Difference between revisions of "WormBase Model:Molecule"
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== Models== | == Models== | ||
− | ===WS252 | + | ===WS254=== |
− | + | <pre> | |
+ | ?Molecule Name ?Text //WBMoleculeID | ||
+ | Public_name ?Text | ||
+ | Formula ?Text //imported from ChEBI | ||
+ | Monoisotopic_mass ?Float //need to set up automated calculation based on formula | ||
+ | IUPAC ?Text //imported from ChEBI | ||
+ | SMILES ?Text //imported from ChEBI | ||
+ | InChi ?Text //imported from ChEBI | ||
+ | InChiKey ?Text //imported from ChEBI | ||
+ | Synonym ?Text //mainly from CTD, but also from papers and ChEBI | ||
+ | DB_info Database ?Database ?Database_field ?Text //links molecule to ChEBI, CTD, KEGG, UniProt | ||
+ | Status Detected #Evidence | ||
+ | Predicted #Evidence | ||
+ | Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics | ||
+ | Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid | ||
+ | Nonspecies_source ?Text //xenobiotic, antibiotic, drug, chemical synthesis, toxin, pollutant, food additive, food, hydrocarbon, pesticide, antihelmintic | ||
+ | Endogenous_in ?Species #Evidence | ||
+ | Biofunction_role Metabolite ?Text #Evidence | ||
+ | Regulator ?Text #Evidence | ||
+ | Structural_component ?Text #Evidence | ||
+ | Cofactor ?Text #Evidence | ||
+ | Activator ?Text #Evidence | ||
+ | Inhibitor ?Text #Evidence | ||
+ | Product ?Text #Evidence | ||
+ | Substrate ?Text #Evidence | ||
+ | Ligand ?Text #Evidence | ||
+ | Receptor ?Text #Evidence | ||
+ | Essential_for ?Species #Evidence | ||
+ | WBProcess ?WBProcess XREF Molecule | ||
+ | Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule // Wen WS228 | ||
+ | Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence | ||
+ | Strain ?Strain ?Phenotype #Evidence | ||
+ | Transgene ?Transgene ?Phenotype #Evidence | ||
+ | RNAi ?RNAi ?Phenotype #Evidence | ||
+ | Rearrangement ?Rearrangement ?Phenotype #Evidence | ||
+ | Interaction ?Interaction XREF Molecule_interactor // Chris WS244 | ||
+ | Molecule_use ?Text #Evidence | ||
+ | Reference ?Paper XREF Molecule | ||
+ | Remark | ||
+ | </pre> | ||
+ | |||
+ | ===WS252=== | ||
+ | <pre> | ||
+ | ?Molecule Name ?Text //WBMoleculeID | ||
+ | Public_name ?Text | ||
+ | Formula ?Text //imported from ChEBI | ||
+ | Monoisotopic_mass ?Float //need to set up automated calculation based on formula | ||
+ | IUPAC ?Text //imported from ChEBI | ||
+ | SMILES ?Text //imported from ChEBI | ||
+ | InChi ?Text //imported from ChEBI | ||
+ | InChiKey ?Text //imported from ChEBI | ||
+ | Synonym ?Text //mainly from CTD, but also from papers and ChEBI | ||
+ | DB_info Database ?Database ?Database_field ?Text //links molecule to ChEBI, CTD, KEGG, etc | ||
+ | Status Detected #Evidence | ||
+ | Predicted #Evidence | ||
+ | Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics | ||
+ | Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid | ||
+ | Nonspecies_source ?Text | ||
+ | Chemical_synthesis #Evidence | ||
+ | Endogenous_in ?Species #Evidence | ||
+ | Biofunction_role Metabolite ?Text #Evidence | ||
+ | Regulator ?Text #Evidence | ||
+ | Structural_component ?Text #Evidence | ||
+ | Cofactor ?Text #Evidence | ||
+ | Activator ?Text #Evidence | ||
+ | Inhibitor ?Text #Evidence | ||
+ | Product ?Text #Evidence | ||
+ | Substrate ?Text #Evidence | ||
+ | Ligand ?Text #Evidence | ||
+ | Receptor ?Text #Evidence | ||
+ | Essential_for ?Species #Evidence | ||
+ | WBProcess ?WBProcess XREF Molecule | ||
+ | Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule // Wen WS228 | ||
+ | Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence | ||
+ | Strain ?Strain ?Phenotype #Evidence | ||
+ | Transgene ?Transgene ?Phenotype #Evidence | ||
+ | RNAi ?RNAi ?Phenotype #Evidence | ||
+ | Rearrangement ?Rearrangement ?Phenotype #Evidence | ||
+ | Interaction ?Interaction XREF Molecule_interactor // Chris WS244 | ||
+ | Molecule_use ?Text #Evidence | ||
+ | Reference ?Paper XREF Molecule | ||
+ | Remark | ||
+ | </pre> | ||
