivial name or a systematic name is to be used preferentially in case a trivial name exists for this monosaccharide)
#is_trivial_name
Indicates whether this is a trivial name that implies modifications, or a systematic name (e.g. KDO vs. D-3-deoxy-manOct2ulo-onic)
#isoleucine
isoleucine
#lc_chromatogram
LC Chromatogram
#lc_column
LC Column
#lc_digest_chromatogram
LC Digest Chromatogram
#lc_peak
LC Peak
#lc_property
Class that contains Liquid Chromatography properties such as gradient, Lc column.
#lc_property
LC Property
#lectin
A class of protein that binds to glycans but is neither an antibody nor an enzyme.
#lectin
Lectin
#leucine
leucine
#linkage_type
List of linkage types that can occur on the monosaccharide side of monosaccharide to substituent linkages.
#linkage_type
Linkage Type
#linkage_type_deoxy
The substituent is linked directly to the basetype backbone by replacing the OH group.
#linkage_type_deoxy
deoxy
#linkage_type_h_at_oh
A standard O-linked substituent, i.e. the substituent replaces the hydrogen of an OH group.
#linkage_type_h_at_oh
h at oh
#linkage_type_h_loss
The substituent is linked directly to the basetype backbone by replacing the hydrogen atom.
#linkage_type_h_loss
h loss
#linkage_type_r_config
The substituent is linked directly to the basetype backbone by replacing a hydrogen atom at a terminal position, which would be non-chiral without the substituent, resulting in an R-configuration of the carbon.
#linkage_type_r_config
r config
#linkage_type_s_config
Same as R_CONFIG, but resulting in an S-Configuration of the carbon.
#linkage_type_s_config
s config
#lipid
Lipid
#lysine
lysine
#lyxo
lyxo
#manno
manno
#mass_spectrometry_device
Mass Spectrometry Device
#mass_spectrum
Mass Spectrum
#methionine
methionine
#modification_type
Modification type is represented due to biological process, typically N-linked or O-linked.
#monosaccharide
Instances of this class represent monosaccharides and their information. These monosaccharides are used to specify the composition of glycans, referenced by glycan:component. Sample URI:
http://www.monosaccharidedb.org/rdf/monosaccharide.action?name=o-dall-HEX-0:0
#monosaccharide
Monosaccharide
#monosaccharide_alias
Alternative names for the monosaccharide in different databases or resources. The aliases consist of the name and the monosaccharide notation scheme.
#monosaccharide_alias
Monosaccharide Alias
#monosaccharide_notation_scheme
List of monosaccharide notation scheme. One monosaccharide can have several different names depending on the notation scheme.
#monosaccharide_notation_scheme
Monosaccharide Notation Scheme
#monosaccharide_notation_scheme_amber_glycam
Two-letter residue names used within the AMBER GLYCAM forcefield. For more information, see Carbohydrate Naming Convention in Glycam.
Note (1): Monosaccharide alias names in GLYCAM notation also encode linkage positions (in the first character of a three-letter-code residue name). These depend on the context of a residue within an oligosaccharide and thus are no monosaccharide properties. GLYCAM names stored in MonosaccharideDB refer to a terminal residue. The first character might have to be adjusted according to the specific context of a residue, i.e. in case other residues linked are to the given one.
Note (2): The GLYCAM notation is not yet supported by the notation parsing routines, i.e. GLYCAM alias names can be created, but not be read yet.
#monosaccharide_notation_scheme_amber_glycam
amber glycam
#monosaccharide_notation_scheme_bcsdb
The notation used by the Russian BCSDB. For more information on this notation, see the description on the BCSDB homepage.
#monosaccharide_notation_scheme_bcsdb
bcsdb
#monosaccharide_notation_scheme_carbbank
The CarbBank notation is based on the IUPAC extended notation. It is used by the Complex Carbohydrate Structure Database (CCSD), which is better known by the name of its query software "carbbank". CarbBank style notation forms the basis of several other notations, such as the Glycosciences.de scheme.
#monosaccharide_notation_scheme_carbbank
carbbank
#monosaccharide_notation_scheme_cfg
The LinearCode notation used by the US Consortium for Functional Glycomics (CFG).
#monosaccharide_notation_scheme_cfg
cfg
#monosaccharide_notation_scheme_glycoct
The nomenclature that is used by EUROCarbDB. For more information see www.eurocarbdb.org/recommendations/encoding/.
#monosaccharide_notation_scheme_glycoct
glycoct
#monosaccharide_notation_scheme_glycosciences_de
The Notation used in the Glycosciences.de web portal. It is based on the CarbBank notation.
