Glyco
- Kiyoko F. Aoki-Kinoshita, Masaaki (Marcus) Shiota, Shinichi Higashimoto, Julien Mariethoz, Daisuke Shinmachi, Issaku Yamada, Evan Bolton
- GitHub: https://github.com/shinmachi/BH1709
- Data model is defined, incl. templates
- Linking to GlyTouCan, Uniprot, Uberon, DiseaseOntology, Pubmed, Cellosaurus
- Discussed with Jerven express fuzzy glycosylation site by FALDO
- Discussed with Nuria express disease that related glycan
- figure link
- Scripting converter rdb2rdf
SNFG Legend Generator prototype done! click here
- Select symbols, options( rows, cols, name format )
- Click submit. Legend PowerPoint file download!
- build the website prototype for GlyCosmos Portal with Ruby on Rails
- User Login system (added social network authentication)
- GlyComb Repository prototype (able to upload an Excel or CSV file)
- Testing MolFileToWURCS software with PubChem (Evan, Issaku)
- we discussed to see what in PubChem can have a computed WURCS2 string to better support Glycomics.
- now provides links to GlyTouCan example
- Download SDFile from ChEBI website
- Modify SDFile (replace “*, R1, R2, R3, R4, R5, R6” to “R”)
- SDFile -> WURCS using "MolfileToWURCS" software
- WURCS -> GlyTouCan ID using GlyTouCan Client CLI (GTCC(http://code.glytoucan.org/system/cli/#glytoucan-client-cli))
- Registered structures: 18,067 glycan structures
- 1,908 entries were mapped to GlyTouCan IDs.
- Among those, 78 GlycoEpitope entries were mapped to 248 IEDB entries (duplicates because same epitopes in different organisms)
KEGG Pathways and genes (Kiyoko, with help from Susumu Goto)
- Extracted 33,134 glycoproteins from UniProt (SPARQL'd entries with Glycosylation annotations)
- Mapped them to KEGG Genes: 9674 unmapped
- Extracted 330 pathways with which the mapped KEGG genes were associated:
| Category | Sub-category | Pathway name |
|---|---|---|
| Metabolism | Carbohydrate metabolism | 00010 Glycolysis / Gluconeogenesis |
| Metabolism | Carbohydrate metabolism | 00020 Citrate cycle (TCA cycle) |
| Metabolism | Carbohydrate metabolism | 00030 Pentose phosphate pathway |
| Metabolism | Carbohydrate metabolism | 00040 Pentose and glucuronate interconversions |
| Metabolism | Carbohydrate metabolism | 00051 Fructose and mannose metabolism |
| Metabolism | Carbohydrate metabolism | 00052 Galactose metabolism |
| Metabolism | Carbohydrate metabolism | 00053 Ascorbate and aldarate metabolism |
| Metabolism | Lipid metabolism | 00061 Fatty acid biosynthesis |
| Metabolism | Lipid metabolism | 00062 Fatty acid elongation |
| Metabolism | Lipid metabolism | 00071 Fatty acid degradation |
| Metabolism | Lipid metabolism | 00072 Synthesis and degradation of ketone bodies |
| Metabolism | Lipid metabolism | 00100 Steroid biosynthesis |
| Metabolism | Lipid metabolism | 00120 Primary bile acid biosynthesis |
| Metabolism | Metabolism of cofactors and vitamins | 00130 Ubiquinone and other terpenoid-quinone biosynthesis |
| Metabolism | Lipid metabolism | 00140 Steroid hormone biosynthesis |
| Metabolism | Energy metabolism | 00190 Oxidative phosphorylation |
| Metabolism | Energy metabolism | 00195 Photosynthesis |
| Metabolism | Amino acid metabolism | 00220 Arginine biosynthesis |
| Metabolism | Nucleotide metabolism | 00230 Purine metabolism |
| Metabolism | Biosynthesis of other secondary metabolites | 00232 Caffeine metabolism |
| Metabolism | Nucleotide metabolism | 00240 Pyrimidine metabolism |
| Metabolism | Amino acid metabolism | 00250 Alanine, aspartate and glutamate metabolism |
| Metabolism | Amino acid metabolism | 00260 Glycine, serine and threonine metabolism |
| Metabolism | Amino acid metabolism | 00270 Cysteine and methionine metabolism |
| Metabolism | Amino acid metabolism | 00280 Valine, leucine and isoleucine degradation |
| Metabolism | Amino acid metabolism | 00310 Lysine degradation |
| Metabolism | Biosynthesis of other secondary metabolites | 00311 Penicillin and cephalosporin biosynthesis |
| Metabolism | Amino acid metabolism | 00330 Arginine and proline metabolism |
| Metabolism | Amino acid metabolism | 00340 Histidine metabolism |
| Metabolism | Amino acid metabolism | 00350 Tyrosine metabolism |
| Metabolism | Amino acid metabolism | 00360 Phenylalanine metabolism |
| Metabolism | Amino acid metabolism | 00380 Tryptophan metabolism |
| Metabolism | Amino acid metabolism | 00400 Phenylalanine, tyrosine and tryptophan biosynthesis |
| Metabolism | Biosynthesis of other secondary metabolites | 00404 Staurosporine biosynthesis |
| Metabolism | Metabolism of other amino acids | 00410 beta-Alanine metabolism |
