Difference between revisions of "WormBase Model:Molecule"
From WormBaseWiki
Jump to navigationJump to searchLine 7: | Line 7: | ||
[[Molecule#mop_tables|postgres molecule tables]] | [[Molecule#mop_tables|postgres molecule tables]] | ||
− | == | + | == Models== |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | + | ===WS251 (proposed)=== | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | ===WS251=== | ||
Based on conversations with Michael Witting to bring in metabolites for C. elegans<br> | Based on conversations with Michael Witting to bring in metabolites for C. elegans<br> | ||
These model changes add tags for curating molecules that are predicted or determined to be metabolites as well as more identifiers for all molecules | These model changes add tags for curating molecules that are predicted or determined to be metabolites as well as more identifiers for all molecules | ||
Line 58: | Line 35: | ||
</pre> | </pre> | ||
− | |||
===WS235=== | ===WS235=== | ||
Reference ?Paper XREF Molecule //Added ability to cite molecules used in a published study | Reference ?Paper XREF Molecule //Added ability to cite molecules used in a published study | ||
Line 71: | Line 47: | ||
===WS227=== | ===WS227=== | ||
Rearrangement ?Rearrangement ?Phenotype #Evidence //KY [110602 pad] | Rearrangement ?Rearrangement ?Phenotype #Evidence //KY [110602 pad] | ||
+ | |||
+ | ===WS217(original)=== | ||
+ | <pre> | ||
+ | ////////////////////////////////////////////////// | ||
+ | // | ||
+ | // 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 | ||
+ | |||
+ | </pre> | ||
==Unused tags== | ==Unused tags== | ||
− | WS219 is the 1st data release that | + | WS219 is the 1st data release that included data |
Revision as of 00:15, 27 August 2015
Contents
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 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
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