#monosaccharide_notation_scheme_glycosciences_de
glycosciences de
#monosaccharide_notation_scheme_monosaccharidedb
MonosaccharideDB's internal notation format. Basetype and substituent names are the same as in GlycoCT, with the exception that 'anhydro' and 'lactone' modifications are included in the basetype here, while they are defined as substituents in GlycoCT. As most glycobiologist and also most carbohydrate databases consider a monosaccharide that contains substituents as one residue, they are defined in this way in MonosaccharideDB as well.
#monosaccharide_notation_scheme_monosaccharidedb
monosaccharidedb
#monosaccharide_notation_scheme_pdb
The 3-letter residue names as used by the Protein Data Bank (PDB). Unlike most of the other notations, these names cannot be generated automatically by conversion routines but have to be assigned manually by the database administrators. Some PDB residue names that encode carbohydrate residues define disaccharides or oligosaccharides. These are not implemented in MonosaccharideDB, as the scope of this database is on monosaccharide residues.
#monosaccharide_notation_scheme_pdb
pdb
#monosaccharide_property
Class that contains all monosaccharides properties such as anomer, basetype etc.
#monosaccharide_property
Monosaccharide Property
#motif
Motif
#ms_annotation
MS Annotation
#ms_fragment_type
MS Fragment Type
#ms_fragment_type_a
A
#ms_fragment_type_b
B
#ms_fragment_type_c
C
#ms_fragment_type_x
X
#ms_fragment_type_y
Y
#ms_fragment_type_z
Z
#ms_peak
Instances represent a peak in a mass spectrometry data consisting of an m/z value, intensity value and optional a charge state.
#ms_peak
MS Peak
#ms_property
Class that contains Mass Spectrometry properties such as adduct, adduct ion etc.
#ms_property
MS Property
#msn_spectrum
Msn Spectrum
#neutral_loss
Neutral Loss
#nmr_property
Parentclass for all classes used in NMR evidences.
#nmr_property
NMR Property
#of_carbon_number
carbon atom number
#open
Open chain sugar that does not form a ring.
#open
open
#peptide
Part of a protein amino acid sequence generated by digestion for analysis.
#peptide
Peptide
#phenylalanine
phenylalanine
#polymerization_degree
A repeat is a property of a polysaccharide that specifies how often the oligomer part is repeated to form the polysaccharide.
#polymerization_degree
Polymerization Degree
#polysaccharide
Polysaccharides are a special form of glycans that consist of large repetitive oligosaccharide units. Often the exact number of repetitions cannot be specified because the experimental technique does not allow this or because the number of repetition in nature varies.
#polysaccharide
Polysaccharide
#profile_spectrum
Profile Spectrum
#proline
proline
#protein
Proteinous part of a glycoprotein that is equivalent to the nascent peptide or protein entities found in UniProt or other protein databases.
#protein
Protein
#published_in
Reference information for the subject.
#pyranose
A Pyranose is any cyclic isomer that has a five carbons and one oxygen in a ring of six atoms.
#pyranose
pyranose
#ratio
Ratio of a solvent in a solvent mixture. (100 if there is only one solvent)
#reaction
Class for reaction process to create or degrade glycans or glycoconjugates.
#reaction
Reaction
#reductive_beta_elimination
Beta elimination that is used reducing a get for stabilize glycan.
#reductive_beta_elimination
reductive beta elimination
#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.
#referenced_compound
Referenced Compound
#relative_configuration
List of relative monosaccharide configurations according to IUPAC.
#relative_configuration
Relative Configuration
#repeat_attribute
List of possible attributes to specify the repeat count. Possible values are average, exact, minimum, maximum or unknown.
#repeat_attribute
Repeat Attribute
#repeat_attribute_average
average
#repeat_attribute_exact
exact
#repeat_attribute_max
max
#repeat_attribute_min
min
#repeat_attribute_unknown
unknown
#resource_entry
A resource entry describes an entry about the glycan in another database.
#resource_entry
Resource Entry
#ribo
ribo
#ring_type
Ringtype of a basetype.
#ring_type
Ring Type
#ring_type_unknown
A monosaccharide whose ring type is unknown.
#ring_type_unknown
unknown
#role
Classification hierarchy for molecular functions.
#role
Role
#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.
#saccharide
Saccharide
#sample_preparation
A process which is the syntesis or preparation of sample for glycan analysis.
#sample_preparation
Sample Preparation
#selenocysteine
selenocysteine
#sequence
A sequence is the textual description of a molecule. For example FASTA sequences for proteins / peptides.
#sequence
Sequence
#serine
serine
#signal
A signal is a NMR data point.
#signal
Signal
#software
Software that has been utilized for the glycan. For example software used to model the glycan.
