Daisuke Shinmachi Hiro Sawaki Issaku Yamada Kiyoko Aoki-Kinoshita Masaaki Matsubara Matthew Campbell Philip Toukach Rene Ranzinger Shin Kawano Shujiro Okuda 2013-02-10T23:11:00 1.2.1 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 #CarbohydrateFormat Instances of this class are the carbohydrate sequence formats. #CarbohydrateFormat Carbohydrate Format #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 #Glycam This class depicts a GlyCAM format of glycans #GlycoCT This class depicts a GlycoCT format of glycans #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 #IupacCondensed This class depicts a IUPAC condensed format of glycans #IupacExtended This class depicts a IUPAC Extended format of glycans. #LinearCode This class depicts a Linear Code format of glycans #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 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 #Source_natural Initial class name is capitalized. "glycan:Source_natural" #Source_natural Source Natural #Wurcs This class depicts a WURCS format of glycans #_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_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_glycan_format This object property links Glycan class to glycanFormat class #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 #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 foaf:Image Image class. foaf:Image Image