| Metabolism | Metabolism of other amino acids | 00430 Taurine and hypotaurine metabolism |
| Metabolism | Metabolism of other amino acids | 00440 Phosphonate and phosphinate metabolism |
| Metabolism | Metabolism of other amino acids | 00460 Cyanoamino acid metabolism |
| Metabolism | Metabolism of other amino acids | 00472 D-Arginine and D-ornithine metabolism |
| Metabolism | Metabolism of other amino acids | 00480 Glutathione metabolism |
| Metabolism | Carbohydrate metabolism | 00500 Starch and sucrose metabolism |
| Metabolism | Glycan biosynthesis and metabolism | 00510 N-Glycan biosynthesis |
| Metabolism | Glycan biosynthesis and metabolism | 00511 Other glycan degradation |
| Metabolism | Glycan biosynthesis and metabolism | 00512 Mucin type O-glycan biosynthesis |
| Metabolism | Glycan biosynthesis and metabolism | 00513 Various types of N-glycan biosynthesis |
| Metabolism | Glycan biosynthesis and metabolism | 00514 Other types of O-glycan biosynthesis |
| Metabolism | Glycan biosynthesis and metabolism | 00515 Mannose type O-glycan biosynthesis |
| Metabolism | Carbohydrate metabolism | 00520 Amino sugar and nucleotide sugar metabolism |
| Metabolism | Glycan biosynthesis and metabolism | 00531 Glycosaminoglycan degradation |
| Metabolism | Glycan biosynthesis and metabolism | 00532 Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate |
| Metabolism | Glycan biosynthesis and metabolism | 00533 Glycosaminoglycan biosynthesis - keratan sulfate |
| Metabolism | Glycan biosynthesis and metabolism | 00534 Glycosaminoglycan biosynthesis - heparan sulfate / heparin |
| Metabolism | Lipid metabolism | 00561 Glycerolipid metabolism |
| Metabolism | Carbohydrate metabolism | 00562 Inositol phosphate metabolism |
| Metabolism | Glycan biosynthesis and metabolism | 00563 Glycosylphosphatidylinositol (GPI)-anchor biosynthesis |
| Metabolism | Lipid metabolism | 00564 Glycerophospholipid metabolism |
| Metabolism | Lipid metabolism | 00565 Ether lipid metabolism |
| Metabolism | Lipid metabolism | 00590 Arachidonic acid metabolism |
| Metabolism | Lipid metabolism | 00591 Linoleic acid metabolism |
| Metabolism | Lipid metabolism | 00592 alpha-Linolenic acid metabolism |
| Metabolism | Lipid metabolism | 00600 Sphingolipid metabolism |
| Metabolism | Glycan biosynthesis and metabolism | 00601 Glycosphingolipid biosynthesis - lacto and neolacto series |
| Metabolism | Glycan biosynthesis and metabolism | 00603 Glycosphingolipid biosynthesis - globo and isoglobo series |
| Metabolism | Glycan biosynthesis and metabolism | 00604 Glycosphingolipid biosynthesis - ganglio series |
| Metabolism | Carbohydrate metabolism | 00620 Pyruvate metabolism |
| Metabolism | Carbohydrate metabolism | 00630 Glyoxylate and dicarboxylate metabolism |
| Metabolism | Carbohydrate metabolism | 00650 Butanoate metabolism |
| Metabolism | Metabolism of cofactors and vitamins | 00730 Thiamine metabolism |
| Metabolism | Metabolism of cofactors and vitamins | 00740 Riboflavin metabolism |
| Metabolism | Metabolism of cofactors and vitamins | 00760 Nicotinate and nicotinamide metabolism |
| Metabolism | Metabolism of cofactors and vitamins | 00770 Pantothenate and CoA biosynthesis |
| Metabolism | Metabolism of cofactors and vitamins | 00780 Biotin metabolism |
| Metabolism | Metabolism of cofactors and vitamins | 00790 Folate biosynthesis |
| Metabolism | Metabolism of cofactors and vitamins | 00830 Retinol metabolism |
| Metabolism | Metabolism of cofactors and vitamins | 00860 Porphyrin and chlorophyll metabolism |
| Metabolism | Metabolism of terpenoids and polyketides | 00900 Terpenoid backbone biosynthesis |
| Metabolism | Biosynthesis of other secondary metabolites | 00901 Indole alkaloid biosynthesis |
| Metabolism | Metabolism of terpenoids and polyketides | 00906 Carotenoid biosynthesis |
| Metabolism | Metabolism of terpenoids and polyketides | 00908 Zeatin biosynthesis |
| Metabolism | Energy metabolism | 00910 Nitrogen metabolism |
| Metabolism | Energy metabolism | 00920 Sulfur metabolism |
| Metabolism | Biosynthesis of other secondary metabolites | 00940 Phenylpropanoid biosynthesis |
| Metabolism | Biosynthesis of other secondary metabolites | 00950 Isoquinoline alkaloid biosynthesis |
| Metabolism | Biosynthesis of other secondary metabolites | 00960 Tropane, piperidine and pyridine alkaloid biosynthesis |
| Metabolism | Xenobiotics biodegradation and metabolism | 00980 Metabolism of xenobiotics by cytochrome P450 |
| Metabolism | Xenobiotics biodegradation and metabolism | 00982 Drug metabolism - cytochrome P450 |