#software
Software
#solvent
A solvent is a substance that dissolves a solute (a chemically different liquid, solid or gas), resulting in a solution.
#solvent
Solvent
#solvent_part
A solvent can consist of a mixture of different molecules. For each molecule a solvent part with the ratio and the molecule is created.
#solvent_part
Solvent Part
#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.
#source
Source
#source_modeled
Class for modeled source. Instance contain information about the software used for modeling and the target organism.
#source_modeled
Source Modeled
#source_natural
Class for sources from biological organism. Instances contain information about the species, cell type, tissue and so on.
#source_natural
Source Natural
#source_sample
Class for source from sample. Instance contain sample type.
#source_sample
Source Sample
#source_synthetic
Class for source for synthetic glycans. In contains information about the type of synthesis approach used and if applicable the original biological source that was tried to mimic.
#source_synthetic
Source Synthetic
#subspectrum
Subspectrum of NMR data. It contains the annotated signals.
#subspectrum
Subspectrum
#substituent
Substition of a monosaccharide by another molecule. The substituent consists of the substituent type and the linkage between monosaccharide and substituent. For example: http://www.monosaccharidedb.org/rdf/substituent/ethyl.rdf
#substituent
Substituent
#substituent_linkage
Linkage between a monosaccharide basetype and a substituent. It consist of the linkage position on the basetype side and the substituent side, and of the linkage type.
#substituent_linkage
Substituent Linkage
#substituent_type
List of substituent types possible on monosaccharides.
#substituent_type
Substituent Type
#substituent_type_acetyl
COCH3
#substituent_type_acetyl
acetyl
#substituent_type_amino
NH2
#substituent_type_amino
amino
#substituent_type_bromo
Br
#substituent_type_bromo
bromo
#substituent_type_chloro
Cl
#substituent_type_chloro
chloro
#substituent_type_ethanolamine
NHCH2CH2OH
#substituent_type_ethanolamine
ethanolamine
#substituent_type_ethyl
CH2CH3
#substituent_type_ethyl
ethyl
#substituent_type_fluoro
F
#substituent_type_fluoro
fluoro
#substituent_type_formyl
CHO
#substituent_type_formyl
formyl
#substituent_type_glycolyl
COCH2OH
#substituent_type_glycolyl
glycolyl
#substituent_type_hydroxymethyl
CH2OH
#substituent_type_hydroxymethyl
hydroxymethyl
#substituent_type_imino
NH
#substituent_type_imino
imino
#substituent_type_iodo
I
#substituent_type_iodo
iodo
#substituent_type_methyl
CH3
#substituent_type_methyl
methyl
#substituent_type_n_acetyl
NHCOCH3
#substituent_type_n_acetyl
n acetyl
#substituent_type_n_alanine
NHCOCHNH2CH3
#substituent_type_n_alanine
n alanine
#substituent_type_n_dimethyl
N(CH3)2
#substituent_type_n_dimethyl
n dimethyl
#substituent_type_n_ethyl
NHCH2CH3
#substituent_type_n_ethyl
n ethyl
#substituent_type_n_formyl
NHCHO
#substituent_type_n_formyl
n formyl
#substituent_type_n_glycolyl
NCOCH2OH
#substituent_type_n_glycolyl
n glycolyl
#substituent_type_n_methyl
NHCH3
#substituent_type_n_methyl
n methyl
#substituent_type_n_succinate
NCOCH2CH2COOH
#substituent_type_n_succinate
n succinate
#substituent_type_n_sulfate
NHSO3H
#substituent_type_n_sulfate
n sulfate
#substituent_type_n_trifluoroacetyl
NHCOCF3
#substituent_type_n_trifluoroacetyl
n trifluoroacetyl
#substituent_type_n_trimethyl
N(CH3)3
#substituent_type_n_trimethyl
n trimethyl
#substituent_type_nitrat
NO2
#substituent_type_nitrat
nitrat
#substituent_type_phosphate
PO3H2
#substituent_type_phosphate
phosphate
#substituent_type_r_lactate
CH3CHCOOH
#substituent_type_r_lactate
r lactate
#substituent_type_r_pyruvate
CH2CCOOH
#substituent_type_r_pyruvate
r pyruvate
#substituent_type_s_lactate
CH3CHCOOH
#substituent_type_s_lactate
s lactate
#substituent_type_s_methyl
SCH3
#substituent_type_s_methyl
s methyl
#substituent_type_s_pyruvate
CH2CCOOH
#substituent_type_s_pyruvate
s pyruvate
#substituent_type_seleno
SeH
#substituent_type_seleno
seleno
#substituent_type_sulfate
SO3H
#substituent_type_sulfate
sulfate
#substituent_type_telluro
TeH
#substituent_type_telluro
telluro
#substituent_type_thio
SH
#substituent_type_thio
thio
#substituent_type_trifluoroacetyl
COCF3
#substituent_type_trifluoroacetyl
trifluoroacetyl
#substituent_type_x_lactate
CH3CHCOOH
#substituent_type_x_lactate
x lactate
#substituent_type_x_pyruvate
CH2CCOOH
#substituent_type_x_pyruvate
x pyruvate
#sulfotransferase_reaction
Instances of this class are sulfotransferase reactions that modifies glycans or glycoconjugates by attaching sulfuric moiety to them.
