WormBase Model:Molecule
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Contents
Curator Comments/Description
Model
////////////////////////////////////////////////// // // 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
Proposed Changes
WS251
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 Classified_as ?Database ?Database_field ?Text //for ChEBI or other database classification system 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 Pathway_database ?Database ?Database_field ?Text //for importing KEGG pathways, for example
Approved Changes
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]
Unused tags
WS219 is the 1st data release that this will be included in.