WormBase Model:Molecule
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Curator Comments/Description
Molecule wiki
postgres molecule tables
Models
WS251 (proposed)
Based on conversations with Michael Witting to bring in metabolites for C. elegans
These model changes add tags for curating molecules that are predicted or determined to be metabolites as well as more identifiers for all molecules
?Molecule Public_name ?Text Formula UNIQUE ?Text Monoisotopic_mass UNIQUE ?Text IUPAC UNIQUE ?Text SMILES ?Text //not unique, there may be many SMILES strings for a given molecule InChi UNIQUE?Text InChi_key UNIQUE ?Text Synonym ?Text DB_info Database ?Database ?Database_field ?Text Status Detected #Evidence Predicted #Evidence //need to add in numeric (float) fields to capture concentrations or ranges Classified_as ?Database ?Database_field ?Text //for ChEBI or other database classification system //this will be way too complicated, any given molecule is classified as many things within any given database, need to capture all classifications? also if classified through an ontology, what level do we take? Source Endogenous ?Species #Evidence //produced within animal Exogenous #Evidence //produced by other living being Pharmaceutical #Evidence //e.g., synthetic drug Industrial #Evidence // e.g., inorganic substance Ligand_for Gene_product_receptor ?Gene Receptor_for_molecule #Evidence Molecule_receptor ?Molecule XREF Receptor_for_molecule #Evidence Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence //Change to Causes_phenotype ?Phenotype_info XREF Caused_by_molecule #Evidence for PATO? Strain ?Strain ?Phenotype #Evidence Transgene ?Transgene ?Phenotype #Evidence RNAi ?RNAi ?Phenotype #Evidence Affected_by_genetics ?Phenotype_info XREF Molecule_affected #Evidence //added by Chris for PATO constructions Molecule_use ?Text #Evidence Remark ?Text #Evidence
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
WS227
Rearrangement ?Rearrangement ?Phenotype #Evidence //KY [110602 pad]
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 data release that included data