| Metabolism | Xenobiotics biodegradation and metabolism | 00983 Drug metabolism - other enzymes |
| Metabolism | Lipid metabolism | 01040 Biosynthesis of unsaturated fatty acids |
| Metabolism | Global and overview maps | 01100 Metabolic pathways |
| Metabolism | Global and overview maps | 01110 Biosynthesis of secondary metabolites |
| Metabolism | Global and overview maps | 01130 Biosynthesis of antibiotics |
| Metabolism | Global and overview maps | 01200 Carbon metabolism |
| Metabolism | Global and overview maps | 01210 2-Oxocarboxylic acid metabolism |
| Metabolism | Global and overview maps | 01212 Fatty acid metabolism |
| Metabolism | Global and overview maps | 01230 Biosynthesis of amino acids |
| Human Diseases | Drug resistance: Antineoplastic | 01521 EGFR tyrosine kinase inhibitor resistance |
| Human Diseases | Drug resistance: Antineoplastic | 01522 Endocrine resistance |
| Human Diseases | Drug resistance: Antineoplastic | 01523 Antifolate resistance |
| Human Diseases | Drug resistance: Antineoplastic | 01524 Platinum drug resistance |
| Environmental Information Processing | Membrane transport | 02010 ABC transporters |
| Environmental Information Processing | Signal transduction | 02020 Two-component system |
| Genetic Information Processing | Translation | 03008 Ribosome biogenesis in eukaryotes |
| Genetic Information Processing | Translation | 03010 Ribosome |
| Genetic Information Processing | Translation | 03013 RNA transport |
| Genetic Information Processing | Folding, sorting and degradation | 03018 RNA degradation |
| Genetic Information Processing | Transcription | 03040 Spliceosome |
| Genetic Information Processing | Folding, sorting and degradation | 03050 Proteasome |
| Genetic Information Processing | Folding, sorting and degradation | 03060 Protein export |
| Organismal Systems | Endocrine system | 03320 PPAR signaling pathway |
| Environmental Information Processing | Signal transduction | 04010 MAPK signaling pathway |
| Environmental Information Processing | Signal transduction | 04011 MAPK signaling pathway - yeast |
| Environmental Information Processing | Signal transduction | 04012 ErbB signaling pathway |
| Environmental Information Processing | Signal transduction | 04013 MAPK signaling pathway - fly |
| Environmental Information Processing | Signal transduction | 04014 Ras signaling pathway |
| Environmental Information Processing | Signal transduction | 04015 Rap1 signaling pathway |
| Environmental Information Processing | Signal transduction | 04016 MAPK signaling pathway - plant |
| Environmental Information Processing | Signal transduction | 04020 Calcium signaling pathway |
| Environmental Information Processing | Signal transduction | 04022 cGMP-PKG signaling pathway |
| Environmental Information Processing | Signal transduction | 04024 cAMP signaling pathway |
| Environmental Information Processing | Signaling molecules and interaction | 04060 Cytokine-cytokine receptor interaction |
| Organismal Systems | Immune system | 04062 Chemokine signaling pathway |
| Environmental Information Processing | Signal transduction | 04064 NF-kappa B signaling pathway |
| Environmental Information Processing | Signal transduction | 04066 HIF-1 signaling pathway |
| Environmental Information Processing | Signal transduction | 04068 FoxO signaling pathway |
| Environmental Information Processing | Signal transduction | 04070 Phosphatidylinositol signaling system |
| Environmental Information Processing | Signal transduction | 04071 Sphingolipid signaling pathway |
| Environmental Information Processing | Signal transduction | 04072 Phospholipase D signaling pathway |
| Environmental Information Processing | Signal transduction | 04075 Plant hormone signal transduction |
| Environmental Information Processing | Signaling molecules and interaction | 04080 Neuroactive ligand-receptor interaction |
| Cellular Processes | Cell growth and death | 04110 Cell cycle |
| Cellular Processes | Cell growth and death | 04111 Cell cycle - yeast |
| Cellular Processes | Cell growth and death | 04113 Meiosis - yeast |
| Cellular Processes | Cell growth and death | 04114 Oocyte meiosis |
| Cellular Processes | Cell growth and death | 04115 p53 signaling pathway |
| Genetic Information Processing | Folding, sorting and degradation | 04120 Ubiquitin mediated proteolysis |
| Genetic Information Processing | Folding, sorting and degradation | 04122 Sulfur relay system |
| Cellular Processes | Transport and catabolism | 04136 Autophagy - other |