#sulfotransferase_reaction
Sulfotransferase Reaction
#symbol_format
Graphical symbol formats used to represent glycans. This includes the symbol format form the CFG and from UOXF.
#symbol_format
Symbol Format
#symbol_format_cfg
A symbol is Consortium for Functional Glycomics (CFG) notation.
#symbol_format_cfg
cfg
#symbol_format_cfg_bw
CFG symbol that is displaied black and white notation.
#symbol_format_cfg_bw
cfg bw
#symbol_format_text
A glycan structure is displayed by text-only form.
#symbol_format_text
text
#symbol_format_uoxf
A symbol is Oxford (UOXF) notations.
#symbol_format_uoxf
uoxf
#symbol_format_uoxf_bw
UOXF symbol that is displayed black and white notation.
#symbol_format_uoxf_bw
uoxf bw
#synthesized_by
Object is a reaction process, which synthesizes the subject.
#synthetic_type
Type of synthesis used for creating the glycan. Possible values are chemical synthesis, enzymatic synthesis and chemoenzymetic synthesis.
#synthetic_type
Synthetic Type
#synthetic_type_chemical
Chemical synthesis that various protecting group manipulations used in the context of glycan synthesis.
#synthetic_type_chemical
chemical
#synthetic_type_chemoenzymatic
Relying on a hybrid of chemical and enzymatic steps that typically begins with chemical synthesis and ends with enzymatic extension.
#synthetic_type_chemoenzymatic
chemoenzymatic
#synthetic_type_enzymatic
Employing glycosyltransferases and glycosidases in a synthetic schema.
#synthetic_type_enzymatic
enzymatic
#talo
talo
#threo
threo
#threonine
threonine
#trifulfonic_acid
Glycan labelled with 9-aminopyrene-1,3,6-trifulfonic acid
#trifulfonic_acid
9-aminopyrene-1,3,6-trifulfonic acid
#trisulfonic_acid
Glycan labelled with 8-aminonaphthalene-1,3,6-trisulfonic acid
#trisulfonic_acid
8-aminonaphthalene-1,3,6-trisulfonic acid
#tryptophan
tryptophan
#tyrosine
tyrosine
#used_amount_mg
sample weight.
#used_buffer
Link to buffer information, such as http://en.wikipedia.org/wiki/Phosphate_buffered_saline.
#used_column_temperature
Column temperature in C.
#used_concentration
sample concentration.
#used_frequency
frequency of NMR spectrometer.
#used_lc_flow_rate
Flow rate refers to the flow of mobile phase through the column and is measured in ml/min.
#used_lc_gradient
Solvent gradient explained by change in composition with respect to time.
#used_lc_run_time
Runtime of the LC
#used_ph
pH of solution
#used_reference_standard
reference_standard is the accepted internal/external standard for calibrating chemical shift for NMR spectroscopy.
#used_software
Software used to model the molecule.
#used_solvent
The predicate links the solvent part with the actually solvent (such as https://www.ebi.ac.uk/chebi/searchId.do?chebiId=41981). Object is an instance of glycan:solvent.
#used_temperature
value or range in K (literal)
#valine
valine
#xylo
xylo
psi:MS_1000008
PSI: The method by which gas phase ions are generated from the sample.
psi:MS_1000008
Ionization Type
psi:MS_1000031
PSI: Instrument model name not including the vendor's name.
psi:MS_1000031
Instrument Model
psi:MS_1000443
PSI: Mass analyzer separates the ions according to their mass-to-charge ratio.
psi:MS_1000443
Mass Analyzer Type
dcterms:issued
Publication year
uniprot:Glycosylation_Annotation
Uniprot term for Glycosylation type (e.g. N-glycosylation)
uniprot:Glycosylation_Annotation
Glycosylation Annotation
uniprot:Protein
Uniprot protein class.
uniprot:Protein
Protein
uniprot:Taxon
Uniprot taxon class.
uniprot:Taxon
Taxon
http://xmlns.com/foaf/0.1/Image
Image class.
http://xmlns.com/foaf/0.1/Image
Image