===WS235=== | ===WS235=== |
Latest revision as of 23:29, 15 March 2016
Contents
Curator Comments/Description
Molecule wiki
postgres molecule tables
Models
WS254
?Molecule Name ?Text //WBMoleculeID Public_name ?Text Formula ?Text //imported from ChEBI Monoisotopic_mass ?Float //need to set up automated calculation based on formula IUPAC ?Text //imported from ChEBI SMILES ?Text //imported from ChEBI InChi ?Text //imported from ChEBI InChiKey ?Text //imported from ChEBI Synonym ?Text //mainly from CTD, but also from papers and ChEBI DB_info Database ?Database ?Database_field ?Text //links molecule to ChEBI, CTD, KEGG, UniProt Status Detected #Evidence Predicted #Evidence Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid Nonspecies_source ?Text //xenobiotic, antibiotic, drug, chemical synthesis, toxin, pollutant, food additive, food, hydrocarbon, pesticide, antihelmintic Endogenous_in ?Species #Evidence Biofunction_role Metabolite ?Text #Evidence Regulator ?Text #Evidence Structural_component ?Text #Evidence Cofactor ?Text #Evidence Activator ?Text #Evidence Inhibitor ?Text #Evidence Product ?Text #Evidence Substrate ?Text #Evidence Ligand ?Text #Evidence Receptor ?Text #Evidence Essential_for ?Species #Evidence WBProcess ?WBProcess XREF Molecule Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule // Wen WS228 Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence Strain ?Strain ?Phenotype #Evidence Transgene ?Transgene ?Phenotype #Evidence RNAi ?RNAi ?Phenotype #Evidence Rearrangement ?Rearrangement ?Phenotype #Evidence Interaction ?Interaction XREF Molecule_interactor // Chris WS244 Molecule_use ?Text #Evidence Reference ?Paper XREF Molecule Remark
WS252
?Molecule Name ?Text //WBMoleculeID Public_name ?Text Formula ?Text //imported from ChEBI Monoisotopic_mass ?Float //need to set up automated calculation based on formula IUPAC ?Text //imported from ChEBI SMILES ?Text //imported from ChEBI InChi ?Text //imported from ChEBI InChiKey ?Text //imported from ChEBI Synonym ?Text //mainly from CTD, but also from papers and ChEBI DB_info Database ?Database ?Database_field ?Text //links molecule to ChEBI, CTD, KEGG, etc Status Detected #Evidence Predicted #Evidence Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid Nonspecies_source ?Text Chemical_synthesis #Evidence Endogenous_in ?Species #Evidence Biofunction_role Metabolite ?Text #Evidence Regulator ?Text #Evidence Structural_component ?Text #Evidence Cofactor ?Text #Evidence Activator ?Text #Evidence Inhibitor ?Text #Evidence Product ?Text #Evidence Substrate ?Text #Evidence Ligand ?Text #Evidence Receptor ?Text #Evidence Essential_for ?Species #Evidence WBProcess ?WBProcess XREF Molecule Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule // Wen WS228 Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence Strain ?Strain ?Phenotype #Evidence Transgene ?Transgene ?Phenotype #Evidence RNAi ?RNAi ?Phenotype #Evidence Rearrangement ?Rearrangement ?Phenotype #Evidence Interaction ?Interaction XREF Molecule_interactor // Chris WS244 Molecule_use ?Text #Evidence Reference ?Paper XREF Molecule Remark
WS235
Reference ?Paper XREF Molecule //Added ability to cite molecules used in a published study
WS228
Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule //Added for molecule regulation of gene expression by Wen
WS224
Interaction ?Interaction XREF Molecule_interactor // Chris WS244
WS217(original)
////////////////////////////////////////////////// // // Molecule class Model - Proposed by Karen Yook WS217 // Connects to: #Phenotype_info // ?Gene_regulation // ////////////////////////////////////////////////// ?Molecule Name ?Text Public_name ?Text Synonym ?Text DB_info Database ?Database ?Database_field ?Accession_number Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence Strain ?Strain ?Phenotype #Evidence Transgene ?Transgene ?Phenotype #Evidence RNAi ?RNAi ?Phenotype #Evidence Molecule_use ?Text #Evidence Remark ?Text #Evidence
Unused tags
WS219 is the 1st release that included data