| Cellular Processes | Transport and catabolism | 04137 Mitophagy - animal |
| Cellular Processes | Transport and catabolism | 04138 Autophagy - yeast |
| Cellular Processes | Transport and catabolism | 04139 Mitophagy - yeast |
| Cellular Processes | Transport and catabolism | 04140 Autophagy - animal |
| Genetic Information Processing | Folding, sorting and degradation | 04141 Protein processing in endoplasmic reticulum |
| Cellular Processes | Transport and catabolism | 04142 Lysosome |
| Cellular Processes | Transport and catabolism | 04144 Endocytosis |
| Cellular Processes | Transport and catabolism | 04145 Phagosome |
| Cellular Processes | Transport and catabolism | 04146 Peroxisome |
| Environmental Information Processing | Signal transduction | 04150 mTOR signaling pathway |
| Environmental Information Processing | Signal transduction | 04151 PI3K-Akt signaling pathway |
| Environmental Information Processing | Signal transduction | 04152 AMPK signaling pathway |
| Cellular Processes | Cell growth and death | 04210 Apoptosis |
| Organismal Systems | Aging | 04211 Longevity regulating pathway |
| Organismal Systems | Aging | 04212 Longevity regulating pathway - worm |
| Organismal Systems | Aging | 04213 Longevity regulating pathway - multiple species |
| Cellular Processes | Cell growth and death | 04214 Apoptosis - fly |
| Cellular Processes | Cell growth and death | 04215 Apoptosis - multiple species |
| Cellular Processes | Cell growth and death | 04216 Ferroptosis |
| Cellular Processes | Cell growth and death | 04217 Necroptosis |
| Cellular Processes | Cell growth and death | 04218 Cellular senescence |
| Organismal Systems | Circulatory system | 04260 Cardiac muscle contraction |
| Organismal Systems | Circulatory system | 04261 Adrenergic signaling in cardiomyocytes |
| Organismal Systems | Circulatory system | 04270 Vascular smooth muscle contraction |
| Environmental Information Processing | Signal transduction | 04310 Wnt signaling pathway |
| Organismal Systems | Development | 04320 Dorso-ventral axis formation |
| Environmental Information Processing | Signal transduction | 04330 Notch signaling pathway |
| Environmental Information Processing | Signal transduction | 04340 Hedgehog signaling pathway |
| Environmental Information Processing | Signal transduction | 04341 Hedgehog signaling pathway - fly |
| Environmental Information Processing | Signal transduction | 04350 TGF-beta signaling pathway |
| Organismal Systems | Development | 04360 Axon guidance |
| Environmental Information Processing | Signal transduction | 04370 VEGF signaling pathway |
| Environmental Information Processing | Signal transduction | 04371 Apelin signaling pathway |
| Organismal Systems | Development | 04380 Osteoclast differentiation |
| Environmental Information Processing | Signal transduction | 04390 Hippo signaling pathway |
| Environmental Information Processing | Signal transduction | 04391 Hippo signaling pathway - fly |
| Environmental Information Processing | Signal transduction | 04392 Hippo signaling pathway - multiple species |
| Cellular Processes | Cellular community - eukaryotes | 04510 Focal adhesion |
| Environmental Information Processing | Signaling molecules and interaction | 04512 ECM-receptor interaction |
| Environmental Information Processing | Signaling molecules and interaction | 04514 Cell adhesion molecules (CAMs) |
| Cellular Processes | Cellular community - eukaryotes | 04520 Adherens junction |
| Cellular Processes | Cellular community - eukaryotes | 04530 Tight junction |
| Cellular Processes | Cellular community - eukaryotes | 04540 Gap junction |
| Cellular Processes | Cellular community - eukaryotes | 04550 Signaling pathways regulating pluripotency of stem cells |
| Organismal Systems | Immune system | 04610 Complement and coagulation cascades |
| Organismal Systems | Immune system | 04611 Platelet activation |
| Organismal Systems | Immune system | 04612 Antigen processing and presentation |
| Organismal Systems | Endocrine system | 04614 Renin-angiotensin system |
| Organismal Systems | Immune system | 04620 Toll-like receptor signaling pathway |
| Organismal Systems | Immune system | 04621 NOD-like receptor signaling pathway |
| Organismal Systems | Immune system | 04622 RIG-I-like receptor signaling pathway |
| Organismal Systems | Immune system | 04623 Cytosolic DNA-sensing pathway |
| Organismal Systems | Immune system | 04624 Toll and Imd signaling pathway |
| Organismal Systems | Environmental adaptation | 04626 Plant-pathogen interaction |
| Environmental Information Processing | Signal transduction | 04630 Jak-STAT signaling pathway |
| Organismal Systems | Immune system | 04640 Hematopoietic cell lineage |
| Organismal Systems | Immune system | 04650 Natural killer cell mediated cytotoxicity |
| Organismal Systems | Immune system | 04657 IL-17 signaling pathway |
| Organismal Systems | Immune system | 04658 Th1 and Th2 cell differentiation |
| Organismal Systems | Immune system | 04659 Th17 cell differentiation |
| Organismal Systems | Immune system | 04660 T cell receptor signaling pathway |
| Organismal Systems | Immune system | 04662 B cell receptor signaling pathway |
| Organismal Systems | Immune system | 04664 Fc epsilon RI signaling pathway |
| Organismal Systems | Immune system | 04666 Fc gamma R-mediated phagocytosis |
| Environmental Information Processing | Signal transduction | 04668 TNF signaling pathway |
| Organismal Systems | Immune system | 04670 Leukocyte transendothelial migration |
| Organismal Systems | Immune system | 04672 Intestinal immune network for IgA production |
| Organismal Systems | Environmental adaptation | 04712 Circadian rhythm - plant |
| Organismal Systems | Environmental adaptation | 04713 Circadian entrainment |
| Organismal Systems | Nervous system | 04720 Long-term potentiation |
| Organismal Systems | Nervous system | 04721 Synaptic vesicle cycle |
| Organismal Systems | Nervous system | 04722 Neurotrophin signaling pathway |
| Organismal Systems | Nervous system | 04723 Retrograde endocannabinoid signaling |
| Organismal Systems | Nervous system | 04724 Glutamatergic synapse |
| Organismal Systems | Nervous system | 04725 Cholinergic synapse |
| Organismal Systems | Nervous system | 04726 Serotonergic synapse |
| Organismal Systems | Nervous system | 04727 GABAergic synapse |
| Organismal Systems | Nervous system | 04728 Dopaminergic synapse |
| Organismal Systems | Nervous system | 04730 Long-term depression |
| Organismal Systems | Sensory system | 04740 Olfactory transduction |
| Organismal Systems | Sensory system | 04742 Taste transduction |
| Organismal Systems | Sensory system | 04744 Phototransduction |
| Organismal Systems | Sensory system | 04745 Phototransduction - fly |
| Organismal Systems | Sensory system | 04750 Inflammatory mediator regulation of TRP channels |
| Cellular Processes | Cell motility | 04810 Regulation of actin cytoskeleton |
| Organismal Systems | Endocrine system | 04910 Insulin signaling pathway |
| Organismal Systems | Endocrine system | 04911 Insulin secretion |
| Organismal Systems | Endocrine system | 04912 GnRH signaling pathway |
| Organismal Systems | Endocrine system | 04913 Ovarian steroidogenesis |
| Organismal Systems | Endocrine system | 04914 Progesterone-mediated oocyte maturation |
| Organismal Systems | Endocrine system | 04915 Estrogen signaling pathway |
| Organismal Systems | Endocrine system | 04916 Melanogenesis |
| Organismal Systems | Endocrine system | 04917 Prolactin signaling pathway |
| Organismal Systems | Endocrine system | 04918 Thyroid hormone synthesis |
| Organismal Systems | Endocrine system | 04919 Thyroid hormone signaling pathway |
| Organismal Systems | Endocrine system | 04920 Adipocytokine signaling pathway |
| Organismal Systems | Endocrine system | 04921 Oxytocin signaling pathway |
| Organismal Systems | Endocrine system | 04922 Glucagon signaling pathway |
| Organismal Systems | Endocrine system | 04923 Regulation of lipolysis in adipocytes |
| Organismal Systems | Endocrine system | 04924 Renin secretion |
| Organismal Systems | Endocrine system | 04925 Aldosterone synthesis and secretion |
| Organismal Systems | Endocrine system | 04926 Relaxin signaling pathway |
| Human Diseases | Endocrine and metabolic diseases | 04930 Type II diabetes mellitus |
| Human Diseases | Endocrine and metabolic diseases | 04931 Insulin resistance |
| Human Diseases | Endocrine and metabolic diseases | 04932 Non-alcoholic fatty liver disease (NAFLD) |
| Human Diseases | Endocrine and metabolic diseases | 04933 AGE-RAGE signaling pathway in diabetic complications |
| Human Diseases | Endocrine and metabolic diseases | 04940 Type I diabetes mellitus |
| Human Diseases | Endocrine and metabolic diseases | 04950 Maturity onset diabetes of the young |
| Organismal Systems | Excretory system | 04960 Aldosterone-regulated sodium reabsorption |
| Organismal Systems | Excretory system | 04961 Endocrine and other factor-regulated calcium reabsorption |
| Organismal Systems | Excretory system | 04962 Vasopressin-regulated water reabsorption |
| Organismal Systems | Excretory system | 04964 Proximal tubule bicarbonate reclamation |
| Organismal Systems | Excretory system | 04966 Collecting duct acid secretion |
| Organismal Systems | Digestive system | 04970 Salivary secretion |
| Organismal Systems | Digestive system | 04971 Gastric acid secretion |
| Organismal Systems | Digestive system | 04972 Pancreatic secretion |
| Organismal Systems | Digestive system | 04973 Carbohydrate digestion and absorption |
| Organismal Systems | Digestive system | 04974 Protein digestion and absorption |
| Organismal Systems | Digestive system | 04975 Fat digestion and absorption |
| Organismal Systems | Digestive system | 04976 Bile secretion |
| Organismal Systems | Digestive system | 04977 Vitamin digestion and absorption |
| Organismal Systems | Digestive system | 04978 Mineral absorption |
| Human Diseases | Neurodegenerative diseases | 05010 Alzheimer's disease |
| Human Diseases | Neurodegenerative diseases | 05012 Parkinson's disease |
| Human Diseases | Neurodegenerative diseases | 05014 Amyotrophic lateral sclerosis (ALS) |
| Human Diseases | Neurodegenerative diseases | 05016 Huntington's disease |
| Human Diseases | Neurodegenerative diseases | 05020 Prion diseases |
| Human Diseases | Substance dependence | 05030 Cocaine addiction |
| Human Diseases | Substance dependence | 05031 Amphetamine addiction |
| Human Diseases | Substance dependence | 05032 Morphine addiction |
| Human Diseases | Substance dependence | 05033 Nicotine addiction |
| Human Diseases | Substance dependence | 05034 Alcoholism |
| Human Diseases | Infectious diseases: Bacterial | 05100 Bacterial invasion of epithelial cells |
| Human Diseases | Infectious diseases: Bacterial | 05110 Vibrio cholerae infection |
| Human Diseases | Infectious diseases: Bacterial | 05120 Epithelial cell signaling in Helicobacter pylori infection |
| Human Diseases | Infectious diseases: Bacterial | 05130 Pathogenic Escherichia coli infection |
| Human Diseases | Infectious diseases: Bacterial | 05131 Shigellosis |
| Human Diseases | Infectious diseases: Bacterial | 05132 Salmonella infection |
| Human Diseases | Infectious diseases: Bacterial | 05133 Pertussis |
| Human Diseases | Infectious diseases: Bacterial | 05134 Legionellosis |
| Human Diseases | Infectious diseases: Parasitic | 05140 Leishmaniasis |
| Human Diseases | Infectious diseases: Parasitic | 05142 Chagas disease (American trypanosomiasis) |
| Human Diseases | Infectious diseases: Parasitic | 05143 African trypanosomiasis |
| Human Diseases | Infectious diseases: Parasitic | 05144 Malaria |
| Human Diseases | Infectious diseases: Parasitic | 05145 Toxoplasmosis |
| Human Diseases | Infectious diseases: Parasitic | 05146 Amoebiasis |
| Human Diseases | Infectious diseases: Bacterial | 05150 Staphylococcus aureus infection |
| Human Diseases | Infectious diseases: Bacterial | 05152 Tuberculosis |
| Human Diseases | Infectious diseases: Viral | 05160 Hepatitis C |
| Human Diseases | Infectious diseases: Viral | 05161 Hepatitis B |
| Human Diseases | Infectious diseases: Viral | 05162 Measles |
| Human Diseases | Infectious diseases: Viral | 05164 Influenza A |
| Human Diseases | Infectious diseases: Viral | 05165 Human papillomavirus infection |
| Human Diseases | Infectious diseases: Viral | 05166 HTLV-I infection |
| Human Diseases | Infectious diseases: Viral | 05167 Kaposi's sarcoma-associated herpesvirus infection |
| Human Diseases | Infectious diseases: Viral | 05168 Herpes simplex infection |
| Human Diseases | Infectious diseases: Viral | 05169 Epstein-Barr virus infection |
| Human Diseases | Cancers: Overview | 05200 Pathways in cancer |
| Human Diseases | Cancers: Overview | 05202 Transcriptional misregulation in cancer |
| Human Diseases | Cancers: Overview | 05203 Viral carcinogenesis |
| Human Diseases | Cancers: Overview | 05204 Chemical carcinogenesis |
| Human Diseases | Cancers: Overview | 05205 Proteoglycans in cancer |
| Human Diseases | Cancers: Overview | 05206 MicroRNAs in cancer |
| Human Diseases | Cancers: Specific types | 05210 Colorectal cancer |
| Human Diseases | Cancers: Specific types | 05211 Renal cell carcinoma |
| Human Diseases | Cancers: Specific types | 05212 Pancreatic cancer |
| Human Diseases | Cancers: Specific types | 05213 Endometrial cancer |
| Human Diseases | Cancers: Specific types | 05214 Glioma |
| Human Diseases | Cancers: Specific types | 05215 Prostate cancer |
| Human Diseases | Cancers: Specific types | 05216 Thyroid cancer |
| Human Diseases | Cancers: Specific types | 05217 Basal cell carcinoma |
| Human Diseases | Cancers: Specific types | 05218 Melanoma |
| Human Diseases | Cancers: Specific types | 05219 Bladder cancer |
| Human Diseases | Cancers: Specific types | 05220 Chronic myeloid leukemia |
| Human Diseases | Cancers: Specific types | 05221 Acute myeloid leukemia |
| Human Diseases | Cancers: Specific types | 05222 Small cell lung cancer |
| Human Diseases | Cancers: Specific types | 05223 Non-small cell lung cancer |
| Human Diseases | Cancers: Specific types | 05224 Breast cancer |
| Human Diseases | Cancers: Overview | 05230 Central carbon metabolism in cancer |
| Human Diseases | Cancers: Overview | 05231 Choline metabolism in cancer |
| Human Diseases | Immune diseases | 05310 Asthma |
| Human Diseases | Immune diseases | 05320 Autoimmune thyroid disease |
| Human Diseases | Immune diseases | 05321 Inflammatory bowel disease (IBD) |
| Human Diseases | Immune diseases | 05322 Systemic lupus erythematosus |
| Human Diseases | Immune diseases | 05323 Rheumatoid arthritis |
| Human Diseases | Immune diseases | 05330 Allograft rejection |
| Human Diseases | Immune diseases | 05332 Graft-versus-host disease |
| Human Diseases | Immune diseases | 05340 Primary immunodeficiency |
| Human Diseases | Cardiovascular diseases | 05410 Hypertrophic cardiomyopathy (HCM) |
| Human Diseases | Cardiovascular diseases | 05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC) |
| Human Diseases | Cardiovascular diseases | 05414 Dilated cardiomyopathy (DCM) |
| Human Diseases | Cardiovascular diseases | 05416 Viral myocarditis |
| Human Diseases | Cardiovascular diseases | 05418 Fluid shear stress and atherosclerosis |
Reactome pathways and genes (Kiyoko)
- Using the same dataset of glycoproteins from UniProt, mapped to Reactome pathways:
- 7446 Genes
- 1771 Pathways
- Shujiro obtained table of glycogenes and metagenome samples containing them from MicrobeDB.jp
- Used ClustVis (with some frustration) to cluster the glycogenes and samples
- Among the results, PCA found, for example, the following samples that were close, both having "Biosynthesis of amino acids" and "Carbon metabolism" as high-scoring functions:
- KO List: K16153 K00712 K02853 K11936 K05946 K12555 K02844 K03669 K02841 K02843 K05365 K12582 K00721 K16148 K02846 K00703 K02527 K07264 K00748 K03814 K16055 K02851 K00694 K05366 K05367 K00697 K13688 K02852 K03693 K03429 K12982
- These KOs map to the following pathways:
| Category | Sub-category | Pathway name |
|---|---|---|
| Metabolism | Carbohydrate metabolism | 00500 Starch and sucrose metabolism |
| Metabolism | Glycan biosynthesis and metabolism | 00510 N-Glycan biosynthesis |
| Metabolism | Glycan biosynthesis and metabolism | 00540 Lipopolysaccharide biosynthesis |
| Metabolism | Glycan biosynthesis and metabolism | 00550 Peptidoglycan biosynthesis |
| Metabolism | Lipid metabolism | 00561 Glycerolipid metabolism |
| Metabolism | Global and overview maps | 01100 Metabolic pathways |
| Metabolism | Global and overview maps | 01110 Biosynthesis of secondary metabolites |
| Human Diseases | Drug resistance: Antimicrobial | 01501 beta-Lactam resistance |
| Human Diseases | Drug resistance: Antimicrobial | 01503 Cationic antimicrobial peptide (CAMP) resistance |
| Cellular Processes | Cellular community - prokaryotes | 02026 Biofilm formation - Escherichia coli |
| Cellular Processes | Cellular community - prokaryotes | 05111 Biofilm formation - Vibrio cholerae |
- add WURCS 2.0 strings into PubChem
- analysis of saccharides to determine definition of "what is a glycan?"
- Discussed with Seth usage of Noctua
- Consider as Glycan-related Pathway editor/visualizer for GlyCosmos
- Discussed with Jerven possibility of linking with SwissLipids once it is RDFized
- GlycoGene DataBase (GGDB) data and PubAnnotation
- GlycoPOD and SmartProtocols
-
- What the relationship each data such as Taxnonomy, Protein, Glycosilation site, Tissue, Structure(glycan) and Disease.
- How to use D2RQ mapper?
-
- create Web Page done
- creating generator docker image
-
- download molecular structure (sdfile) from ChEBI ftp-site (ftp://ftp.ebi.ac.uk/pub/databases/chebi/SDF/).
- convert to WURCS.
- ChEBI SDFile is not standard format, modified atomic symbols (R1, R2, R3, R4, R5, R#).
- generating WURCS using MolfileToWURCS2.0 (https://github.com/glycoinfo/MolfileToWURCS2.0).
-
- Glycosylation site including in Glycosuite database.
- We drew position graph for make sample RDF.
@prefix glycan: <http://purl.jp/bio/12/glyco/glycan#> .
@prefix faldo: <http://biohackathon.org/resource/faldo#>.
@prefix glyconnect: <http://biohackathon.org/resource/glyconnect#>.
@prefix gcs: <http://biohackathon.org/resource/glyconnect/structure/>.
@prefix gcgs: <http://biohackathon.org/resource/glyconnect/glycosylation_site/>.
@prefix gcl: <http://biohackathon.org/resource/glyconnect/>.
@prefix gcp: <http://biohackathon.org/resource/protein/>.
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix up: <http://www.uniprot.org/core/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
### Saccharide
gcs:8118
a glycan:Saccharide;
glycan:glycosylates gcgs:730_1424.
gcs:8048
a glycan:Saccharide;
rdfs:seeAlso <https://glytoucan.org/Structures/Glycans/G22208HN>;
foaf:primaryTopic <https://glytoucan.org/Structures/Glycans/G22208HN>;
glycan:glycosylates gcgs:730_1424.
gcs:8128
a glycan:Saccharide;
glycan:glycosylates gcgs:730_869.
### Glycosylation_site
gcgs:730_869
a glycan:Glycosylation_site;
faldo:location gcl:730_869.
gcgs:730_1424
a glycan:Glycosylation_site;
faldo:location gcl:730_1424.
### Exact Position.
gcl:730_869
a faldo:ExactPosition;
faldo:position "869"^^xsd:int;
rdfs:seeAlso <http://www.uniprot.org/blast/?about=P01023[872]>;
faldo:reference gcp:730.
gcl:730_1424
a faldo:ExactPosition;
faldo:position "1424"^^xsd:int;
faldo:reference gcp:730.
### Protein
gcp:730
a up:Protein;
rdfs:label "Alpha-2-macroglobulin";
rdfs:seeAlso <http://purl.uniprot.org/uniprot/P01023>.
-
- Create Legend Generator docker image done
- Generator can create PowerPoint file, but all function does not work
- Sample System deploy at RINGS2
-
- convert to WURCS done.
- mapping ChEBI and GlyTouCan done.
@prefix glycan: <http://purl.jp/bio/12/glyco/glycan#> .
@prefix faldo: <http://biohackathon.org/resource/faldo#>.
@prefix glyconnect: <http://biohackathon.org/resource/glyconnect#>.
@prefix gcs: <http://biohackathon.org/resource/glyconnect/structure/>.
@prefix gcgs: <http://biohackathon.org/resource/glyconnect/glycosylation_site/>.
@prefix gcl: <http://biohackathon.org/resource/glyconnect/locations/>.
@prefix gclp: <http://biohackathon.org/resource/glyconnect/locations/position/>.
@prefix gcp: <http://biohackathon.org/resource/protein/>.
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix up: <http://www.uniprot.org/core/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
## Fuzzy positongg
## one saccharide, some glycosylation site
### Saccharide
gcs:4225
a glycan:Saccharide;
foaf:primaryTopic <https://identifiers.org/G10225UW>;
rdfs:seeAlso <https://glytoucan.org/Structures/Glycans/G10225UW>;
glycan:glycosylates gcgs:285_666o118o675o691o673.
### Glycosylation_site
gcgs:285_666o118o675o691o673
a glycan:Glycosylation_site;
faldo:location gcl:285_666o118o675o691o673.
### One Of Position
gcl:285_666o118o675o691o673
a faldo:OneOfPosition;
faldo:location gclp:285_666;
faldo:location gclp:285_118;
faldo:location gclp:285_675;
faldo:location gclp:285_691;
faldo:location gclp:285_673.
### Exact Position
gclp:285_666
a faldo:ExactPosition;
faldo:position "666"^^xsd:int;
faldo:reference gcp:285.
gclp:285_118
a faldo:ExactPosition;
faldo:position "118"^^xsd:int;
faldo:reference gcp:285.
gclp:285_675
a faldo:ExactPosition;
faldo:position "675"^^xsd:int;
faldo:reference gcp:285.
gclp:285_691
a faldo:ExactPosition;
faldo:position "691"^^xsd:int;
faldo:reference gcp:285.
gclp:285_673
a faldo:ExactPosition;
faldo:position "673"^^xsd:int;
faldo:reference gcp:285.
### Protein
gcp:285
a up:Protein;
rdfs:label "Inter-Alpha-Trypsin Inhibitor Heavy Chain H2";
foaf:primaryTopic <http://identifiers.org/uniprot/P19823>;
rdfs:seeAlso <http://purl.uniprot.org/uniprot/P19823>.
-
- Testing MolFileToWURCS software with PubChem (Evan, Issaku)
- we discussed to see what in PubChem can have a computed WURCS2 string to better support Glycomics.
- Testing MolFileToWURCS software with PubChem (Evan, Issaku)
Development of referenced glycan graph to encapsulate diseases and references for glycans and glycoproteins
SNFG Legend Generator prototype done! click here
- Select symbols, options( rows, cols, name format )
- Click submit. Legend PPowerPoint file download!
- mapping IEDB and GlyTouCan done.
- 1,908 entries were mapped.